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Lichtarge Computational Biology Lab

Houston, Texas

Lichtarge Computational Biology Lab
Lichtarge Computational Biology Lab
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PyETV: An Application for Mapping Evolutionary Traces onto Protein Structures in PyMOL


Requirements
Installation
User Interface and Screenshots
Videos
Input Examples
Notes
Citation

Requirements

A Tcl/Tk-based version of PyMOL. Downloads are available at delsci.com. Older PyMOL builds (0.99) should work just fine.

Installation

  1. Download the plugin: PyETV.py
  2. Install the plugin using either of the following methods (might require administrator privileges on your computer):
    • On the PyMOL Tcl/Tk user interface, follow the menu options "Plugin" -> "Install Plugin..."

    • (OR) Copy PyETV.py into the PyMOL plugins directory.
      On Windows, this is usually: C:\Program Files\DeLano Scientific\PyMOL\modules\pmg_tk\startup
      On Macintosh, with the X11/Hybrid version, the location is probably: PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup
      On a linux machine, it might be under: /var/lib/python-support/python2.4/pmg_tk/startup/

If you are using a Mac and your version of PyMOL does not support plugins, visit: http://www.pymolwiki.org/index.php/Plugins

User Interface

PyETV should now be on your list of plugins:

Screen capture depicting basic viewing.



Annotated screenshots of each page of the plugin are available in PowerPoint and PDF formats.

Videos

(New Video 9/7/10) Installing and running PyETV (Version 1.1) on a Mac:

For quick loading of a trace and basic ET viewing (Windows XP): .

More videos:
Mapping Evolutionary Trace results from a selected ranks file to a PDB chain
Viewing the Evolutionary Trace of biological assemblies predicted by PISA
(View Trace results on a complex obtained from PISA (http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html), select protein-protein interface residues,...)
Loading Evolutionary Trace server results through a link to a PyMOL script (View Trace results on a complex of unique PDB chains from the ET server, select protein-protein interface residues,...)

Input examples

  1. Loading multiple traces
    To load an arbitrary number of structures and to map as many traces,
    write a PyMOL script in the format shown below. Run the script in PyMOL,
    then open the PyETV plugin.
    Each trace will be allocated its own tabbed folder in the plugin.
    Evolutionary Trace ranks files may be loaded from a URL (internet) or local directory.
    For example: 
    
#Load the structures
load query_1gotA.pdb, 1gotA
load query_1gotB.pdb, 1gotB
load query_1gotG.pdb, 1gotG
zoom
#Values used by the plugin when it is opened
#Specify Python list of structure names
cmd._et_tools_structurenamelist=['1gotA','1gotB','1gotG']
#Specify Python list of ET ranks files, one for each structure
cmd._et_tools_etvxurllist=['C:\ET_1gotA.ranks','C:\\1gotB.ranks','http://mammoth.bcm.tmc.edu/ETserver2/pdbeasytrace/1gotG.ranks']
    Example pymol scripts: 1got.pml, 1gotBA.pml
  2. Ranks files
    By default, the PyETV maps information from ET ranks files onto a structure.
    ET ranks files are included in the zip files that are part of the search results
    returned by the ET server (http://mammoth.bcm.tmc.edu/ETserver.html)
    An example ET ranks file is ET_1gotA.ranks

    PyETV can also map information from a file containing only two columns.
    The first column lists the residue numbers and the second column the ranks or raw scores.
    The filename should have the .simple extension.
    For example: 
    
#comment                      
#filename example.simple      
#columns separated by space(s)
#  residue      rho           
      1       4.51            
      2       8.48            
      3       6.38            
      4       6.71            
      5       8.62            
      6       3.89            
      7       4.72

Notes

  • To see the formulas used to evaluate the various z-scores, visit this page.
  • Letting the mouse cursor hover over a user-interface component in PyETV, such as a button or checkbox, would prompt a tooltip, or short descriptive text, to appear.
  • PyETC is another PyMOL plugin complementary to PyETV. Instructions are under construction.

Citation


Lua RC and Lichtarge O.
"PyETV: A PyMOL Evolutionary Trace viewer to analyze functional site predictions in protein complexes"
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq566