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<TITLE>RE: [Chimera-users] Multiscale models and surface coloring</TITLE>
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<P><FONT SIZE=2>Dave,<BR>
<BR>
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:<BR>
<BR>
runCommand('color red #0:.a; color blue #0:.b')<BR>
runCommand('select #1')<BR>
MultiScale.color_surfaces_to_match_atoms()<BR>
<BR>
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.<BR>
<BR>
I'd be interested to know if you figured out something else or use different set of python commands to accomplish the "runCommand" tasks.<BR>
<BR>
Thanks for your post, I was able to steal a few useful things from your test.py!<BR>
<BR>
Ed Brignole<BR>
Asturias Lab<BR>
The Scripps Research Institute<BR>
<BR>
-----Original Message-----<BR>
From: chimera-users-bounces@cgl.ucsf.edu on behalf of David Sept<BR>
Sent: Tue 7/8/2008 11:14 AM<BR>
To: chimera-users@cgl.ucsf.edu<BR>
Subject: [Chimera-users] Multiscale models and surface coloring<BR>
<BR>
<BR>
I need to create a series of images of large protein complexes, and <BR>
since it is tedious to do this through the menus, I am trying to <BR>
script this for Chimera. I want to create low-res, EM looking <BR>
surfaces and color the individual protein chains different colors. So <BR>
far, I can read in multiple structures and create the surfaces, but I <BR>
can't figure out how to change the coloring. Here's what I have:<BR>
<BR>
---- test.py -------<BR>
from chimera import openModels<BR>
m = openModels.open('model-1.pdb')[0]<BR>
<BR>
import MultiScale<BR>
<BR>
d = MultiScale.show_multiscale_model_dialog()<BR>
d.make_multimers([m])<BR>
<BR>
chimera.viewer.viewAll()<BR>
---- test.py -------<BR>
<BR>
The above python script work and makes very nice blobs. I can color <BR>
the entire structure (say red) by adding something like:<BR>
<BR>
d.select_all_chains_cb()<BR>
d.change_color_cb((1, 0, 0, 1))<BR>
<BR>
but I can't figure out how to select individual chains and color them <BR>
(not sure how to use select_chains). This also gets more complicated <BR>
when I load in two structures at the same time and they have common <BR>
chain letters. Since I found a way to get this (almost) working in <BR>
python, I've been sticking with it, but if this can easily be done <BR>
directly using a chimera command file, I'm happy to do that. Any help <BR>
is appreciated.<BR>
<BR>
Thanks,<BR>
<BR>
Dave<BR>
<BR>
----------------------------------------------------<BR>
David Sept, Ph.D. Associate Professor<BR>
Biomedical Engineering and Center for Computational Biology<BR>
Washington University, Campus Box 1097, St. Louis, MO 63130<BR>
Phone: (314) 935-8837 Fax: (314) 935-7448<BR>
dsept@biomed.wustl.edu <A HREF="http://habanero.ibme.wustl.edu">http://habanero.ibme.wustl.edu</A><BR>
<BR>
<BR>
<BR>
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