Difference between revisions of "Cheshift"

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{{Infobox script-repo
 
{{Infobox script-repo
 
|type      = plugin
 
|type      = plugin
|filename = plugins/cheshift.py
+
|download = https://github.com/aloctavodia/cheshift/archive/v3.1.zip
 
|author    = [[User:OsvaldoMartin|Osvaldo Martin]]
 
|author    = [[User:OsvaldoMartin|Osvaldo Martin]]
 
|license  = GPL
 
|license  = GPL
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The differences between observed and predicted <sup>13</sup>C<sup>α</sup> and <sup>13</sup>C<sup>β</sup> chemical shifts can be used as a sensitive probe with which to detect possible local flaws in protein structures. For this reason exist [http://www.cheshift.com CheShift], a Web server for protein structure validation.
 
The differences between observed and predicted <sup>13</sup>C<sup>α</sup> and <sup>13</sup>C<sup>β</sup> chemical shifts can be used as a sensitive probe with which to detect possible local flaws in protein structures. For this reason exist [http://www.cheshift.com CheShift], a Web server for protein structure validation.
  
This plugin provides a way to use PyMOL to validate a protein model using observed chemical shifts. All computations run on <i>Che</i>Shift server,
+
This plugin provides a way to use PyMOL to validate a protein model using observed chemical shifts.
and the results are retrieved to PyMOL, hence an Internet connection is needed.  
 
  
 
=== Version ===
 
=== Version ===
The current version of this plugin is 3.0
+
The current version of this plugin is 3.1
  
 
== Installation ==
 
== Installation ==
 
=== Linux ===
 
=== Linux ===
1) The plugin can be downloaded from here [[https://github.com/Pymol-Scripts/Pymol-script-repo/raw/master/plugins/cheshift.py Pymol-script-repo]]
+
1) The plugin can be downloaded from here [[https://github.com/aloctavodia/cheshift/archive/v3.1.zip Here]]
  
2) You should install mechanize, a python module. This module is available from the repositories of the main Linux distributions. Just use your default package manager (or command line) to install it. In Ubuntu/Debian the package name is "python-mechanize".
+
2) If you are using the incentive version of PyMOL skip the next step and go directly to step 4.
 +
 
 +
3) You should install NumPy and Scipy. This python packages are available from the repositories of the main Linux distributions. Just use your default package manager (or command line) to install it. In Ubuntu/Debian you could do "sudo apt-get install python-numpy python-scipy".
 +
 
 +
4) Open PyMOL and then go to plugin --> plugin manager --> Install New Plugin --> Install from local file --> Choose file. and choose the zip file you download in step 1. Now the plugin should be installed.
 +
If you have an old version of PyMOL without the plugin manager then, unzip the file downloaded in step 1 and copy the "cheshift" folder to the plugin directory, probably something like "/usr/lib/python2.7/dist-packages/pmg_tk/startup"
  
 
=== Windows ===
 
=== Windows ===
 
This plugin have not been extensively tested on Windows machines, but it passed all the test I have done...
 
This plugin have not been extensively tested on Windows machines, but it passed all the test I have done...
  
1) The plugin can be downloaded from here [[https://github.com/Pymol-Scripts/Pymol-script-repo/raw/master/plugins/cheshift.py Pymol-script-repo]]
+
1) The plugin can be downloaded from here [[https://github.com/aloctavodia/cheshift/archive/v3.1.zip Here]]
  
2) You should install mechanize, a python module. In order to do that, download [http://208.84.148.45/mechanize.zip this] unzip and copy the mechanize folder were you have installed PyMOL, usually is C:\Program Files\DeLano Scientific\PyMOL\modules\pmg_tk\startup
+
2) If you are using the incentive version of PyMOL skip the next step and go directly to step 4.
 +
 
 +
3) You should install NumPy and SciPy. Probably the easiest way to do this on a Windows machine is to install a Python Distribution like [[https://store.continuum.io/cshop/anaconda/ Anaconda]] or [[https://www.enthought.com/products/canopy/  Canopy]]
 +
 
 +
4) Open PyMOL and then go to plugin --> plugin manager --> Install New Plugin --> Install from local file --> Choose file. and choose the zip file you download in step 1. Now the plugin should be installed.
 +
If you have an old version of PyMOL without the plugin manager then, unzip the file downloaded in step 1 and copy the "cheshift" folder to the plugin directory, probably something like "C:\Python27\Lib\site-packages\pmg_tk\startup\"
  
 
=== Mac OsX ===
 
=== Mac OsX ===
This plugin have not been tested on a Mac OsX machine, but it should work...
+
This plugin have not been extensively tested on Windows machines, but it passed all the test I have done...
  
