https://pymolwiki.org/api.php?action=feedcontributions&user=Gha&feedformat=atomPyMOLWiki - User contributions [en]2024-03-28T20:48:21ZUser contributionsMediaWiki 1.35.7https://pymolwiki.org/index.php?title=MtsslDock&diff=13300MtsslDock2020-05-21T19:03:05Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGui.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslDock is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2020-05-21:<br />
If you are having trouble with installation, give [http://www.mtsslsuite.isb.ukbonn.de this] a try!<br />
<br />
2017-01-18:<br />
[http://www-hagelueken.thch.uni-bonn.de/index.php/en/2014-08-04-13-28-34/mtssldock Version 2.0 available]<br />
<br />
2013-07-04:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Installation==<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the PLUGINS menu. <br />
Alternatively install the plugin via the Plugin Manager.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). Download it and check the contents of the downloaded folder (It is probably called "tkintertable-1.1.2" or similar). There should be a folder in it that is called "tkintertable" put this folder into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
==Docking==<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
===C2 symmetric structures, e.g. symmetric dimers===<br />
If you try the C2 dimer feature: Make a copy of your monomer and leave it at the exact same position. Then, label both monomers independently and import them as protein A and B.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips. Also to Damien Farrell for the tkintertable class.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=13299MtsslDock2020-05-21T19:02:41Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGui.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslDock is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2020-05-21:<br />
If you are having trouble with installation, give [this http://www.mtsslsuite.isb.ukbonn.de] a try!<br />
<br />
2017-01-18:<br />
[http://www-hagelueken.thch.uni-bonn.de/index.php/en/2014-08-04-13-28-34/mtssldock Version 2.0 available]<br />
<br />
2013-07-04:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Installation==<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the PLUGINS menu. <br />
Alternatively install the plugin via the Plugin Manager.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). Download it and check the contents of the downloaded folder (It is probably called "tkintertable-1.1.2" or similar). There should be a folder in it that is called "tkintertable" put this folder into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
==Docking==<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
===C2 symmetric structures, e.g. symmetric dimers===<br />
If you try the C2 dimer feature: Make a copy of your monomer and leave it at the exact same position. Then, label both monomers independently and import them as protein A and B.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips. Also to Damien Farrell for the tkintertable class.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=13298MtsslWizard2020-05-21T19:00:46Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
2020-05-21<br />
*If you are having trouble with installation give [http://www.mtsslsuite.isb.ukbonn.de this] a try<br />
<br />
2017-01-17:<br />
*[http://www-hagelueken.thch.uni-bonn.de/index.php/en/2014-08-04-13-28-34/mtssldock Version 2.0 available]! <br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature. Plots can be viewed with [[mtsslPlotter]].<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported. In "distance map" mode, the program quickly estimates the inter-label distances between all possible spin pairs in a protein molecule. The result is saved as a color coded distance map. It is also possible to calculate difference distance maps between two conformations of a protein.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.7. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed<br />
*Pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
*On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
#The calculated distributions can be viewed with [[mtsslPlotter]].<br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
<br />
===Distance maps===<br />
#change "Mode" to "Distance map"<br />
#For a simple distance map: click twice on the protein of interest<br />
#For a difference distance map between two conformations of a protein: click once on each of the two conformations. For this feature to work properly, both conformations should have the same number of residues. This can be easily achieved using standard PyMOL commands.<br />
#The maps can be viewed with [[mtsslPlotter]]<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at' uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=13297MtsslWizard2020-05-21T18:59:54Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
2020-05-21<br />
*If you are having trouble with installation give [http://www.mtsslsuite.isb.ukbonn.de this] a try<br />
<br />
2017-01-17:<br />
*[http://www-hagelueken.thch.uni-bonn.de/index.php/en/2014-08-04-13-28-34/mtssldock Version 2.0 available]! <br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature. Plots can be viewed with [[mtsslPlotter]].<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported. In "distance map" mode, the program quickly estimates the inter-label distances between all possible spin pairs in a protein molecule. The result is saved as a color coded distance map. It is also possible to calculate difference distance maps between two conformations of a protein.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.7. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed<br />
*Pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
*On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
#The calculated distributions can be viewed with [[mtsslPlotter]].<br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
<br />
===Distance maps===<br />
#change "Mode" to "Distance map"<br />
#For a simple distance map: click twice on the protein of interest<br />
#For a difference distance map between two conformations of a protein: click once on each of the two conformations. For this feature to work properly, both conformations should have the same number of residues. This can be easily achieved using standard PyMOL commands.<br />
#The maps can be viewed with [[mtsslPlotter]]<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=12513MtsslDock2017-01-18T10:23:47Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGui.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslDock is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2017-01-18:<br />
[http://www-hagelueken.thch.uni-bonn.de/index.php/en/2014-08-04-13-28-34/mtssldock Version 2.0 available]<br />
<br />
2013-07-04:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Installation==<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the PLUGINS menu. <br />
Alternatively install the plugin via the Plugin Manager.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). Download it and check the contents of the downloaded folder (It is probably called "tkintertable-1.1.2" or similar). There should be a folder in it that is called "tkintertable" put this folder into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
==Docking==<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
===C2 symmetric structures, e.g. symmetric dimers===<br />
If you try the C2 dimer feature: Make a copy of your monomer and leave it at the exact same position. Then, label both monomers independently and import them as protein A and B.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips. Also to Damien Farrell for the tkintertable class.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=12512MtsslWizard2017-01-18T10:21:51Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2017-01-17:<br />
*[http://www-hagelueken.thch.uni-bonn.de/index.php/en/2014-08-04-13-28-34/mtssldock Version 2.0 available]! <br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature. Plots can be viewed with [[mtsslPlotter]].<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported. In "distance map" mode, the program quickly estimates the inter-label distances between all possible spin pairs in a protein molecule. The result is saved as a color coded distance map. It is also possible to calculate difference distance maps between two conformations of a protein.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.7. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed<br />
*Pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
*On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
#The calculated distributions can be viewed with [[mtsslPlotter]].<br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
<br />
===Distance maps===<br />
#change "Mode" to "Distance map"<br />
#For a simple distance map: click twice on the protein of interest<br />
