Thanks for the help Tom! Adjusting the ribbon quality did speed up the morph substantially. I appreciate the added benefit of being able to move the structure around while it's progressing through the coordset. Cheers, Chad ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Friday, September 27, 2024 5:48 PM To: Altobelli, Chad <http://Chad.Altobelli@ucsf.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Increasing ChimeraX speed? One other trick is to just take bigger steps in your morph morph #1,2 frames 10 https: //www. cgl. ucsf. edu/chimerax/docs/user/commands/morph. html Or you could play back the morph skipping frames coordset #3 1,50,5 https: //www. cgl. ucsf. edu/chimerax/docs/user/commands/coordset. html ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd One other trick is to just take bigger steps in your morph morph #1,2 frames 10 https://www.cgl.ucsf.edu/chimerax/docs/user/commands/morph.html Or you could play back the morph skipping frames coordset #3 1,50,5 https://www.cgl.ucsf.edu/chimerax/docs/user/commands/coordset.html This plays frames 1 to 50 stepping 5 at a time. Tom On Sep 27, 2024, at 5:44 PM, Tom Goddard <goddard@sonic.net> wrote: Hi Chad, If the ribbon shape is not recomputed then your morph would not move, probably not the best result. A faster CPU might make a small difference, probably not significant. The ribbon calculation is not multi-threaded so it can only use a single CPU core. Here are two ideas. First you can record a movie using that button at the far right of the morph slider. The movie can be played back and forth as fast as you like in a movie player. The second idea is that maybe it would compute the ribbon faster if the ribbon is at lower quality. Try a command like graphics quality ribbonSides 4 ribbonDivisions 5 The ribbonDivisions option is how many segments of the smooth ribbon curve lie between two amino acids. The ribbonSides is how many segments around a cross-section of the ribbon. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality I have never investigated if that is the speed bottleneck. It well may be earlier parts of the computation computing the cubic spline. Most likely it is some part of the computation that is done in Python instead of C++. I optimized the ribbon code many years ago so there are probably not simple code changes that will speed it up. Tom On Sep 27, 2024, at 5:10 PM, Altobelli, Chad via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Ah, much faster! Is there a way to show ribbons without having it recompute the shape at every step? Is this something a more powerful computer could handle? I'm not driving a Rolls Royce yet, but maybe one day. Cheers, Chad ________________________________ From: Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> Sent: Friday, September 27, 2024 5:03 PM To: Altobelli, Chad <http://Chad.Al<mailto:Chad.Altobelli@ucsf.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] Increasing ChimeraX speed? This Message Is From an External Sender This message came from outside your organization. Ok, next thought is if you are showing ribbons it has to recompute the ribbon shape every time step and that takes some time. How fast is it in sphere display style? Tom On Sep 27, 2024, at 4:57 PM, Altobelli, Chad <http://Chad.Al<mailto:Chad.Altobelli@ucsf.edu>> wrote: Hi Tom, Interesting, changing the lighting to "simple" does cut the 3D GPU usage by ~50% but doesn't increase the pace of coordset advancement (~7 frames per second). Thanks, Chad ________________________________ From: Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> Sent: Friday, September 27, 2024 4:49 PM To: Altobelli, Chad <http://Chad.Al<mailto:Chad.Altobelli@ucsf.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] Increasing ChimeraX speed? This Message Is From an External Sender This message came from outside your organization. Hi Chad, The problem is probably you are using "soft" or "full" lighting which computes ambient shadows from 64 directiions each time the shape of the protein changes. That is done on the graphics card and is time consuming. Switch to simple lighting (command "light simple") or use the icon in the toolbar. Tom On Sep 27, 2024, at 4:41 PM, Altobelli, Chad via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hi, I love using ChimeraX to make morphs, but my protein is quite a large hexamer (500kda) and the progression through the coordset can be quite slow during playback. When I look at my Windows taskmanager, I can see that neither my CPU (12th Gen Intel i7-12700H), RAM, or GPU (NVIDIA RTX 3050 Laptop) are maxed out. Is there a way to speed up Chimera morphs? Thanks, Chad _______________________________________________ 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/