1) The plugin can be downloaded from here [[https://github.com/Pymol-Scripts/Pymol-script-repo/raw/master/plugins/cheshift.py Pymol-script-repo]]
+
1) The plugin can be downloaded from here [[https://github.com/aloctavodia/cheshift/archive/v3.1.zip Here]]
  
2) You should install mechanize, a python module. In order to do that download [http://208.84.148.45/mechanize.zip this] unzip and copy the mechanize folder were you have installed PyMOL. For the X11/Hybrid version, the location is probably: PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup
+
2) If you are using the incentive version of PyMOL skip the next step and go directly to step 4.
  
 +
3) You should install NumPy and SciPy. Probably the easiest way to do this on a Windows machine is to install a Python Distribution like [[https://store.continuum.io/cshop/anaconda/ Anaconda]] or [[https://www.enthought.com/products/canopy/  Canopy]]
  
== Using the Plugin ==
+
4) Open PyMOL and then go to plugin --> plugin manager --> Install New Plugin --> Install from local file --> Choose file. and choose the zip file you download in step 1. Now the plugin should be installed.
1) Launch PyMOL and select "Cheshift" from the plugin menu. <br>
+
If you have an old version of PyMOL without the plugin manager then, unzip the file downloaded in step 1 and copy the "cheshift" folder to the plugin directory, probably something like "/usr/lib/python2.7/dist-packages/pmg_tk/startup"
2) Select a PDB file of your protein model (using the <i>Che</i>Shift plugin menu).<br>
+
 
 +
== Using the Plugin for predicting <sup>13</sup>C<sup>α</sup> and <sup>13</sup>C<sup>β</sup> chemical shifts==
 +
1) Launch PyMOL and select a PDB file <br>
 +
2) Select "Cheshift" from the plugin menu. <br>
 +
3) Click the "Run" button.<br>
 +
4) The results will be saved in your working directory as a .txt file<br>
 +
 
 +
== Using the Plugin for validation protein models ==
 +
1) Launch PyMOL and select a PDB file <br>
 +
2) Select "Cheshift" from the plugin menu. <br>
 
3) Select a file with the experimental chemical shift values.<br>
 
3) Select a file with the experimental chemical shift values.<br>
4) Click the "Submit" button.<br>
+
4) Click the "Run" button.<br>
5) Wait until results are displayed (this could from seconds to a few minutes, depending  
+
5) Wait until results are displayed (this could take from seconds to a few minutes, depending on the size of your protein and the speed of your computer<br>
on all existing request on the server.<br>
 
 
 
  
 
<b>Note:</b>
 
<b>Note:</b>
* If more than 20 conformers are uploaded only the 20 first will be analysed.
 
 
* If the PDB file has more than one chain only the first one will be analysed.
 
* If the PDB file has more than one chain only the first one will be analysed.
* The PDB file must not have missing residues.
+
* The PDB file must have no missing residues.
 
* Missing observed <sup>13</sup>C<sup>α</sup> and <sup>13</sup>C<sup>β</sup> chemical shifts are tolerated.
 
