Hi Eric, I've done the following commands on 3 .pdb files and used matchmaker on the 200th frame and 10,000th frame, respectively. open */md.nc structureModel #1 step 50 (slider shows 200 frames loaded) I've also tried open */md.nc structureModel #1 start 1 end 10000 step 50 (same result as above) vs open */md.nc structureModel #2 (slider shows 10,000 frames loaded - original) Both the 200/200 frames versions match the 200/10,000 frames version. If it worked, would 200/200 frames match 10,000/10,000 frames? Alex Lee Woods Lab ahl63010@uga.edu ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Friday, September 29, 2023 4:54 PM To: Alexander Hung Lee <Alexander.Lee@uga.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Speeding up commands from cxc You don't often get email from pett@cgl.ucsf.edu. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi Alex, I didn't even notice that you were already only showing every 50th frame. In that case you should use "step 50" in the open command and your play-through command becomes simply "coordset #1 1,200; wait 200". You have to realize that by default when you run the hbonds command on a trajectory model, it computes the H-bonds for every frame of the trajectory (controllable with the "coordsets" keyword). So using a trajectory of 200 frames vs. 10,000 will produce a 50x speedup, so the H-bonds calculation for 200 frames should take on the order of a half minute or so in your case. --Eric On Sep 28, 2023, at 8:18 PM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Eric, Thanks for the clarification. Little disappointed that hbond step can't leverage my hardware, but it's good to know I might be able to go around it by manipulating the frames. I'm using 10,000 frames for 100 ns MD simulation. Currently, my cxc workflow is producing ~ 1 min long movie by playing 10,000 frames in 50 frame increments and encoding at 4 fps. I'm visualizing the trajectory with "open *.pdb" followed by "open *.nc format Amber". If I were to use "open *.nc format Amber step 10" instead, would calculations be faster and I should change coordset #1 1,10000,50; wait 200 > coordset #1 1,1000,5; wait 200 ? Surface and hbond calculations should be significantly shorter (hbonds alone take 20 mins)? Thanks, Alex Lee Woods Lab ahl63010@uga.edu<mailto:ahl63010@uga.edu> ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Sent: Thursday, September 28, 2023 10:12 PM To: Alexander Hung Lee <Alexander.Lee@uga.edu<mailto:Alexander.Lee@uga.edu>> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Speeding up commands from cxc You don't often get email from pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi Alex, Yes, the bottlenecks are likely the surface recomputations as the trajectory plays, and the H-bonds calculation for 10,000 frames. I believe the surface calculation automatically uses multiple processors if available, so there's nothing you can do there, and the H-bonds calculation is very complicated and has not been parallelized (nor would it be easy to). My advice would be to use fewer frames. A 10,000 frame trajectory shown at 25 frames/sec would produce a movie close to 7 minutes long. Is that really what you want? If you used every 10th frame ("step 10" in the open command) then the movie would be 40 seconds long and take 3 minutes to record. --Eric Eric Pettersen UCSF Computer Graphics Lab On Sep 28, 2023, at 5:55 PM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto: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 1080 set bgColor white view zalign ligand inFrontOf #1 sel protein surface; surface color salmon; transparency protein 60 target s sel :UNL color sel dark slate gray; color sel byhetero sel :SIA color sel dim gray; color sel byhetero sel :UNL hbonds :UNL reveal true surface zone #1 nearAtoms ligand distance 15 select zone ligand 15; select add ligand select ~sel ~cartoon sel delete sel ~sel view ligand movie record supersample 4 perframe "~label; label hbondatoms" ; coordset #1 1,10000,50; wait 200; ~perframe movie 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 Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010@uga.edu<mailto:ahl63010@uga.edu> Mobile: (470) 641-3884 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/