October 2023 - ChimeraX-users - RBVI Mailing Lists

Speeding up commands from cxc
by Alexander Hung Lee 02 Oct '23

02 Oct '23

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(a)uga.edu Mobile: (470) 641-3884

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Bright light while using fly command
by Haselbach,David 02 Oct '23

02 Oct '23

Hi, I am trying to make a fly movie in which I move from one rotation state of the molecule to the next. Unfortunately, the lighting during the flight is not nice. The light goes very bright while moving and in the end jumps back to normal. However, if I do the turn life with mouse the light is fine. I am using soft lighting. Find attached an example movie. What could I do? Can anyone help? Best, David

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ChimeraX Alphafold Question
by Vincent Candela 02 Oct '23

02 Oct '23

Hello, I am an undergraduate researcher at McGill University using the Alphafold feature of ChimeraX to study the role of tau on microtubule dimers, and I was wondering if you could point me to detailed documentation on the energy-minimization feature of Alphafold. I’ve been looking at the ChimeraX documentation and couldn’t find an in-depth documentation on what it does. Thank you so much, Vincent Candela

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