* Missing observed <sup>13</sup>C<sup>α</sup> and <sup>13</sup>C<sup>β</sup> chemical shifts are tolerated.
* A file with observed <sup>13</sup>C<sup>α</sup> and/or <sup>13</sup>C<sup>β</sup> chemical shift values is needed. The format of this file should be the one used in the BMRB or the PDB. Alternatively, you can provide a simple 4 column file : The first column should be the residue number, the second the residue name (three-letter code) and the third column the <sup>13</sup>C<sup>α</sup> experimental chemical shifts and the last column the <sup>13</sup>C<sup>β</sup> chemical shifts. Spaces should be used to separates the columns.
+
* A file with observed <sup>13</sup>C<sup>α</sup> and/or <sup>13</sup>C<sup>β</sup> chemical shift values is needed. The format of this file should be the one used in the BMRB or the PDB. Alternatively, you can provide a file with the following format the first line should contain the name of the reference compound i.e DSS, TSP or TMS. The following lines should have four columns. The first column should be the residue number, the second the residue name (three-letter code) and the third column the <sup>13</sup>C<sup>α</sup> experimental chemical shifts and the last column the <sup>13</sup>C<sup>β</sup> chemical shifts. Spaces should be used to separates the columns.
  
 +
DSS<br>
 
1  MET 55.63 32.95<br>
 
1  MET 55.63 32.95<br>
 
2  TYR 62.81 39.27<br>
 
2  TYR 62.81 39.27<br>
Line 65: Line 82:
 
6  ILE  56.38 38.59<br>
 
6  ILE  56.38 38.59<br>
  
=== Proxy Configuration ===
 
If you are behind a proxy the <i>Che</i>Shift plugin will try to correctly guess your proxy configuration, but this is a tricky business and many things could fail. In that scenario you will be prompted to manually set your proxy settings. In case you manually set the proxy configuration the plugin will save your proxy settings and next time it will attempt to use those saved settings to connect to the Internet.
 
  
 
== License ==
 
== License ==
 
<i>Che</i>Shift plugin is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License. A complete copy of the GNU General Public License can be accessed here http://www.gnu.org/licenses/.
 
<i>Che</i>Shift plugin is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License. A complete copy of the GNU General Public License can be accessed here http://www.gnu.org/licenses/.
  
<i>Che</i>Shift Server ([http://www.cheshift.com www.cheshift.com]) is available free of charge ONLY for academic use.
+
<i>Che</i>Shift uses data derived from the [[http://dunbrack.fccc.edu/ndrd/ Neighbor-Dependent Ramachandran Distributions]] obtained by the Dunbrack Lab. This derived data is also released under the GPL license, with the permission of Professor Roland Dunbrack. The full NDRD data is released using a different [[http://dunbrack.fccc.edu/ndrd/license/index.html license]].
 
 
  
 
== Citation ==
 
== Citation ==

Revision as of 15:50, 23 May 2014

Type PyMOL Plugin
Download https://github.com/aloctavodia/cheshift/archive/v3.1.zip
Author(s) Osvaldo Martin
License GPL


Description

Result of a CheShift analysis.
Colors indicate the difference between predicted and observed 13Cα and/or 13Cβchemical shifts values averaged over all uploaded conformers. Green, yellow and red colors represent small, medium and large differences, respectively. White is used if either the prediction failed or the observed value is missing.
Blue is used to highlight residues for which the agreement between observed and predicted 13Cα and 13Cβchemical shifts can be improved, i.e., if the (χ12 ) side-chain

The differences between observed and predicted 13Cα and 13Cβ chemical shifts can be used as a sensitive probe with which to detect possible local flaws in protein structures. For this reason exist CheShift, a Web server for protein structure validation.

This plugin provides a way to use PyMOL to validate a protein model using observed chemical shifts.

Version

The current version of this plugin is 3.1

Installation

Linux

1) The plugin can be downloaded from here [Here]

2) If you are using the incentive version of PyMOL skip the next step and go directly to step 4.

3) You should install NumPy and Scipy. This python packages are available from the repositories of the main Linux distributions. Just use your default package manager (or command line) to install it. In Ubuntu/Debian you could do "sudo apt-get install python-numpy python-scipy".

4) Open PyMOL and then go to plugin --> plugin manager --> Install New Plugin --> Install from local file --> Choose file. and choose the zip file you download in step 1. Now the plugin should be installed. If you have an old version of PyMOL without the plugin manager then, unzip the file downloaded in step 1 and copy the "cheshift" folder to the plugin directory, probably something like "/usr/lib/python2.7/dist-packages/pmg_tk/startup"

Windows

This plugin have not been extensively tested on Windows machines, but it passed all the test I have done...

