PyETV: An Application for Mapping Evolutionary Traces onto Protein Structures in PyMOL

Requirements

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/

User Interface

• Normal multi-chain ET
  
• Difference ET
  

Examples

1. Difference ET example
   Run the following PyMOL script: 2phyA_diffET.pml
   After opening the PyETV plugin, click the button labeled "Map ranks to structure".
2. 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.

   #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']
   #Specify default tab folder when plugin is opened
   cmd._et_tools_selectpage='1gotA'
   

   Example pymol scripts: 1got.pml, 1gotBA.pml
3. Ranks files
   By default, the PyETV maps information from ET ranks files onto a structure. ET ranks are included as output in
   the ET server (http://mammoth.bcm.tmc.edu/ETserver.html)
   and the Difference ET server (http://mammoth.bcm.tmc.edu/gpcr/diffET_proteins.html).
   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.
   The filename should have the .simple extension.

   #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