Cheshift

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The differences between observed and predicted <sup>13</sup>C<sup>α</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>  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 CheShift server,  
+
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,  
 
and the results are retrieved to PyMOL, hence an Internet connection is needed.  
 
and the results are retrieved to PyMOL, hence an Internet connection is needed.  
  
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== Using the Plugin ==
 
== Using the Plugin ==
 
1) Launch PyMOL and select "Cheshift" from the plugin menu. <br>
 
1) Launch PyMOL and select "Cheshift" from the plugin menu. <br>
2) Select a PDB file of your protein model (using the CheShift plugin menu).<br>
+
2) Select a PDB file of your protein model (using the <i>Che</i>Shift 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 "Submit" button.<br>
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== License ==
 
== 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/.
+
<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/.
  
CheShift Server ([http://www.cheshift.com www.cheshift.com]) is available free of charge ONLY for academic use.
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<i>Che</i>Shift Server ([http://www.cheshift.com www.cheshift.com]) is available free of charge ONLY for academic use.
  
  
 
== Citation ==
 
== Citation ==
Martin O.A. Vila J.A. and Scheraga H.A. CheShift-2: Graphic validation of protein structures. Bioinformatics 2012 (submitted)
+
Martin O.A. Vila J.A. and Scheraga H.A. <i>Che</i>Shift-2: Graphic validation of protein structures. Bioinformatics 2012 (submitted)
  
  
 
== References ==
 
== References ==
Martin O.A. Vila J.A. and Scheraga H.A. (2012). CheShift-2: Graphic validation of protein structures. Bioinformatics 2012 (submitted).
+
Martin O.A. Vila J.A. and Scheraga H.A. (2012). <i>Che</i>Shift-2: Graphic validation of protein structures. Bioinformatics 2012 (submitted).
  
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. Arnautova Y.A. Martin O.A. and Scheraga, H.A. (2009). Quantum-mechanics-derived 13C chemical shift server (<i>Che</i>Shift) 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 <sup>13</sup>C<sup>α</sup> chemical shifts. Accounts of chemical research, 42(10), 1545-53.
 
Vila, J.A. and Scheraga H.A. (2009). Assessing the accuracy of protein structures by quantum mechanical computations of <sup>13</sup>C<sup>α</sup> chemical shifts. Accounts of chemical research, 42(10), 1545-53.

Revision as of 18:23, 28 February 2012

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


Contents

Description

Result of a CheShift analysis

The differences between observed and predicted 13Cα 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. All computations run on CheShift server, and the results are retrieved to PyMOL, hence an Internet connection is needed.

Version

The current version of this plugin is 1.0


Installation

Linux

1) The plugin can be downloaded from here [Pymol-script-repo]

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".

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 [Pymol-script-repo]

2) You should install mechanize, a python module. In order to do that, download this unzip and copy the mechanize folder were you have installed PyMOL, usually is C:\Program Files\DeLano Scientific\PyMOL\modules\pmg_tk\startup

Mac OsX

This plugin have not been tested on a Mac OsX machine, but it should work...

1) The plugin can be downloaded from here [Pymol-script-repo]

2) You should install mechanize, a python module. In order to do that download 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


Using the Plugin

1) Launch PyMOL and select "Cheshift" from the plugin menu.
2) Select a PDB file of your protein model (using the CheShift plugin menu).
3) Select a file with the experimental chemical shift values.
4) Click the "Submit" button.
5) Wait until results are displayed (this could take a few minutes, depending on all existing request on the server. Analyzing 20 conformations of a 100 residues protein takes ~4 minutes).

Note:

the 13Cα are needed, the others nuclei could be present but are ignored).

you can use a complete BMRB file or just a file with only the experimental chemical shifts. In the latter case you can use this format:

       1  21 MET N    N 121.0  0.25 1 
       2  21 MET H    H   8.36 0.01 1 
       3  21 MET CA   C  55.9  0.20 1 
       4  21 MET HA   H   4.39 0.01 1 
       5  21 MET CB   C  31.8  0.20 1 
       6  21 MET HB2  H   2.15 0.01 2 
       7  21 MET HG2  H   2.54 0.01 2 
       8  21 MET HE   H   2.09 0.01 1 
       9  21 MET C    C 176.6  0.10 1 
      10  22 GLY N    N 111.4  0.25 1 
      11  22 GLY H    H   8.55 0.01 1 
      12  22 GLY CA   C  44.9  0.20 1 
      13  22 GLY HA2  H   4.15 0.01 2 
      14  22 GLY HA3  H   3.91 0.01 2 
      15  22 GLY C    C 173.2  0.10 1 

or this format:

        1   1   1 SER HA   H   4.44 0.005 1 
        2   1   1 SER HB2  H   3.85 0.005 2 
        3   1   1 SER HB3  H   3.88 0.005 2 
        4   1   1 SER C    C 168.6  0.2   1 
        5   1   1 SER CA   C  58.4  0.2   1 
        6   1   1 SER CB   C  63.8  0.2   1 
        7   2   2 ALA H    H   8.23 0.005 1 
        8   2   2 ALA HA   H   4.87 0.005 1 
        9   2   2 ALA HB   H   1.37 0.005 1 
       10   2   2 ALA C    C 174.5  0.2   1 
       11   2   2 ALA CA   C  51.7  0.2   1 
       12   2   2 ALA CB   C  23.3  0.2   1 
       13   2   2 ALA N    N 120.2  0.2   1 

Proxy Configuration

If you are behind a proxy the CheShift 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

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 Server (www.cheshift.com) is available free of charge ONLY for academic use.


Citation

Martin O.A. Vila J.A. and Scheraga H.A. CheShift-2: Graphic validation of protein structures. Bioinformatics 2012 (submitted)


References

Martin O.A. Vila J.A. and Scheraga H.A. (2012). CheShift-2: Graphic validation of protein structures. Bioinformatics 2012 (submitted).

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.

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