[Chimera-users] Multiscale models command
goddard at sonic.net
Tue Dec 20 15:49:57 PST 2016
To show the 2qa0 virus capsid as ribbons
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!
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