Cheshift

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


Description

This plug-in provides a way to validate a protein model using observed chemical shifts. All computations run on CheShift server (www.cheshift.com), and the results are retrieved to PyMOL, hence an Internet connection is needed.

Version : 1.0 Citation: Martin O.A. Vila J.A. and Scheraga H.A. CheShift-2: Graphic validation of protein structures. Bioinformatics 2012 (submitted)


Installation

Linux

1) The plug-in 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 plug-in have not been extensively tested on a Windows machines, but it should work...

1) The plug-in 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 plug-in have not been tested on a Mac OsX machine, but it should work...

1) The plug-in 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 Plug-in

1) Launch PyMOL and select "CheShift" from the Plug-ins menu. 2) Select a PDB file of your protein model (using the CheShift plug-in). 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:

  • If more than 20 conformers are uploaded only the 20 first will be analyzed
  • If the PDB file has more than one chain only the first one will be analyzed
  • The PDB file must not have missing residues
  • Missing observed 13Cα chemical shifts are tolerated
  • The observed 13Cα chemical shifts values should be in BMRB-Star format (only

the 13Cα are needed, the other nucleus 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 


Result of a CheShift analysis

Proxy Configuration

The CheShift plug-in 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 plug-in will save your proxy settings and next time it will attempt to use those saved settings to connect to the Internet.

License

CheShift plug-in 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.

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.