[Chimera-users] Multiscale models command

[Ian Holmes]

Thank you very much Elaine and Tom!
Ian

On Tue, Dec 20, 2016 at 3:56 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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