[Chimera-users] Deleting a surface on command line, not just hiding it

Rebecca Swett Rebecca_Swett at vrtx.com
Thu Jan 12 13:51:46 PST 2017


Thank you very much Eric. I will happily use the not-so-horrible Python way. :)
Cheers,
Rebecca

From: Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>>
Date: Thursday, January 12, 2017 at 4:50 PM
To: Vertex <rebecca_swett at vrtx.com<mailto:rebecca_swett at vrtx.com>>
Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] Deleting a surface on command line, not just hiding it

Hi Rebecca,
There’s a horrible non-Python way to do it, and a not-so-horrible Python way to do it.  The horrible non-Python way is whenever you need a surface you open a second copy of your trajectory (“open” command), change it to the right coordinate set (“coordset” command), show the surface and then close the second trajectory.  Open it again when you need another surface, etc.
The Python way is to run this Python code whenever to need to close a surface only (it will close all surfaces):

from chimera import openModels, MSMSModel
openModels.close(openModels.list(modelTypes=[MSMSModel]))

You should put it in a file whose name ends in “.py” (e.g. closeSurfs.py) and then just use the open command to open/run it when you need it.

—Eric

Eric Pettersen
UCSF Computer Graphics Lab

On Jan 11, 2017, at 10:54 AM, Rebecca Swett <Rebecca_Swett at vrtx.com<mailto:Rebecca_Swett at vrtx.com>> wrote:

Hi all,
I'm working on an animation, and I'd like to know if there's a way I can delete or close a calculated surface from the command line. For my purposes, I'd like to show the surface representation of the protein, remove it, then show a dynamics trajectory, and show the surface again at a separate point (while the trajectory is stopped). Currently, without being able to close the surface, it tries to recalculate the surface at each trajectory frame, which doesn't work for my purposes. Let me know if this is possible.
Cheers,
Rebecca


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