#For a difference distance map between two conformations of a protein: click once on each of the two conformations. For this feature to work properly, both conformations should have the same number of residues. This can be easily achieved using standard PyMOL commands.<br />
#The maps can be viewed with [[mtsslPlotter]]<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=12511MtsslWizard2017-01-18T10:20:21Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2017-01-17:<br />
*[Check out version 2.0 of the mtsslSuite | http://www-hagelueken.thch.uni-bonn.de/index.php/en/2014-08-04-13-28-34/mtssldock]! <br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature. Plots can be viewed with [[mtsslPlotter]].<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported. In "distance map" mode, the program quickly estimates the inter-label distances between all possible spin pairs in a protein molecule. The result is saved as a color coded distance map. It is also possible to calculate difference distance maps between two conformations of a protein.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.7. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed<br />
*Pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
*On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
#The calculated distributions can be viewed with [[mtsslPlotter]].<br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
<br />
===Distance maps===<br />
#change "Mode" to "Distance map"<br />
#For a simple distance map: click twice on the protein of interest<br />
#For a difference distance map between two conformations of a protein: click once on each of the two conformations. For this feature to work properly, both conformations should have the same number of residues. This can be easily achieved using standard PyMOL commands.<br />
#The maps can be viewed with [[mtsslPlotter]]<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=12510MtsslWizard2017-01-18T10:19:15Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2017-01-17:<br />
*[Check out version 2.0 of the mtsslSuite http://www-hagelueken.thch.uni-bonn.de/index.php/en/2014-08-04-13-28-34/mtssldock]! <br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature. Plots can be viewed with [[mtsslPlotter]].<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported. In "distance map" mode, the program quickly estimates the inter-label distances between all possible spin pairs in a protein molecule. The result is saved as a color coded distance map. It is also possible to calculate difference distance maps between two conformations of a protein.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.7. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed<br />
*Pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
*On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
#The calculated distributions can be viewed with [[mtsslPlotter]].<br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
<br />
===Distance maps===<br />
#change "Mode" to "Distance map"<br />
#For a simple distance map: click twice on the protein of interest<br />
#For a difference distance map between two conformations of a protein: click once on each of the two conformations. For this feature to work properly, both conformations should have the same number of residues. This can be easily achieved using standard PyMOL commands.<br />
#The maps can be viewed with [[mtsslPlotter]]<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=12057MtsslWizard2015-07-28T10:07:31Z<p>Gha: /* Usage */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature. Plots can be viewed with [[mtsslPlotter]].<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported. In "distance map" mode, the program quickly estimates the inter-label distances between all possible spin pairs in a protein molecule. The result is saved as a color coded distance map. It is also possible to calculate difference distance maps between two conformations of a protein.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.7. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed<br />
*Pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
*On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
#The calculated distributions can be viewed with [[mtsslPlotter]].<br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
<br />
===Distance maps===<br />
#change "Mode" to "Distance map"<br />
#For a simple distance map: click twice on the protein of interest<br />
#For a difference distance map between two conformations of a protein: click once on each of the two conformations. For this feature to work properly, both conformations should have the same number of residues. This can be easily achieved using standard PyMOL commands.<br />
#The maps can be viewed with [[mtsslPlotter]]<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=12056MtsslWizard2015-07-28T10:06:35Z<p>Gha: /* News */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature. Plots can be viewed with [[mtsslPlotter]].<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported. In "distance map" mode, the program quickly estimates the inter-label distances between all possible spin pairs in a protein molecule. The result is saved as a color coded distance map. It is also possible to calculate difference distance maps between two conformations of a protein.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.7. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed<br />
*Pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
*On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
#The calculated distributions can be viewed with mtsslPlotter.<br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
<br />
===Distance maps===<br />
#change "Mode" to "Distance map"<br />
#For a simple distance map: click twice on the protein of interest<br />
#For a difference distance map between two conformations of a protein: click once on each of the two conformations. For this feature to work properly, both conformations should have the same number of residues. This can be easily achieved using standard PyMOL commands.<br />
#The maps can be viewed with mtsslPlotter<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslPlotter&diff=12055MtsslPlotter2015-07-28T10:05:51Z<p>Gha: /* mtsslPlotter */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslPlotter.py<br />
|author = Dinar Abdullin<br />
|license = -<br />
}}<br />
= mtsslPlotter =<br />
mtsslPlotter is a plotting tool for the visualisation of [[mtsslWizard]] results.<br />
It depends on the wxPython and Matplotlib libraries.<br />
<br />
==Use==<br />
Any plots created by mtsslWizard can be loaded by clicking the "Load Graphs" button.<br />
The graph of interest can then be selected from the "Current Graph" pulldown menu.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslPlotter&diff=12054MtsslPlotter2015-07-28T09:55:22Z<p>Gha: Created page with "{{Infobox script-repo |type = plugin |filename = plugins/mtsslPlotter.py |author = Dinar Abdullin |license = - }} = mtsslPlotter = mtsslPlotter is a plotting tool for ..."</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslPlotter.py<br />
|author = Dinar Abdullin<br />
|license = -<br />
}}<br />
= mtsslPlotter =<br />
mtsslPlotter is a plotting tool for the visualisation of [[mtsslWizard]] results.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=12053MtsslWizard2015-07-28T09:51:09Z<p>Gha: /* News */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature. Plots can be viewed with mtsslPlotter.<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported. In "distance map" mode, the program quickly estimates the inter-label distances between all possible spin pairs in a protein molecule. The result is saved as a color coded distance map. It is also possible to calculate difference distance maps between two conformations of a protein.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.7. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed<br />
*Pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
*On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
#The calculated distributions can be viewed with mtsslPlotter.<br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
<br />
===Distance maps===<br />
#change "Mode" to "Distance map"<br />
#For a simple distance map: click twice on the protein of interest<br />
#For a difference distance map between two conformations of a protein: click once on each of the two conformations. For this feature to work properly, both conformations should have the same number of residues. This can be easily achieved using standard PyMOL commands.<br />
#The maps can be viewed with mtsslPlotter<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=12052MtsslWizard2015-07-28T09:50:09Z<p>Gha: /* Distance maps */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature.<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported. In "distance map" mode, the program quickly estimates the inter-label distances between all possible spin pairs in a protein molecule. The result is saved as a color coded distance map. It is also possible to calculate difference distance maps between two conformations of a protein.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.7. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed<br />
*Pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
*On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
#The calculated distributions can be viewed with mtsslPlotter.<br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
<br />
===Distance maps===<br />
#change "Mode" to "Distance map"<br />
#For a simple distance map: click twice on the protein of interest<br />
#For a difference distance map between two conformations of a protein: click once on each of the two conformations. For this feature to work properly, both conformations should have the same number of residues. This can be easily achieved using standard PyMOL commands.<br />
#The maps can be viewed with mtsslPlotter<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=12051MtsslWizard2015-07-28T09:48:08Z<p>Gha: /* Usage */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature.<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported. In "distance map" mode, the program quickly estimates the inter-label distances between all possible spin pairs in a protein molecule. The result is saved as a color coded distance map. It is also possible to calculate difference distance maps between two conformations of a protein.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.7. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed<br />
*Pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
*On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
#The calculated distributions can be viewed with mtsslPlotter.<br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
<br />
===Distance maps===<br />
#change "Mode" to "Distance map"<br />
#For a simple distance map: click twice on the protein of interest<br />
#For a difference distance map between two conformations of a protein: click once on each of the two conformations<br />
#The maps can be viewed with mtsslPlotter<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=12050MtsslWizard2015-07-28T09:39:39Z<p>Gha: /* Installation */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature.<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported. In "distance map" mode, the program quickly estimates the inter-label distances between all possible spin pairs in a protein molecule. The result is saved as a color coded distance map. It is also possible to calculate difference distance maps between two conformations of a protein.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.7. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed<br />
*Pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
*On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=12049MtsslWizard2015-07-28T09:37:01Z<p>Gha: /* Program features */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature.<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported. In "distance map" mode, the program quickly estimates the inter-label distances between all possible spin pairs in a protein molecule. The result is saved as a color coded distance map. It is also possible to calculate difference distance maps between two conformations of a protein.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.5. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed for v1.1<br />
*On some systems pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=12048MtsslWizard2015-07-27T14:27:24Z<p>Gha: /* News */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2015-07-27:<br />
<br />
*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature.<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.5. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed for v1.1<br />
*On some systems pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=11533MtsslWizard2014-03-04T09:34:37Z<p>Gha: /* News */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2014-03-04:<br />
<br />
* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.5. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed for v1.1<br />
*On some systems pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=11380MtsslWizard2013-08-06T07:37:51Z<p>Gha: /* Usage */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Installation==<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.5. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed for v1.1<br />
*On some systems pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
==Usage==<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=11379MtsslWizard2013-08-06T07:37:18Z<p>Gha: /* How people get it to run... */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Usage==<br />
===Installation===<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.5. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed for v1.1<br />
*On some systems pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people got it to run...====<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=11378MtsslWizard2013-08-06T07:36:44Z<p>Gha: /* Installation */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Usage==<br />
===Installation===<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.5. It does not work with PyMOL 1.3. Here are manuals on how to install it on [[MAC_Install | Mac]] or [[Windows_Install | Windows]].<br />
<br />
Additional requirements:<br />
*SciPy has to be installed for v1.1<br />
*On some systems pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people get it to run...====<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=11377MtsslWizard2013-08-06T07:34:46Z<p>Gha: /* Installation */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Usage==<br />
===Installation===<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.5. It does not work with PyMOL 1.3. [[MAC_Install | Here]] is how to install it.<br />
<br />
Additional requirements:<br />
*SciPy has to be installed for v1.1<br />
*On some systems pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
====How people get it to run...====<br />
"I installed Pymol 1.5 via MacPorts. After putting pyperclip in the python 2.6 library folder, I then downloaded mtsslWizard and used the plugin installer to incorporate it. This was very simple and trouble-free."<br />
<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11367MtsslDock2013-07-25T12:29:50Z<p>Gha: /* Installation */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGui.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Installation==<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the PLUGINS menu. <br />
Alternatively install the plugin via the Plugin Manager.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). Download it and check the contents of the downloaded folder (It is probably called "tkintertable-1.1.2" or similar). There should be a folder in it that is called "tkintertable" put this folder into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
==Docking==<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
===C2 symmetric structures, e.g. symmetric dimers===<br />
If you try the C2 dimer feature: Make a copy of your monomer and leave it at the exact same position. Then, label both monomers independently and import them as protein A and B.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips. Also to Damien Farrell for the tkintertable class.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslTrilaterate&diff=11349MtsslTrilaterate2013-07-09T07:54:56Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslTrilaterate.py<br />
|author = [[User:DinarAbdullin|Dinar Abdullin]]<br />
|license = -<br />
}}<br />
= mtsslTrilaterate =<br />
mtsslTrilaterate is a PyMOL plugin for the trilateration of objects based on distance restraints.<br />
<br />
The mtsslTrilaterate program calculates the coordinates of an object which is defined by the distances from this object to several known objects in a 3D space. This program can be used to localize spin centers in biomolecules by measuring the distances between these metal ions and artificially attached spin labels.<br />
The mtsslTrilaterate program is a part of the mtsslSuite package and it is optimized to work in pair with mtsslWizard program. <br />
The mtsslTrilaterate program is a python code and it works as a plugin for the PyMOL (www.pymol.org) program. It was tested on the Windows 7 64 bit platform. Due to some problems with the wx library in PyMOL the program temporarily does not work on the Mac platform.<br />
<br />
<br />
==News==<br />
2013-07-09:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslTrilaterate screenshot.png |640px]]<br />
<br />
==Installation==<br />
*mtsslTrilaterate requires python 2.7 or higher to be installed. It can be downloaded free of charge from official web site http://www.python.org/. The program also uses wx and numpy modules. If the basic version of Python does not contain these modules they should be installed subsequently (e.g. from http://www.lfd.uci.edu/~gohlke/pythonlibs/).<br />
