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: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-July/002791.html Tom 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@cgl.ucsf.edu on behalf of David Sept Sent: Tue 7/8/2008 11:14 AM To: chimera-users@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