January 2021 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax
by Elaine Meng 26 Jan '21

26 Jan '21

On Jan 25, 2021, at 7:47 PM, sunyeping <sunyeping(a)aliyun.com> wrote: > > Dear all, > I wish to color an model by an attribute in chimerax. The attribute is the entropy which is calculted by an external software. I wrote the entropy values of each residue in a text file (attr.txt) like the following: > > attribute: entropy > match mode: 1-to-1 > recipient: residues > :1 0.0 > :2 0.0014948 > :3 0.0090952 > :4 0.0004805 > :5 0.1102497 > :6 0.0095258 > :7 0.0008226 > :8 0.0042205 > :9 0.0037255 > :10 0.0006678 > :11 0.0027988 > :12 0.0193925 > :13 0.0153925 > :14 0.0052115 > :15 0.0020136 > .......... > However, when I input the command "color byattr attr.txt", I get the following error information: > "No known/Registered attribute attr.txt" > > Could anyone tell me what is the correct way to do this? > With many thanks. > Best regards Hello, Since this is a ChimeraX question, better to send to the chimerax-users(a)cgl.ucsf.edu address CC'd here instead of the chimera-users list. (1) First you need to make sure the text file is the right format. It should be tabs (not just a space) before the residue number and between the residue number and the value, e.g. as described here: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html> (2) Then (after the atomic structure is open), open the attribute file with the "open" command, e.g. with pathname of your file, or if you want use a file browser window to find the file, "open browse". It is easiest to first name the file ending in .defattr so that ChimeraX will know what kind of file it is supposed to be. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#defattr> (3) then the Log should report that the attribute named entropy is assigned and you are ready to do the coloring. The coloring command could be something like color byattribute entropy palette rainbow ...there are several other options, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [chimerax-users] windows 10 GPU acceleration?
by Tom Goddard 25 Jan '21

25 Jan '21

Hi Chuck, Glad you figured it out. I wonder what that graphics scheduling option is doing. Tom > On Jan 24, 2021, at 3:36 PM, Sindelar, Charles <charles.sindelar(a)yale.edu> wrote: > > Hey, I figured it out! There is some kind of new windows option called hardware-accelerated graphics scheduling, in the graphics settings->change default graphics settings control panel. I turned it off, and boom- ChimeraX started using the Nvidia. Thanks for the pointers- definitely helped me guess the solution. Maybe this will help someone else… cheers! > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Sunday, January 24, 2021 2:38 PM > To: Sindelar, Charles <charles.sindelar(a)yale.edu> > Cc: chimerax-users(a)cgl.ucsf.edu > Subject: Re: [chimerax-users] windows 10 GPU acceleration? > > Hi Chuck! > > Yes ChimeraX and Chimera should both be using your laptop Nvidia 2080 GPU and not the Intel graphics. Chimera(X) does not choose the GPU and does not even know that there is more than one -- nothing in the OpenGL graphics library gives that information. It is up to the Windows operating system to decide what GPU used, and it usually makes the right choice. There is in fact a flag in ChimeraX that tells Windows it should use the Nvidia GPU if available. > > You can see for certain which GPU is being used in Chimera with the command > > graphics driver > > Here's what it reports in the log on my laptop > > OpenGL version: 4.1 ATI-3.10.18 > OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine > OpenGL vendor: ATI Technologies Inc. > > Yours should either save Nvidia or Intel in the output. It may say Nvidia but your 2080 GPU use does not seem to get much use. The GPU will only be used when the graphics are changing -- for instance, use the command "roll" to set the models in motion (and command "stop" to halt them). Even when the graphics is constantly changing if your model is small and lighting mode is simple, it will probably show the GPU is hardly working. Use "full" or "soft" lighting to get ambient shadows and that should load the GPU some ("lighting full", or "lighting soft"). > > The high performance graphics mode you set in Windows should certainly make the Nvidia GPU get chosen. > > If ChimeraX "graphics driver" says the Intel GPU is being used then something is clearly messed up. But it must have something to do with your Windows and graphics driver configuration. In fact are you sure you have a working Niovida graphics driver installed? Are there any other apps you use where you see the Nvidia GPU in use? > > Tom > > > > > On Jan 24, 2021, at 10:09 AM, Sindelar, Charles <charles.sindelar(a)yale.edu <mailto:charles.sindelar@yale.edu>> wrote: > > Dear Tom, Elain, Eric et al, happy new year to you and I hope all is well. > > I was wondering how much GPU acceleration I can hope for with my new Dell XPS 17, for either ChimeraX or Chimera? Right now I am noticing that when I use the programs, all the graphics load goes to my integrated Intel graphics GPU, and frame rates are not impressive. The Nvidia 2080, which should be awesome, sits idling. This is on Windows 10. I tried setting the Windows “Graphics Settings” control panel for “high performance”, which should try to make Chimera(X) use the NVidia, as far as I know, but nothing happens. > > Thanks and cheers! - Chuck > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl…>

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windows 10 GPU acceleration?
by Sindelar, Charles 24 Jan '21

24 Jan '21

Dear Tom, Elain, Eric et al, happy new year to you and I hope all is well. I was wondering how much GPU acceleration I can hope for with my new Dell XPS 17, for either ChimeraX or Chimera? Right now I am noticing that when I use the programs, all the graphics load goes to my integrated Intel graphics GPU, and frame rates are not impressive. The Nvidia 2080, which should be awesome, sits idling. This is on Windows 10. I tried setting the Windows "Graphics Settings" control panel for "high performance", which should try to make Chimera(X) use the NVidia, as far as I know, but nothing happens. Thanks and cheers! - Chuck

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CastP surfaces in ChimeraX/ Chimera
by Y. Mutum 20 Jan '21

20 Jan '21

Hi Is there a way to open the results from CastP results in 'ChimeraX' and visualise the surfaces calculated using CastP? In this case, the pdb is 3cx5, and the surfaces are calculated from CastP webserver. Just on using Chimera (version 1.15c) - I have also tried to open the CastP results using 'Chimera', but the molecular surfaces display are failing (picture attached). I followed up the abberant surface-calculation problems in https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html. However, the display surfaces are all still failing - I tried the first 2 suggestions relevant to mine, but they are still failing. The first - which involves splitting the chain using the command 'split', shuts down the Castp: surfaces-window in Chimera and I can't see of a way to retrieve this CastP window with the list of surfaces. As, I do not want to split the model, I tried the second suggestion of 'surfcat one' (as CastP server selects atoms from multiple chains to create surfaces). I am not sure if I want to mess up with the Vanderwaal radii (the third suggestion) either, as these surfaces were calculated in CastP with a specific probe radius. Would you have any suggestions of how to use ChimeraX to open and analyse molecular surfaces calculated by CastP? Last, but not the least, if suppose you have to end up using Chimera if ChimeraX doesn't support .poc files, could you please suggest this work-around for opening these problematic CastP-calculated-surfaces in Chimera? Thanks Yaikhomba [cid:8c139fcc-51aa-496c-9f20-9c01badbbe12]

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Re: [chimerax-users] video of digestion kinetics
by Elaine Meng 18 Jan '21

18 Jan '21

Hi Tynan, Besides abruptly hiding atoms and bonds, you could fade them in or out over time (spread hiding across multiple movie frames), or don't hide them but select them (shown as green outline), or color them differently, or show them with different styling like fatter or thinner sticks, etc. These are all things you can do with the commands of either program, normal stuff that people frequently do when making figures or movies. Or instead of (or in addition to) changing how the peptide is shown, you could show a 2D label that is an arrow pointing to the cleavage point (see 2dlabels command of either program). Elaine > On Jan 18, 2021, at 12:04 PM, Tynan A. Becker <tabecker(a)alaska.edu> wrote: > > Hi Elaine, > Thank you for the very quick response. The info does help. I was thinking that I might be able to take this approach. And I don't mind learning the command line > > However, I was also wondering if there was a way to highlight the peptide bonds between residues to show the actual cleavage points and what gets added as time goes on. This would be a more accurate representation of my data because some peptides are "lost" due to limitations in mass spec rather than the digestion (a very short peptide might not have been digested, but also wasn't IDed by the instrument). > Thank you! > Tynan > > -------- Forwarded Message -------- > Subject: Re: [chimerax-users] video of digestion kinetics > Date: Mon, 18 Jan 2021 11:47:07 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Reply-To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > To: Tynan A. Becker <tabecker(a)alaska.edu> > CC: chimerax-users(a)cgl.ucsf.edu > > > Hi Tynan, > I'm not sure if you meant to send this to the chimera-users(a)cgl.ucsf.edu list or the chimerax-users(a)cgl.ucsf.edu list. Anyway, using either program, UCSF Chimera or UCSF ChimeraX, in general you would need to make a command file for what happens during the movie. The command file could include hide successive parts of the peptide, i.e. if residues 10-12 get cut off first, hide them, then several steps (movie frames) later hide the next set of residues to get cut off, etc. > > In either program, making a command script would require learning the commands, so you would need to invest some time. In Chimera, however, there is also a graphical interface to movie recording, so if you are able to use the menus instead of commands to get to various states you want in your movie (e.g. with more and more of the peptide hidden), with this Movie Recorder interface you can save them as scenes and place them on a timeline. Still, however, at a minimum it will require learning how to use the menus of Chimera to do all the coloring, styles, 2D labels etc. that you want in your movie. > ChimeraX "making movies" page: > <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> > > Chimera "making movies" page: > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html> > Chimera Movie Recorder tool: > <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorde…> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Jan 18, 2021, at 10:32 AM, Tynan A. Becker <tabecker(a)alaska.edu> wrote: >> >> Good morning, I have kinetics data from the in vitro digestion of a protein by several enzymes. For each enzyme, I have 8 time points with peptides that remain intact at that point of time (which also gives me the cleavage sites added between adjacent time points). I was trying to figure out to model this in Chimera, including being able to show the protein from multiple sides. Looking online, I see that you have some videos with proteins showing alternate conformations. Do you think it possible for me to show the cleavage sites that develop sequentially over time in a specific protein as it is digested? >> Thanks, Tynan >

