[Chimera-users] Multiscale models command

Tom Goddard goddard at sonic.net
Tue Dec 20 15:49:57 PST 2016

Hi Ian,

  To show the 2qa0 virus capsid as ribbons

	open 2qa0
	sym #0

Then to zoom to show the full virus


The sym command also has options to make surfaces like the multiscale model if you want those.


> On Dec 20, 2016, at 3:39 PM, Ian Holmes 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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