Latest revision as of 14:00, 21 May 2020

mtsslWizard

Type	PyMOL Plugin
Download	plugins/mtsslWizard.py
Author(s)	Gregor Hagelueken
License	-
	This code has been put under version control in the project Pymol-script-repo

mtsslWizard is a PyMOL wizard for in silico spin labeling of proteins.

News

2020-05-21

If you are having trouble with installation give this a try

2017-01-17:

Version 2.0 available!

2015-07-27:

uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature. Plots can be viewed with mtsslPlotter.

2014-03-04:

uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!

2013-07-05:

added two new labels: DOTA and K1 (pAcPhe based)

2013-01-31:

Version 1.1 in script repository.

Some new features of v1.1:

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.

New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.

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

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).

The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.

Version 1.0 is still available here.

Program features

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.

Please reference:

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

Screen shot

Installation

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. Alternatively install the wizard via the plugins menu.

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 or Windows.

Additional requirements:

SciPy has to be installed
Pyperclip or xerox have to be installed for the clipboard support.

How people got it to run...

On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.

"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."

Usage

Labeling

Open a structure in PyMOL and remove any unwanted solvent molecules or ligands.
Start the mtsslWizard via Wizards>mtsslWizard
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.
Click "Search conformers!" to start the calculation.

Distance calculation

change "Mode" to "Distance"
click the first and second ensemble
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!
The calculated distributions can be viewed with mtsslPlotter.

Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:

distances
bins for histogram
histogram frequencies
histogram frequencies with highest value normalized to 1.0 for comparisons

Distance maps

change "Mode" to "Distance map"
For a simple distance map: click twice on the protein of interest
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.
The maps can be viewed with mtsslPlotter

Reference

If you find this program useful, please cite this paper:

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

It also contains detailed informations about the program, examples and a discussion of limitations of the approach.

Older versions

Version 1.0

Contact

hagelueken'at' uni-bonn.de

Acknowledgement

Thanks to Jason Vertrees and Thomas Holder for some programming tips.

@@ Line 1: / Line 1: @@
+{{Infobox script-repo
+|type      = plugin
+|filename  = plugins/mtsslWizard.py
+|author    = [[User:Gha|Gregor Hagelueken]]
+|license   = -
+}}
 = mtsslWizard =
 mtsslWizard is a PyMOL wizard for ''in silico'' spin labeling of proteins.
+==News==
+-05-21
+*If you are having trouble with installation give [http://www.mtsslsuite.isb.ukbonn.de this] a try
+-01-17:
+*[http://www-hagelueken.thch.uni-bonn.de/index.php/en/2014-08-04-13-28-34/mtssldock Version 2.0 available]!
+-07-27:
+*uploaded a new version (1.3) to repository. Includes some new spin labels and a distance map feature. Plots can be viewed with [[mtsslPlotter]].
+-03-04:
+* uploaded a new version (1.12) to repository. Fixes a bug that occurred on some machines. Thanks to C. Engelhard for noticing!
+-07-05:
+* added two new labels: DOTA and K1 (pAcPhe based)
+-01-31:
+Version 1.1 in script repository.
+Some new features of v1.1:
+* 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.
+* New spin labels. The program now contains MTSSL, PROXYL and two labels for nucleic acids. Additional spin labels can be added upon request.
+* 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
+* 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).
+The new version was thoroughly tested. If you encounter any bugs or problems, please use the contact address below.
+Version 1.0 is still available [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py here].
 ==Program features==
-An MTSSL spin label can be attached to any position of a protein just by pointing and clicking. The program can then search the conformational space of the label (5 chi angles) and determine which conformations of the label do not clash with the protein surface. In "distance mode", distances between MTSSL ensembles can be determined and exported.
+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.
-For symmetric molecules, the MTSSL ensemble can be copied to symmetry related positions simply by pointing and clicking ("Copy & Move" mode).
+Please reference:
+[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]
 ==Screen shot==
-[[File:MtsslWizard_gui.jpg]]
+[[File:MtsslWizardv1-1.jpg]]
+==Installation==
+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.
+Alternatively install the wizard via the plugins menu.
+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]].
+Additional requirements:
+*SciPy has to be installed
+*Pyperclip or xerox have to be installed for the clipboard support.
+====How people got it to run...====
+*On a Mac it is easiest to install Pymol, Numpy, WxPython, Scipy and Matplotlib via fink.
+"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."
 ==Usage==
-===labeling===
+===Labeling===
-#Open a protein structure in PyMOL and remove any unwanted solvent molecules or ligands.
+#Open a structure in PyMOL and remove any unwanted solvent molecules or ligands.
 #Start the mtsslWizard via Wizards>mtsslWizard
-#If needed, vary the search parameters like "Thoroughness", "Cutoff" and "Clashes allowed". Thoroughness determines how many conformations of MTSSL will be checked. The cutoff value determines the minimum allowed distance between label and protein before the conformation is sorted out as clashing. "Clashes allowed" should usually be set to zero. If this value is changed  to e.g. "5", a conformation can violate the "cutoff" parameter five times before the conformation is discarded.
+#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.
-#click "Go" to start the calculation. Depending on the size of the protein, the "Thoroughness" parameter and of course the speed of your computer the duration of the search can vary quite considerably. With the default settings it does usually not take longer than 10-15 seconds.
+#Click "Search conformers!" to start the calculation.
-===distance calculation===
+===Distance calculation===
 #change "Mode" to "Distance"
 #click the first and second ensemble
-#The program will now calculate all possible distances between the conformations in the two ensembles. If both ensembles have many conformations, this can take quite a while!
+#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!
-===Reference===
+#The calculated distributions can be viewed with [[mtsslPlotter]].
-please read this paper for detailed information on the limitations of the approach:
-MtsslWizard: In silico Spin-Labeling and Generation of Distance Distributions in PyMOL. (2012) Appl. Magn. Res. accepted for publication
+Distances and a histogram are directly copied to the clipboard or written out to a file. The result file contains 4 columns:
-===Contact===
+#distances
-gh50'at'st-andrews.ac.uk
+#bins for histogram
+#histogram frequencies
+#histogram frequencies with highest value normalized to 1.0 for comparisons
+===Distance maps===
+#change "Mode" to "Distance map"
+#For a simple distance map: click twice on the protein of interest
+#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.
+#The maps can be viewed with [[mtsslPlotter]]
+==Reference==
+If you find this program useful, please cite this paper:
+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
+It also contains detailed informations about the program, examples and a discussion of limitations of the approach.
+==Older versions==
+*[https://github.com/Pymol-Scripts/Pymol-script-repo/blob/5935bdad82a480a4e004c8c902ef69dc75389ac8/plugins/mtsslWizard.py Version 1.0]
+==Contact==
+hagelueken'at' uni-bonn.de
+==Acknowledgement==
+Thanks to Jason Vertrees and Thomas Holder for some programming tips.

MtsslWizard: Difference between revisions