*mtsslTrilaterate requires PyMOL version compatible with Python 2.7.<br />
*Save mtsslTrilaterate.py file somewhere in your computer.<br />
*Run PyMOL. In the Plugin menu select Plugin Manager. Then open the Install New Plugin page and click on Choose file. Select the trilater.py file and choose a plugin directory. If installation is finished successfully a message “Plugin Trilateration has been installed” would appear.<br />
*Run mtsslTrilaterate from the Plugin menu.<br />
<br />
<br />
mtsslTrilaterate has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*wx<br />
*NumPy<br />
<br />
==Trilateration==<br />
===User interface===<br />
<br />
The graphical user interface of mtsslTrilaterate is shown above. It contains a small menu and a main working window. The main window consists of 2 main panels called “INPUT” and “OUTPUT”. <br />
The “INPUT” panel represents all input data as a table. Each row of this table is related to a certain label (spin label) that was introduced to the structural model. The identifiers of these labels are listed in the first column. The following three columns correspond to the average coordinate (x, y, z) of the label. The last two columns represent the mean value and the standard deviation of the distances between the particular label and a target. <br />
<br />
<br />
*Load biomolecule structure to current PyMOL session. It can be done either in PyMOL selecting File → Open or in mtsslTrilaterate selecting PyMOL → Load structure to PyMOL. <br />
*Create spin labels by means of mtsslWizard selecting in PyMOL Wizard → mtsslWizard. This wizard performs site-directed spin labelling in silico (look http://pymolwiki.org/index.php/MtsslWizard for more information).<br />
*The coordinates of the selected label can be entered in three different ways. Firstly, they can be entered manually to the table. Secondly, the parameters related to a particular spin label can be imported from the current PyMOL session by pushing the “Import from PyMOL” button. The identifiers and average coordinates of spin labels that were generated inside PyMOL beforehand are in this way imported into the program and can be assigned to rows in the data table. Thirdly, the label coordinates can be loaded from an ASCII data file by selecting the label in the table and then clicking the “Load coordinates” button. The data file should contain 3 columns corresponding to x, y, z coordinates. If the label is flexible (i.e. has a set of the coordinates) an average label coordinates will be calculated after loading the data file. <br />
*The distance between the selected label and the target can be entered manually to the corresponding fields of the table or loaded from an ASCII data file clicking the “Load distances” button. This way an interspin distance distribution generated within the DeerAnalysis program (Jeschke, G.; Chechik, V.; Ionita, P.; Godt, A.; Zimmermann, H.; Banham, J.; Timmel, C. R.; Hilger, D.; Jung, H. Appl. Magn. Reson. 2006, 30, 473) can be imported to the program.<br />
*If all input data entered press “Accept” button. At this stage the program checks if at least four spin labels were described completely. Four spin labels is a minimal number of labels that allows to solve the trilateration problem.<br />
*Click “Compute” button. After calculations, the coordinates of the target and their standard deviations should appear in the “OUTPUT” panel. The program also displays an obtained χ2 value and a number of iterations which was required to reach this χ2 value.<br />
Push Export to PyMOL button to get a graphical representation of trilateration in the current PyMOL session. Two PyMOL objects, called “trilateration” and “target”, will be created inside PyMOL (Figure 1). *The “trilateration” object represents a ‘trilateration-sphere’ plotted around each used spin label. The radius of each sphere equals to the average distance between the corresponding spin label and the unlocalized spin center. The space where these spheres intersect each other determines the location of the spin center. This space is depicted by the “target” ellipsoid. The center of the ellipsoid corresponds to the most probable coordinates of the spin center, whereas the legths of its semi-principal axes equal to the obtained standard errors of these coordinates. The scale of semi-principal axes, i.e. the confidence level of the solution, can be incresed in the File → Preferences → Output panel. <br />
*Click “Save as” button or select File → Save as in the File menu to save current section as a ASCII data file. Afterwards this session can be reinitialized by opening this data file through File → Open.<br />
<br />
<br />
The “OUTPUT” panel is used to displays the results of the trilateration process. After the calculation is started by pushing the “Compute” button, the program solves the trilateration problem and displays the most probable coordinates of the target and their standard errors.<br />
The File menu contains the Open, Save as, and Close commands to work with data files. It also incorporates the Preferences window which allows user to format the input and output data of the program as well as to adjuxt some calculation parameters.<br />
The PyMOL menu allows user to open and close the PyMOL data files within the program.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
abdullin'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslTrilaterate&diff=11348MtsslTrilaterate2013-07-09T07:54:05Z<p>Gha: /* Trilateration */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslTrilaterate.py<br />
|author = [[User:DinarAbdullin|Dinar Abdullin]]<br />
|license = -<br />
}}<br />
= mtsslTrilaterate =<br />
mtsslTrilaterate is a PyMOL plugin for the trilateration of objects based on distance restraints.<br />
<br />
The mtsslTrilaterate program calculates the coordinates of an object which is defined by the distances from this object to several known objects in a 3D space. This program can be used to localize spin centers in biomolecules by measuring the distances between these metal ions and artificially attached spin labels.<br />
The mtsslTrilaterate program is a part of the mtsslSuite package and it is optimized to work in pair with mtsslWizard program. <br />
The mtsslTrilaterate program is a python code and it works as a plugin for the PyMOL (www.pymol.org) program. It was tested on the Windows 7 64 bit platform. Due to some problems with the wx library in PyMOL the program temporarily does not work on the Mac platform.<br />
<br />
<br />
==News==<br />
2013-07-09:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslTrilaterate screenshot.png |640px]]<br />
<br />
==Installation==<br />
*mtsslTrilaterate requires python 2.7 or higher to be installed. It can be downloaded free of charge from official web site http://www.python.org/. The program also uses wx and numpy modules. If the basic version of Python does not contain these modules they should be installed subsequently (e.g. from http://www.lfd.uci.edu/~gohlke/pythonlibs/).<br />
*mtsslTrilaterate requires PyMOL version compatible with Python 2.7.<br />
*Save mtsslTrilaterate.py file somewhere in your computer.<br />
*Run PyMOL. In the Plugin menu select Plugin Manager. Then open the Install New Plugin page and click on Choose file. Select the trilater.py file and choose a plugin directory. If installation is finished successfully a message “Plugin Trilateration has been installed” would appear.<br />
*Run mtsslTrilaterate from the Plugin menu.<br />
<br />
<br />
mtsslTrilaterate has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*wx<br />
*NumPy<br />
<br />
==Trilateration==<br />
===User interface===<br />
<br />
The graphical user interface of mtsslTrilaterate is shown above. It contains a small menu and a main working window. The main window consists of 2 main panels called “INPUT” and “OUTPUT”. <br />
The “INPUT” panel represents all input data as a table. Each row of this table is related to a certain label (spin label) that was introduced to the structural model. The identifiers of these labels are listed in the first column. The following three columns correspond to the average coordinate (x, y, z) of the label. The last two columns represent the mean value and the standard deviation of the distances between the particular label and a target. <br />
<br />
<br />
*Load biomolecule structure to current PyMOL session. It can be done either in PyMOL selecting File → Open or in mtsslTrilaterate selecting PyMOL → Load structure to PyMOL. <br />
*Create spin labels by means of mtsslWizard selecting in PyMOL Wizard → mtsslWizard. This wizard performs site-directed spin labelling in silico (look http://pymolwiki.org/index.php/MtsslWizard for more information).<br />