1) The plugin can be downloaded from here [Here]

2) If you are using the incentive version of PyMOL skip the next step and go directly to step 4.

3) You should install NumPy and SciPy. Probably the easiest way to do this on a Windows machine is to install a Python Distribution like [Anaconda] or [Canopy]

4) Open PyMOL and then go to plugin --> plugin manager --> Install New Plugin --> Install from local file --> Choose file. and choose the zip file you download in step 1. Now the plugin should be installed. If you have an old version of PyMOL without the plugin manager then, unzip the file downloaded in step 1 and copy the "cheshift" folder to the plugin directory, probably something like "C:\Python27\Lib\site-packages\pmg_tk\startup\"

Mac OsX

This plugin have not been extensively tested on Windows machines, but it passed all the test I have done...

1) The plugin can be downloaded from here [Here]

2) If you are using the incentive version of PyMOL skip the next step and go directly to step 4.

3) You should install NumPy and SciPy. Probably the easiest way to do this on a Windows machine is to install a Python Distribution like [Anaconda] or [Canopy]

4) Open PyMOL and then go to plugin --> plugin manager --> Install New Plugin --> Install from local file --> Choose file. and choose the zip file you download in step 1. Now the plugin should be installed. If you have an old version of PyMOL without the plugin manager then, unzip the file downloaded in step 1 and copy the "cheshift" folder to the plugin directory, probably something like "/usr/lib/python2.7/dist-packages/pmg_tk/startup"

Using the Plugin for predicting 13Cα and 13Cβ chemical shifts

1) Launch PyMOL and select a PDB file
2) Select "Cheshift" from the plugin menu.
3) Click the "Run" button.
4) The results will be saved in your working directory as a .txt file

Using the Plugin for validation protein models

1) Launch PyMOL and select a PDB file
2) Select "Cheshift" from the plugin menu.
3) Select a file with the experimental chemical shift values.
4) Click the "Run" button.
5) Wait until results are displayed (this could take from seconds to a few minutes, depending on the size of your protein and the speed of your computer

Note:

  • If the PDB file has more than one chain only the first one will be analysed.
  • The PDB file must have no missing residues.
  • Missing observed 13Cα and 13Cβ chemical shifts are tolerated.
  • A file with observed 13Cα and/or 13Cβ chemical shift values is needed. The format of this file should be the one used in the BMRB or the PDB. Alternatively, you can provide a file with the following format the first line should contain the name of the reference compound i.e DSS, TSP or TMS. The following lines should have four columns. The first column should be the residue number, the second the residue name (three-letter code) and the third column the 13Cα experimental chemical shifts and the last column the 13Cβ chemical shifts. Spaces should be used to separates the columns.

DSS
1 MET 55.63 32.95
2 TYR 62.81 39.27
3 ALA 53.78 18.97
4 GLY 47.24 999.00
5 LYS 57.55 32.77
6 ILE 56.38 38.59


License

CheShift plugin is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License. A complete copy of the GNU General Public License can be accessed here http://www.gnu.org/licenses/.

CheShift uses data derived from the [Neighbor-Dependent Ramachandran Distributions] obtained by the Dunbrack Lab. This derived data is also released under the GPL license, with the permission of Professor Roland Dunbrack. The full NDRD data is released using a different [license].

Citation

Martin O.A. Arnautova Y.A. Icazatti A.A. Scheraga H.A. and Vila J.A. A Physics-Based Method to Validate and Repair Flaws in Protein Structures. Proc Natl Acad Sci USA 2013, vol. 110 16826-16831.

Martin O.A. Vila J.A. and Scheraga H.A. (2012). CheShift-2: Graphic validation of protein structures. Bioinformatics 2012. 28(11), 1538-1539.

Other References

Vila J.A. Arnautova Y.A. Martin O.A. and Scheraga, H.A. (2009). Quantum-mechanics-derived 13C chemical shift server (CheShift) for protein structure validation. PNAS, 106(40), 16972-16977.

Vila, J.A. and Scheraga H.A. (2009). Assessing the accuracy of protein structures by quantum mechanical computations of 13Cα chemical shifts. Accounts of chemical research, 42(10), 1545-53.