[Chimera-users] Multiscale models and surface coloring

Tom Goddard goddard at cgl.ucsf.edu
Wed Jul 9 21:17:38 PDT 2008

Hi Ed,

  I replied to the chimera-users question about low resolution 
surfaces.  The email might not have reached you because it had an 
attachment with a *.cmd suffix which may have caused your email server 
to reject it.  Here is the URL to my reply:



Edward Brignole wrote:
> Dave,
> 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')
> MultiScale.color_surfaces_to_match_atoms()
> 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()
> d.make_multimers([m])
> chimera.viewer.viewAll()
> ---- 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.select_all_chains_cb()
> 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.
> Thanks,
> Dave

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