*The coordinates of the selected label can be entered in three different ways. Firstly, they can be entered manually to the table. Secondly, the parameters related to a particular spin label can be imported from the current PyMOL session by pushing the “Import from PyMOL” button. The identifiers and average coordinates of spin labels that were generated inside PyMOL beforehand are in this way imported into the program and can be assigned to rows in the data table. Thirdly, the label coordinates can be loaded from an ASCII data file by selecting the label in the table and then clicking the “Load coordinates” button. The data file should contain 3 columns corresponding to x, y, z coordinates. If the label is flexible (i.e. has a set of the coordinates) an average label coordinates will be calculated after loading the data file. <br />
*The distance between the selected label and the target can be entered manually to the corresponding fields of the table or loaded from an ASCII data file clicking the “Load distances” button. This way an interspin distance distribution generated within the DeerAnalysis program (Jeschke, G.; Chechik, V.; Ionita, P.; Godt, A.; Zimmermann, H.; Banham, J.; Timmel, C. R.; Hilger, D.; Jung, H. Appl. Magn. Reson. 2006, 30, 473) can be imported to the program.<br />
*If all input data entered press “Accept” button. At this stage the program checks if at least four spin labels were described completely. Four spin labels is a minimal number of labels that allows to solve the trilateration problem.<br />
*Click “Compute” button. After calculations, the coordinates of the target and their standard deviations should appear in the “OUTPUT” pane. The program also displays an obtained χ2 value and a number of iterations which was required to reach this χ2 value.<br />
Push Export to PyMOL button to get a graphical representation of trilateration in the current PyMOL session. Two PyMOL objects, called “trilateration” and “target”, will be created inside PyMOL (Figure 1). *The “trilateration” object represents a ‘trilateration-sphere’ plotted around each used spin label. The radius of each sphere equals to the average distance between the corresponding spin label and the unlocalized spin center. The space where these spheres intersect each other determines the location of the spin center. This space is depicted by the “target” ellipsoid. The center of the ellipsoid corresponds to the most probable coordinates of the spin center, whereas the legths of its semi-principal axes equal to the obtained standard errors of these coordinates. The scale of semi-principal axes, i.e. the confidence level of the solution, can be incresed in the File → Preferences → Output pane. <br />
*Click “Save as” button or select File → Save as in the File menu to save current section as a ASCII data file. Afterwards this session can be reinitialized by opening this data file through File → Open.<br />
<br />
<br />
The “OUTPUT” panel is used to displays the results of the trilateration process. After the calculation is started by pushing the “Compute” button, the program solves the trilateration problem and displays the most probable coordinates of the target and their standard errors.<br />
The File menu contains the Open, Save as, and Close commands to work with data files. It also incorporates the Preferences window which allows user to format the input and output data of the program as well as to adjuxt some calculation parameters.<br />
The PyMOL menu allows user to open and close the PyMOL data files within the program.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
abdullin'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslTrilaterate&diff=11347MtsslTrilaterate2013-07-09T07:51:45Z<p>Gha: /* Installation */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslTrilaterate.py<br />
|author = [[User:DinarAbdullin|Dinar Abdullin]]<br />
|license = -<br />
}}<br />
= mtsslTrilaterate =<br />
mtsslTrilaterate is a PyMOL plugin for the trilateration of objects based on distance restraints.<br />
<br />
The mtsslTrilaterate program calculates the coordinates of an object which is defined by the distances from this object to several known objects in a 3D space. This program can be used to localize spin centers in biomolecules by measuring the distances between these metal ions and artificially attached spin labels.<br />
The mtsslTrilaterate program is a part of the mtsslSuite package and it is optimized to work in pair with mtsslWizard program. <br />
The mtsslTrilaterate program is a python code and it works as a plugin for the PyMOL (www.pymol.org) program. It was tested on the Windows 7 64 bit platform. Due to some problems with the wx library in PyMOL the program temporarily does not work on the Mac platform.<br />
<br />
<br />
==News==<br />
2013-07-09:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslTrilaterate screenshot.png |640px]]<br />
<br />
==Installation==<br />
*mtsslTrilaterate requires python 2.7 or higher to be installed. It can be downloaded free of charge from official web site http://www.python.org/. The program also uses wx and numpy modules. If the basic version of Python does not contain these modules they should be installed subsequently (e.g. from http://www.lfd.uci.edu/~gohlke/pythonlibs/).<br />
*mtsslTrilaterate requires PyMOL version compatible with Python 2.7.<br />
*Save mtsslTrilaterate.py file somewhere in your computer.<br />
*Run PyMOL. In the Plugin menu select Plugin Manager. Then open the Install New Plugin page and click on Choose file. Select the trilater.py file and choose a plugin directory. If installation is finished successfully a message “Plugin Trilateration has been installed” would appear.<br />
*Run mtsslTrilaterate from the Plugin menu.<br />
<br />
<br />
mtsslTrilaterate has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*wx<br />
*NumPy<br />
<br />
==Trilateration==<br />
User interface<br />
<br />
The graphical user interface of mtsslTrilaterate is presented on Figure 1. It contains a small menu and a main working window. The main window consists of 2 main panes called “INPUT” and “OUTPUT”. <br />
The “INPUT” pane represents all input data as a table. Each row of this table is related to a certain label (spin label) that was introduced to the structural model. The identifiers of these labels are listed in the first column. The following three columns correspond to the average coordinate (x, y, z) of the label. The last two columns represent the mean value and the standard deviation of the distances between the particular label and a target. <br />
<br />
<br />
1. Load biomolecule structure to current PyMOL session. It can be done either in PyMOL selecting File → Open or in mtsslTrilaterate selecting PyMOL → Load structure to PyMOL. <br />
2. Create spin labels by means of mtsslWizard selecting in PyMOL Wizard → mtsslWizard. This wizard performs site-directed spin labelling in silico (look http://pymolwiki.org/index.php/MtsslWizard for more information).<br />
3. The coordinates of the selected label can be entered in three different ways. Firstly, they can be entered manually to the table. Secondly, the parameters related to a particular spin label can be imported from the current PyMOL session by pushing the “Import from PyMOL” button. The identifiers and average coordinates of spin labels that were generated inside PyMOL beforehand are in this way imported into the program and can be assigned to rows in the data table. Thirdly, the label coordinates can be loaded from an ASCII data file by selecting the label in the table and then clicking the “Load coordinates” button. The data file should contain 3 columns corresponding to x, y, z coordinates. If the label is flexible (i.e. has a set of the coordinates) an average label coordinates will be calculated after loading the data file. <br />
4. The distance between the selected label and the target can be entered manually to the corresponding fields of the table or loaded from an ASCII data file clicking the “Load distances” button. This way an interspin distance distribution generated within the DeerAnalysis program (Jeschke, G.; Chechik, V.; Ionita, P.; Godt, A.; Zimmermann, H.; Banham, J.; Timmel, C. R.; Hilger, D.; Jung, H. Appl. Magn. Reson. 2006, 30, 473) can be imported to the program.<br />
5. If all input data entered press “Accept” button. At this stage the program checks if at least four spin labels were described completely. Four spin labels is a minimal number of labels that allows to solve the trilateration problem.<br />
6. Click “Compute” button. After calculations, the coordinates of the target and their standard deviations should appear in the “OUTPUT” pane. The program also displays an obtained χ2 value and a number of iterations which was required to reach this χ2 value.<br />
7. Push Export to PyMOL button to get a graphical representation of trilateration in the current PyMOL session. Two PyMOL objects, called “trilateration” and “target”, will be created inside PyMOL (Figure 1). The “trilateration” object represents a ‘trilateration-sphere’ plotted around each used spin label. The radius of each sphere equals to the average distance between the corresponding spin label and the unlocalized spin center. The space where these spheres intersect each other determines the location of the spin center. This space is depicted by the “target” ellipsoid. The center of the ellipsoid corresponds to the most probable coordinates of the spin center, whereas the legths of its semi-principal axes equal to the obtained standard errors of these coordinates. The scale of semi-principal axes, i.e. the confidence level of the solution, can be incresed in the File → Preferences → Output pane. <br />
8. Click “Save as” button or select File → Save as in the File menu to save current section as a ASCII data file. Afterwards this session can be reinitialized by opening this data file through File → Open.<br />
<br />
<br />
The “OUTPUT” pane is used to displays the results of the trilateration process. After the calculation is started by pushing the “Compute” button, the program solves the trilateration problem and displays the most probable coordinates of the target and their standard errors.<br />
The File menu contains the Open, Save as, and Close commands to work with data files. It also incorporates the Preferences window which allows user to format the input and output data of the program as well as to adjuxt some calculation parameters.<br />
The PyMOL menu allows user to open and close the PyMOL data files within the program.<br />
<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
abdullin'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslTrilaterate&diff=11346MtsslTrilaterate2013-07-09T07:47:17Z<p>Gha: Created page with "{{Infobox script-repo |type = plugin |filename = plugins/mtsslTrilaterate.py |author = Dinar Abdullin |license = - }} = mtsslTrilaterate = mtssl..."</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslTrilaterate.py<br />
|author = [[User:DinarAbdullin|Dinar Abdullin]]<br />
|license = -<br />
}}<br />
= mtsslTrilaterate =<br />
mtsslTrilaterate is a PyMOL plugin for the trilateration of objects based on distance restraints.<br />
<br />
The mtsslTrilaterate program calculates the coordinates of an object which is defined by the distances from this object to several known objects in a 3D space. This program can be used to localize spin centers in biomolecules by measuring the distances between these metal ions and artificially attached spin labels.<br />
The mtsslTrilaterate program is a part of the mtsslSuite package and it is optimized to work in pair with mtsslWizard program. <br />
The mtsslTrilaterate program is a python code and it works as a plugin for the PyMOL (www.pymol.org) program. It was tested on the Windows 7 64 bit platform. Due to some problems with the wx library in PyMOL the program temporarily does not work on the Mac platform.<br />
<br />
<br />
==News==<br />
2013-07-09:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslTrilaterate screenshot.png |640px]]<br />
<br />
==Installation==<br />
1. mtsslTrilaterate requires python 2.7 or higher to be installed. It can be downloaded free of charge from official web site http://www.python.org/. The program also uses wx and numpy modules. If the basic version of Python does not contain these modules they should be installed subsequently (e.g. from http://www.lfd.uci.edu/~gohlke/pythonlibs/).<br />
2. mtsslTrilaterate requires PyMOL version compatible with Python 2.7.<br />
3. Save trilater.py file somewhere in your computer.<br />
4. Run PyMOL. In the Plugin menu select Plugin Manager. Then open the Install New Plugin page and click on Choose file. Select the trilater.py file and choose a plugin directory. If installation is finished successfully a message “Plugin Trilateration has been installed” would appear.<br />
5. Run mtsslTrilaterate from the Plugin menu.<br />
<br />
<br />
mtsslTrilaterate has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*wx<br />
*NumPy<br />
<br />
<br />
==Trilateration==<br />
User interface<br />
<br />
The graphical user interface of mtsslTrilaterate is presented on Figure 1. It contains a small menu and a main working window. The main window consists of 2 main panes called “INPUT” and “OUTPUT”. <br />
The “INPUT” pane represents all input data as a table. Each row of this table is related to a certain label (spin label) that was introduced to the structural model. The identifiers of these labels are listed in the first column. The following three columns correspond to the average coordinate (x, y, z) of the label. The last two columns represent the mean value and the standard deviation of the distances between the particular label and a target. <br />
<br />
<br />
1. Load biomolecule structure to current PyMOL session. It can be done either in PyMOL selecting File → Open or in mtsslTrilaterate selecting PyMOL → Load structure to PyMOL. <br />
2. Create spin labels by means of mtsslWizard selecting in PyMOL Wizard → mtsslWizard. This wizard performs site-directed spin labelling in silico (look http://pymolwiki.org/index.php/MtsslWizard for more information).<br />
3. The coordinates of the selected label can be entered in three different ways. Firstly, they can be entered manually to the table. Secondly, the parameters related to a particular spin label can be imported from the current PyMOL session by pushing the “Import from PyMOL” button. The identifiers and average coordinates of spin labels that were generated inside PyMOL beforehand are in this way imported into the program and can be assigned to rows in the data table. Thirdly, the label coordinates can be loaded from an ASCII data file by selecting the label in the table and then clicking the “Load coordinates” button. The data file should contain 3 columns corresponding to x, y, z coordinates. If the label is flexible (i.e. has a set of the coordinates) an average label coordinates will be calculated after loading the data file. <br />
4. The distance between the selected label and the target can be entered manually to the corresponding fields of the table or loaded from an ASCII data file clicking the “Load distances” button. This way an interspin distance distribution generated within the DeerAnalysis program (Jeschke, G.; Chechik, V.; Ionita, P.; Godt, A.; Zimmermann, H.; Banham, J.; Timmel, C. R.; Hilger, D.; Jung, H. Appl. Magn. Reson. 2006, 30, 473) can be imported to the program.<br />
5. If all input data entered press “Accept” button. At this stage the program checks if at least four spin labels were described completely. Four spin labels is a minimal number of labels that allows to solve the trilateration problem.<br />
6. Click “Compute” button. After calculations, the coordinates of the target and their standard deviations should appear in the “OUTPUT” pane. The program also displays an obtained χ2 value and a number of iterations which was required to reach this χ2 value.<br />
7. Push Export to PyMOL button to get a graphical representation of trilateration in the current PyMOL session. Two PyMOL objects, called “trilateration” and “target”, will be created inside PyMOL (Figure 1). The “trilateration” object represents a ‘trilateration-sphere’ plotted around each used spin label. The radius of each sphere equals to the average distance between the corresponding spin label and the unlocalized spin center. The space where these spheres intersect each other determines the location of the spin center. This space is depicted by the “target” ellipsoid. The center of the ellipsoid corresponds to the most probable coordinates of the spin center, whereas the legths of its semi-principal axes equal to the obtained standard errors of these coordinates. The scale of semi-principal axes, i.e. the confidence level of the solution, can be incresed in the File → Preferences → Output pane. <br />
8. Click “Save as” button or select File → Save as in the File menu to save current section as a ASCII data file. Afterwards this session can be reinitialized by opening this data file through File → Open.<br />
<br />
<br />
The “OUTPUT” pane is used to displays the results of the trilateration process. After the calculation is started by pushing the “Compute” button, the program solves the trilateration problem and displays the most probable coordinates of the target and their standard errors.<br />
The File menu contains the Open, Save as, and Close commands to work with data files. It also incorporates the Preferences window which allows user to format the input and output data of the program as well as to adjuxt some calculation parameters.<br />
The PyMOL menu allows user to open and close the PyMOL data files within the program.<br />
<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
abdullin'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=File:MtsslTrilaterate_screenshot.png&diff=11345File:MtsslTrilaterate screenshot.png2013-07-09T07:41:23Z<p>Gha: </p>
<hr />
<div></div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11344MtsslDock2013-07-08T11:20:41Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGui.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Installation==<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). Download it and check the contents of the downloaded folder (It is probably called "tkintertable-1.1.2" or similar). There should be a folder in it that is called "tkintertable" put this folder into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
