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|type      = plugin
 
|type      = plugin
 
|filename  = plugins/cheshift.py
 
|filename  = plugins/cheshift.py
|author    = [[mailto:aloctavodia@gmail.com|Osvaldo Martin]]
+
|author    = [[User:OsvaldoMartin|Osvaldo Martin]]
 
|license  = GPL
 
|license  = GPL
 
}}
 
}}
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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.  
  
Version : 1.0
+
 
Citation: Martin O.A. Vila J.A. and Scheraga H.A. CheShift-2: Graphic
+
=== Version ===
validation of protein structures. Bioinformatics 2012 (submitted)
+
The current version of this plug-in is 1.0
 +
 
  
  
Line 25: Line 26:
  
 
=== Windows ===
 
=== Windows ===
This plug-in have not been extensively tested on a Windows machines, but it should work...
+
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 [[git_intro | Pymol-script-repo]]
 
1) The plug-in can be downloaded from here [[git_intro | Pymol-script-repo]]
  
2) You should install mechanize, a python module. In order to do that, download [http://208.84.148.45/ 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) 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
  
  
Line 37: Line 38:
 
1) The plug-in can be downloaded from here [[git_intro | Pymol-script-repo]]
 
1) The plug-in can be downloaded from here [[git_intro | Pymol-script-repo]]
  
2) You should install mechanize, a python module. In order to do that download [http://208.84.148.45/ 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) 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
  
  
Line 53: Line 54:
 
* If the PDB file has more than one chain only the first one 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
 
* The PDB file must not have missing residues
* Missing observed 13Cα chemical shifts are tolerated
+
* Missing observed <sup>13</sup>C<sup>α</sup> chemical shifts are tolerated
* The observed 13Cα chemical shifts values should be in BMRB-Star format (only  
+
* The observed <sup>13</sup>C<sup>α</sup> chemical shifts values should be in BMRB-Star format (only  
the 13Cα are needed, the other nucleus could be present but are ignored)
+
the <sup>13</sup>C<sup>α</sup> 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:
 
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:
Line 95: Line 96:
  
 
=== Proxy Configuration ===
 
=== 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.
+
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 ===
+
== 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 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.
 
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 ==
 
== 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). 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. 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 <sup>13</sup>C<sup>α</sup> chemical shifts. Accounts of chemical research, 42(10), 1545-53.
  
  

Revision as of 07:04, 14 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


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

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). 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 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 


Result of a CheShift analysis

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 13Cα chemical shifts. Accounts of chemical research, 42(10), 1545-53.