[Chimera-users] Multiscale models command

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 20 15:56:07 PST 2016


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 at 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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