Hi Ian, You would use the “sym” command. There is an option to create the multiscale-type low-resolution surfaces instead of loading all the atomic copies, but since you want ribbons rather than the surfaces, there is no need. So, I’m thinking commands: open 2qa0 sym #0 focus sel :300,600 (this file doesn’t have residues 10,20,30) I think you can just use the runcommand thing to convert to python: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> sym: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 20, 2016, at 3:39 PM, Ian Holmes <ihholmes@gmail.com> wrote:
Hello Chimera gurus,
I am using multiscale models to view a virus capsid (PDB 2QA0) in Chimera. I would like to create a Python script to render the capsid as a multiscale model and then highlight (i.e. select) certain residues. However, I can't figure out the command-line syntax to create a multiscale model. The docs also suggest the Midas Python module as an alternative way of scripting Chimera in Python, but I haven't yet found that module.
Here is the rough order of what I am doing from the graphical user interface:
Open model 2QA0 Tools menu -> Higher-order structure -> Multiscale Models panel (The following actions are all in the Multiscale Models panel) Click "Make models" button in "Models from molecules and matrices" section Click "All" button in "Select chains:" section Click "Hide" button in "Act on selected chains" section, "Selected chains" subsection Click "All" button in "Select chains:" section (again) Select "Ribbon" from "Style" menu in "Act on selected chains" section (then back to the main view) Zoom out (with mouse wheel) Favorites menu -> Command Line Type "select :10,20,30" (amino acids I want to highlight)
Here is what I've got so far in terms of equivalent Python code:
import os from chimera import runCommand as rc rc("open 2QA0") # make multiscale model here? rc("select :10,20,30") # select some residues
Your help would be appreciated - thanks! Ian
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