Deleting a surface on command line, not just hiding it
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 This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.
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@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
This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you very much Eric. I will happily use the not-so-horrible Python way. :) Cheers, Rebecca From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Date: Thursday, January 12, 2017 at 4:50 PM To: Vertex <rebecca_swett@vrtx.com<mailto:rebecca_swett@vrtx.com>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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@vrtx.com<mailto:Rebecca_Swett@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 This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Dusers&d=DwMFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=-DBoUvsYlwp-GCB0_VgwXtV_gtnFa4g6gyPMur-PDU0&s=LWiSONYl0QbQXtGe1tJKcXqdBOHThOZLeFm1QinYFj0&e=> This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.
participants (2)
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Eric Pettersen -
Rebecca Swett