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
[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> 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
From: Eric Pettersen <pett@cgl.ucsf.edu>
Sent: Thursday, September 28, 2023 10:12 PM
To: Alexander Hung Lee <Alexander.Lee@uga.edu>
Cc: chimerax-users@cgl.ucsf.edu <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
[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> 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
Department of Biochemistry & Molecular Biology
Complex Carbohydrate Research Center
University of Georgia 

315 Riverbend Rd.
Athens, GA  30602
Mobile: (470) 641-3884
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