[Chimera-users] Multiscale models and surface coloring

Edward Brignole brignole at scripps.edu
Wed Jul 9 20:47:39 PDT 2008


I'm interested in the reply to your post, but since I didn't see one... try this to color your multiscale model after applying the desired colors to the atoms with something like this:

runCommand('color red #0:.a; color blue #0:.b')
runCommand('select #1')

This assumes your pdb was #0 and your surfaces are #1. As far as I can tell, the color_surfaces_to_match_atoms() only works after selecting the multiscale model.

I'd be interested to know if you figured out something else or use different set of python commands to accomplish the "runCommand" tasks.

Thanks for your post, I was able to steal a few useful things from your test.py!

Ed Brignole
Asturias Lab
The Scripps Research Institute

-----Original Message-----
From: chimera-users-bounces at cgl.ucsf.edu on behalf of David Sept
Sent: Tue 7/8/2008 11:14 AM
To: chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] Multiscale models and surface coloring

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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