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> 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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