PyETV

Requirements

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

Installation

1. Download the plugin:

   PyETV_v1.3.py (Newest)
   PyETV.py (python2 version)

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 and Screenshots

PyETV should now be on your list of plugins:

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 viewer
   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