Hi Józef,
This is some bad behavior of ChimeraX where the surface automatically updates itself right before rendering to use the new coordinates erasing the surface zone. Two ways to fix it are 1) don't use a zone, just show surface patches around specific residues that line your channel
coord #1 perframe "surface #1:4,7,8,16,17"
or 2) if you have markers in the channel and want to use a zone around those markers use the tricky "update false" option to the surface command like so
coord #1 perframe "surface close #1 ; surface #1 update false ; surface zone #1 near #2"
This makes the surface not auto-update with coordinate changes and instead you explicitly close the preceding surface, make the new one, and make the zone. More details are in the bug report Elaine alluded to
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6252 https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6252
Tom
On Feb 25, 2022, at 3:11 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Józef, I can reproduce this problem. I'll create a bug ticket and put your e-mail address on it so you will receive notifications about our findings on this issue. Sorry for the inconvenience, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 25, 2022, at 5:42 AM, Lewandowski, Jozef via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I would like to use “surface zone” command to visualise a substrate channel in an animation of an MD trajectory. For that I would like to regenerate the surface every frame with “perframe”. However, if I do that when I record the movie the entire surface (instead of just the selected zone) will flash before the zone is displayed. Is there any way so that only the surface zone will be displayed from frame to frame without the entire surface flashing? I essentially just would like to follow the changes to the substrate channel without any distractions.
Thank you, Józef
Józef R. Lewandowski Professor | Department of Chemistry | University of Warwick j.r.lewandowski@warwick.ac.uk | External: +44 (0) 24 76151355 | Internal: 51355 Millburn House: F07 | Coventry CV4 7AL | Find us on the interactive map Lewandowski group website | Warwick solid-state NMR group website
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