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On Sep 28, 2023, at 5:55 PM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello everyone,
I'm working to automate making movies from 10,000 frame trajectories. Currently, my cxc contains the following commands
windowsize 1920 1080set bgColor whiteview zalign ligand inFrontOf #1sel proteinsurface; surface color salmon; transparency protein 60 target ssel :UNLcolor sel dark slate gray; color sel byheterosel :SIAcolor sel dim gray; color sel byheterosel :UNLhbonds :UNL reveal truesurface zone #1 nearAtoms ligand distance 15select zone ligand 15; select add ligandselect ~sel~cartoon seldelete sel~selview ligandmovie record supersample 4perframe "~label; label hbondatoms" ; coordset #1 1,10000,50; wait 200; ~perframemovie encode output hbond.mp4 bitrate 6000 framerate 4
The above takes ~ 30 mins, and it's something I would like to do for whole libraries I'm screening. I think the longest process is "hbonds :UNL reveal true" while second longest is movie record and perframe. Is there a way to speed this up? Is there a way to take advantage of multi-threading if it isn't already enabled? If multi-threading is already being used, what can I change to be more efficient?
I deleted the parts that I didn't need "delete sel" since they're not involved in the binding site, and I thought it would help speed up surface calculations while recording.Regards,
_______________________________________________Alex LeePhD StudentDepartment of Biochemistry & Molecular Biology
Complex Carbohydrate Research CenterUniversity of Georgia
315 Riverbend Rd.Athens, GA 30602
Email: ahl63010@uga.eduMobile: (470) 641-3884
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