[Chimera-users] Multiscale models and surface coloring

Tom Goddard goddard at cgl.ucsf.edu
Tue Jul 8 12:00:37 PDT 2008

Hi Dave,

  While you could use multiscale and Python to make low resolution 
surfaces for your complexes I think it will be easier to use the 
"molmap" Chimera command in a command script.  The molmap command can 
produce surfaces of nice quality at any desired resolution.  I've 
attached an example script.  I tested it with Chimera 1.2539 (July 3, 
2008 daily build).  It should work with current Chimera snapshots and 
daily builds, but not the  Nov 2007 production release (1.2470) because 
that does not have the molmap command.


David Sept wrote:
> 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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