==Docking==<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
===C2 symmetric structures, e.g. symmetric dimers===<br />
If you try the C2 dimer feature: Make a copy of your monomer and leave it at the exact same position. Then, label both monomers independently and import them as protein A and B.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips. Also to Damien Farrell for the tkintertable class.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11343MtsslDock2013-07-08T11:20:02Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGui.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Installation==<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). Download it and check the contents of the downloaded folder (It is probably called "tkintertable-1.1.2" or similar). There should be a folder in it that is called "tkintertable" put this folder into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
==Docking==<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
===C2 symmetric structures, e.g. symmetric dimers===<br />
If you try the C2 dimer feature: Make a copy of your monomer and leave it at the exact same position. Then, label both monomers independently and import them as protein A and B.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips. Also to Damien Farrell for the tkintertable class.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11342MtsslDock2013-07-08T11:18:50Z<p>Gha: /* C2 symmetric structures, e.g. symmetric dimers */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGui.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). Download it and check the contents of the downloaded folder (It is probably called "tkintertable-1.1.2" or similar). There should be a folder in it that is called "tkintertable" put this folder into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
==C2 symmetric structures, e.g. symmetric dimers==<br />
If you try the C2 dimer feature: Make a copy of your monomer and leave it at the exact same position. Then, label both monomers independently and import them as protein A and B.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips. Also to Damien Farrell for the tkintertable class.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11341MtsslDock2013-07-08T11:18:27Z<p>Gha: /* Usage */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGui.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). Download it and check the contents of the downloaded folder (It is probably called "tkintertable-1.1.2" or similar). There should be a folder in it that is called "tkintertable" put this folder into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
==C2 symmetric structures, e.g. symmetric dimers==<br />
if you try the C2 dimer feature: Make a copy of your monomer and leave it at the exact same position. Then, label both monomers independently and import them as protein A and B.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips. Also to Damien Farrell for the tkintertable class.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11340MtsslDock2013-07-08T09:56:39Z<p>Gha: /* Installation */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGui.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). Download it and check the contents of the downloaded folder (It is probably called "tkintertable-1.1.2" or similar). There should be a folder in it that is called "tkintertable" put this folder into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips. Also to Damien Farrell for the tkintertable class.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslWizard&diff=11339MtsslWizard2013-07-05T09:47:40Z<p>Gha: /* News */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslWizard.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslWizard =<br />
mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.<br />
<br />
==News==<br />
<br />
2013-07-05:<br />
<br />
* added two new labels: DOTA and K1 (pAcPhe based)<br />
<br />
2013-01-31:<br />
<br />
Version 1.1 in script repository.<br />
<br />
Some new features of v1.1:<br />
* Much faster. The algorithm was optimized and the speed of the program is now almost independent off the size of the molecule. Due to this, 'thorough search' is now set as default and the 'copy and move' mode has been dropped.<br />
<br />
* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.<br />
<br />
* Distances and histogram are directly copied to the clipboard or written out to a file as before. The result file contains 4 columns: 1-distances, 2-bins for histogram, 3-histogram frequencies, 4-histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
* Improved interface. Amongst other things, the clash control settings were simplified: There are now only two settings for vdW restraints: 'tight' and 'loose'. Also, only the average and c-Beta distances are displayed in the PyMOL viewer to avoid screen clutter (see screenshot).<br />
<br />
The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.<br />
<br />
Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].<br />
<br />
==Program features==<br />
Spin labels can be attached to any position of a protein or nucleic acid just by pointing and clicking. The program then searches the conformational space of the label and determines which conformations of the label do not clash with the macromolecule. In "distance mode", distances between label ensembles can be determined and exported.<br />
<br />
Please reference: <br />
<br />
[http://www.springerlink.com/content/7148j5k2ppk475wu/ '''MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL''', Gregor Hagelueken, Richard Ward, James H. Naismith and Olav Schiemann, DOI: 10.1007/s00723-012-0314-0]<br />
<br />
==Screen shot==<br />
[[File:MtsslWizardv1-1.jpg]]<br />
<br />
==Usage==<br />
===Installation===<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslWizard.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
<br />
mtsslWizard has been tested with PyMOL 1.5.<br />
<br />
Additional requirements:<br />
*SciPy has to be installed for v1.1<br />
*On some systems pyperclip or xerox have to be installed for the clipboard support.<br />
<br />
===Labeling===<br />
#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands. <br />
#Start the mtsslWizard via Wizards>mtsslWizard<br />
#If needed, vary the search parameters: "Speed" and "vdW restraints". 'Speed' determines how many conformations of the label will be generated and checked for clashes. The 'vdW restraints' parameter determines how stringent conformations are checked for clashes with the macromolecular surface.<br />
#Click "Search conformers!" to start the calculation.<br />
<br />
===Distance calculation===<br />
#change "Mode" to "Distance"<br />
#click the first and second ensemble<br />
#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take a couple of seconds! <br />
<br />
Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:<br />
#distances<br />
#bins for histogram<br />
#histogram frequencies<br />
#histogram frequencies with highest value normalized to 1.0 for comparisons<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
Hagelueken G, Ward R, Naismith JH, Schiemann O (2012) MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. Appl. Magn. Res. accepted for publication<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
==Older versions==<br />
*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11338MtsslDock2013-07-05T08:09:08Z<p>Gha: /* Acknowledgement */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGui.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). You can just download it and put it into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips. Also to Damien Farrell for the tkintertable class.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11337MtsslDock2013-07-04T15:19:16Z<p>Gha: /* mtsslDock */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGui.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 in repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). You can just download it and put it into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11336MtsslDock2013-07-04T15:18:48Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGui.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 submitted to script repository. Should be accessible soon.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). You can just download it and put it into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11335MtsslDock2013-07-04T14:53:23Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDockGUI.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 submitted to script repository. Should be accessible soon.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). You can just download it and put it into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11334MtsslDock2013-07-04T14:46:27Z<p>Gha: /* Installation */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDock.