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. Colors indicate the difference between predicted and observed 13Cα and/or 13Cβ chemical shifts values averaged over all uploaded conformers. Green, yellow and red colors represent small, medium and large differences, respectively. Red is a warning that a possible flaw may exist. 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 ¹³C^α and ¹³C^βchemical shifts can be improved, i.e., if the (χ¹ /χ² ) side-chain

The differences between observed and predicted ¹³C^α and ¹³C^β 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 3.0

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 from seconds to a few minutes, depending on all existing request on the server.

Note:

• 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.
• The PDB file must not have missing residues.
• Missing observed ¹³C^α and ¹³C^β chemical shifts are tolerated.
• A file with observed ¹³C^α and/or ¹³C^β 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 ¹³C^α experimental chemical shifts and the last column the ¹³C^β chemical shifts. Spaces should be used to separates the columns.

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

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. 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. (in press).

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