<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Józef,<div class=""><br class=""></div><div class=""> 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</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>coord #1</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>perframe "surface #1:4,7,8,16,17"</div><div class=""><br class=""></div><div class="">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</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>coord #1</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>perframe "surface close #1 ; surface #1 update false ; surface zone #1 near #2"</div><div class=""><br class=""></div><div class="">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</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6252" class="">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6252</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Feb 25, 2022, at 3:11 PM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Józef,<br class="">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.<br class="">Sorry for the inconvenience,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><blockquote type="cite" class="">On Feb 25, 2022, at 5:42 AM, Lewandowski, Jozef via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hi, <br class=""><br class="">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”.<br class="">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?<br class="">I essentially just would like to follow the changes to the substrate channel without any distractions.<br class=""><br class="">Thank you,<br class="">Józef<br class=""><br class="">------------------------------------------------------------------------------------------------------<br class="">Józef R. Lewandowski<br class="">Professor | Department of Chemistry | University of Warwick<br class=""><a href="mailto:j.r.lewandowski@warwick.ac.uk" class="">j.r.lewandowski@warwick.ac.uk</a> | External: +44 (0) 24 76151355 | Internal: 51355 <br class="">Millburn House: F07 | Coventry CV4 7AL | Find us on the interactive map<br class="">Lewandowski group website | Warwick solid-state NMR group website<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>