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 submitted to script repository. Should be accessible soon.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). You can just download it and put it into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11333MtsslDock2013-07-04T14:45:03Z<p>Gha: /* News */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDock.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 submitted to script repository. Should be accessible soon.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: You will need scipy, numpy and a module called tkintertable (http://code.google.com/p/tkintertable/). You can just download it and put it into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11332MtsslDock2013-07-04T14:39:44Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDock.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 submitted to script repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: You will need scipy, numpy and a module called tkintertable (http://code.google.com/p/tkintertable/). You can just download it and put it into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with [[MtsslWizard | mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11331MtsslDock2013-07-04T14:39:21Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDock.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 submitted to script repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: You will need scipy, numpy and a module called tkintertable (http://code.google.com/p/tkintertable/). You can just download it and put it into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with [[MtsslWizard mtsslWizard (1.1)]] and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11330MtsslDock2013-07-04T14:38:12Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDock.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 submitted to script repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: You will need scipy, numpy and a module called tkintertable (http://code.google.com/p/tkintertable/). You can just download it and put it into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with mtsslWizard (1.1) and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Reference==<br />
If you find this program useful, please cite this paper:<br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
It also contains detailed informations about the program, examples and a discussion of limitations of the approach.<br />
<br />
<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11329MtsslDock2013-07-04T14:36:35Z<p>Gha: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDock.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 submitted to script repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: You will need scipy, numpy and a module called tkintertable (http://code.google.com/p/tkintertable/). You can just download it and put it into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with mtsslWizard (1.1) and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0":<br />
<br />
[[File:MtsslDock distanceTable.jpg | 500px]]<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
[[File:MtsslDock results.jpg | 500px]]<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
The program was tested with a crystal structure of a protein:protein complex and it works well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=File:MtsslDock_results.jpg&diff=11328File:MtsslDock results.jpg2013-07-04T14:35:19Z<p>Gha: </p>
<hr />
<div></div>Ghahttps://pymolwiki.org/index.php?title=File:MtsslDock_distanceTable.jpg&diff=11327File:MtsslDock distanceTable.jpg2013-07-04T14:33:36Z<p>Gha: </p>
<hr />
<div></div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11326MtsslDock2013-07-04T14:32:29Z<p>Gha: /* Docking */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDock.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 submitted to script repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: You will need scipy, numpy and a module called tkintertable (http://code.google.com/p/tkintertable/). You can just download it and put it into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with mtsslWizard (1.1) and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
[[File:MtsslDock Import Labels.jpg | 500px]]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0".<br />
<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
I have tested the program with a crystal structure of a protein:protein complex and it seems to work well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=MtsslDock&diff=11325MtsslDock2013-07-04T14:32:11Z<p>Gha: /* Docking */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = plugins/mtsslDock.py<br />
|author = [[User:Gha|Gregor Hagelueken]]<br />
|license = -<br />
}}<br />
= mtsslDock =<br />
mtsslWizard is a PyMOL plugin for distance constrained rigid-body docking.<br />
<br />
==News==<br />
2013-07-04:<br />
<br />
Version 1.0 submitted to script repository.<br />
<br />
<br />
If you use this program, please reference: <br />
<br />
[http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.809804#.UdWAzha3n6s/ '''mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI: 10.1080/00268976.2013.809804]<br />
<br />
==Screen shot==<br />
[[File:MtsslDock screenshot.jpg |640px]]<br />
<br />
==Usage==<br />
===Installation===<br />
*Step 1:<br />
Install the program by copying the code from the link above into an empty text file (e.g. "mtsslDock.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the WIZARDS menu. <br />
Alternatively install the wizard via the plugins menu.<br />
<br />
*Step 2:<br />
This might be a bit tricky: You will need scipy, numpy and a module called tkintertable (http://code.google.com/p/tkintertable/). You can just download it and put it into the 'site-packages' folder of the Python installation that PyMOL uses. On Windows it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages<br />
<br />
On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:<br />
http://sourceforge.net/projects/pmw/files/Pmw/Pmw.1.3.3/<br />
Install it to /Applications/PyMOLX11Hybrid.app/pymol/modules into a folder called 'Pmw'. You might want to rename the original Pmw folder in case something gets messed up…<br />
<br />
mtsslDock has been tested with PyMOL 1.5.<br />
<br />
===Additional requirements:===<br />
*SciPy<br />
*NumPy<br />
*[http://code.google.com/p/tkintertable/ tkintertable]<br />
<br />
===Docking===<br />
To do a docking run, label the two proteins with mtsslWizard (1.1) and then start mtsslDock from the Plugins menu. <br />
The GUI should then appear and look like this:<br />
[File:MtsslDock Import Labels.jpg | 500px]<br />
<br />
First select the two proteins that you want to dock using the pulldown menus at the top of the 'Import Labels' dialog. Protein A will be held fixed, protein B will be moved. In the list below these two pulldowns, the program will list all mtsslWizard labels that it found in the PyMOL session. You can assign each of them to either A or B using the radiobuttons. Once you are happy with everything, click "OK".<br />
<br />
The program will then build up a table for the docking constraints and you can enter your distance data (the rows are proteinA labels, the columns protein B labels). If a distance was not measured, enter "0", otherwise enter the distance and uncertainty separated by semicolon, e.g. "12.4;5.0".<br />
<br />
<br />
You can then save this table for later reference in the file menu. Note that if you do save it, you have to use the exact same order of labels if you want to use it again.<br />
If you want you can then change some docking settings in the 'Settings' menu, but the defaults should be fine.<br />
<br />
Hit "Dock" at the bottom. The program will do 10 independent docking runs. Depending on the size of the molecules this might take 5-30 min. There is a progress bar on the bottom right.<br />
Once the docking has finished, a "Results" tab will be added to the GUI:<br />
<br />
Here, the solutions are listed on the left, clashing ones are marked by "-clash" added to their names. The table on the right shows the log of the docking or the difference between docked and experimental distances for the selected solution, depending on what you select with the three buttons below the table. The box on the bottom left shows you the settings that were used for this docking run.<br />
<br />
I have tested the program with a crystal structure of a protein:protein complex and it seems to work well when you have at least 6 or better 8 distance constraints. See the paper for a discussion of performance.<br />
<br />
==Contact==<br />
hagelueken'at'pc.uni-bonn.de<br />
<br />
==Acknowledgement==<br />
Thanks to Jason Vertrees and Thomas Holder for some programming tips.</div>Ghahttps://pymolwiki.org/index.php?title=File:MtsslDock_Import_Labels.jpg&diff=11324File:MtsslDock Import Labels.jpg2013-07-04T14:31:26Z<p>Gha: </p>
<hr />
<div></div>Gha