[Chimera-users] Multiscale models and surface coloring

David Sept dsept at biomed.wustl.edu
Tue Jul 8 11:14:49 PDT 2008

I need to create a series of images of large protein complexes, and  
since it is tedious to do this through the menus, I am trying to  
script this for Chimera.  I want to create low-res, EM looking  
surfaces and color the individual protein chains different colors.  So  
far, I can read in multiple structures and create the surfaces, but I  
can't figure out how to change the coloring.  Here's what I have:

---- test.py -------
from chimera import openModels
m = openModels.open('model-1.pdb')[0]

import MultiScale

d = MultiScale.show_multiscale_model_dialog()

---- test.py -------

The above python script work and makes very nice blobs.  I can color  
the entire structure (say red) by adding something like:

d.change_color_cb((1, 0, 0, 1))

but I can't figure out how to select individual chains and color them  
(not sure how to use select_chains).  This also gets more complicated  
when I load in two structures at the same time and they have common  
chain letters.  Since I found a way to get this (almost) working in  
python, I've been sticking with it, but if this can easily be done  
directly using a chimera command file, I'm happy to do that.  Any help  
is appreciated.



David Sept, Ph.D.  Associate Professor
Biomedical Engineering and Center for Computational Biology
Washington University,  Campus Box 1097, St. Louis, MO  63130
Phone: (314) 935-8837          Fax:  (314) 935-7448
dsept at biomed.wustl.edu      http://habanero.ibme.wustl.edu

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