Cheshift

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

Description

Result of a CheShift analysis

The differences between observed and predicted ¹³C^α 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 plug-in 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 plug-in is 1.0

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 Windows machines, but it passed all the test I have done...

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 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:

• 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 ¹³C^α chemical shifts are tolerated.
• The observed ¹³C^α chemical shifts values should be in BMRB-Star format (only

the ¹³C^α 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 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.

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 ¹³C^α chemical shifts. Accounts of chemical research, 42(10), 1545-53.