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 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
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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
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