[Chimera-users] Gorgon EM modeling / visualization software

Tom Goddard goddard at sonic.net
Mon Sep 27 16:59:35 PDT 2010

  Hi Tom,

   I found in Keren Lasker's book chapter a reference to an EM modeling 
program called Gorgon from Washington University at St Louis.  It was 
developed in collaboration with NCMI (Wah) and seems to be aimed at 
modeling high resolution EM maps where protein backbones can be traced.  
It is embarrassing that I didn't know about this, and also that they 
didn't leverage Chimera.  I guess Chimera code was deemed too complex to 
reuse so they wrote their own molecule/map display and editor.  Ugh.  
This Gorgon software is a relative of the pipeline for EM modeling that 
Keren describes in her book chapter, only it is really the NCMI pipeline 
-- focused on how to model 4 Angstrom EM maps.

   I think this would be a good case study to investigate why they 
didn't make use of Chimera extensibility or Chimera code modules.  
Another recent case of massive reimplementing computer graphics 
capabilities is a fitting package called UROX from Jorge Navaza's lab.  
It would be interesting to survey new molecular and EM graphics 
packages, talk to the authors, and see what we could have done to make 
Chimera more attractive to them as a development platform or code base.


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