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. Tom 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
# Chimera script to open a PDB and make low resolution surfaces for each chain open 0 /tmp/1a0m.pdb # Make surfaces. Default grid spacing is 1/3 resolution. molmap #0:.A 8.0 modelId 1 molmap #0:.B 8.0 modelId 2 molmap #0:.water 3.5 gridSpacing 0.5 modelId 3 # Color surfaces volume #1 color blue volume #2 color limegreen volume #3 color .7,.5,0,.5