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video of digestion kinetics
by Tynan A. Becker 18 Jan '21

18 Jan '21

Good morning, I have kinetics data from the in vitro digestion of a protein by several enzymes. For each enzyme, I have 8 time points with peptides that remain intact at that point of time (which also gives me the cleavage sites added between adjacent time points). I was trying to figure out to model this in Chimera, including being able to show the protein from multiple sides. Looking online, I see that you have some videos with proteins showing alternate conformations. Do you think it possible for me to show the */cleavage sites/* that develop sequentially over time in a specific protein as it is digested? Thanks, Tynan

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Black/Dark Theme
by Petrychenko, Valentyn 13 Jan '21

13 Jan '21

Dear ChimeraX Developers Team, Do you have in your features list an dark or black GUI theme? I understand that stylistic features have lover priority than a really useful ones, but during many hours of work every day in ChimeraX white GUI eyes getting tired especially at late hours and especially when it contrasts with dark interface of the rest of the system and other dark themed software. I really looking forward to see a dark theme feature in future updates. Respectfully yours, Valentyn Petrychenko

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Question about the comparative homology modelling tool
by Moradkhan, Tiglath A 12 Jan '21

12 Jan '21

Hi I have two questions about the homology modelling tool: 1. Why is the default number of models to be built five? Does having five models provide a better choice for choosing the best model? 2. In evaluating a protein model which of the following parameters plays a much more dominating role: zDOPE, predicted RMSD or the predicted native overlap? Or do all three measures contribute the same effect on model evaluation? For instance a model might have a low zDOPE score but have a higher RMSD while another model might have a much more positive zDOPE score but a lower RMSD. Based on this, would the first model be the better one to pick or do both models have equal weight in terms of overall model quality? I would be very glad for advice. Thanks Tiglath

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high results tiff
by Fabian Glaser 10 Jan '21

10 Jan '21

Dear experts, I am sorry to bug with this issue again, but I dont’ find a good tutorial or clear instructions about the right way to prepare figures with high quality for publication with chimeraX, and I find myself again and again making them with chimera, since it seems I am able to produce 300 dpi with chimera on tiff for example using the save image dialogue, but on chimeraX I am only able to produce them with 72 dpi using the save command. I have tried all kind of sizes but… well for me it does not work yet. Again, may this is trivial, but I am not an expert in graphics, and if somebody could guide me would be really thankful. Thanks in advance, Fabian Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ Tel +972 (0) 4 8293701

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Re: [chimerax-users] Stereo mode error
by Tom Goddard 07 Jan '21

07 Jan '21

Hi J.C., Since Chimera works in stereo and ChimeraX does not I think the problem is almost surely that ChimeraX requires a "core" OpenGL context (ie using modern OpenGL) while Chimera requires a "legacy" OpenGL context. I assume ChimeraX is working for you not in stereo. So it can get a core context, but apparently not a core stereo context. It looks like the Nvidia driver is not providing a core OpenGL stereo context. But Nvidia has clearly stated that it does support this in their 3D Vision FAQ https://nvidia.custhelp.com/app/answers/detail/a_id/4845 "Without 3D Vision, will NVIDIA Quadro GPUs still support OpenGL Quad-buffered Stereo? Absolutely YES. OpenGL Quad-buffered Stereo is not affected by changes to the 3D Vision driver." ChimeraX is asking for quad-buffered stereo core context and "core" contexts are the standard of current OpenGL. So if we believe Nvidia's statement then their driver will give this kind of context. And that suggests that you have a driver configuration setting that prevents it. It is certainly also possible that the Nvidia driver you are using is simply broken in its ability to provide core stereo contexts. But I think it is more likely you have it configured to not give such a context, possibly your X server "Option "Stereo" "10"" setting is the cause. When the Nvidia driver provides a core OpenGL stereo context this does not mean your 3D Vision glasses will work. In fact the above 3D Vision FAQ very clearly says it will not work with a current Nvidia driver unless a separate 3D Vision USB driver is installed. "NVIDIA announced it is no longer supporting 3D Vision. What does this mean? Hardware: NVIDIA is no longer selling the 3D Vision emitters and glasses. Drivers: R418 graphics drivers will be the last driver to contain the 3D Vision driver package. The R418 branch will be supported until January 2020. In addition, NVIDIA will decouple the 3D Vision USB driver from the graphics driver. NVIDIA will provide the 3D Vision USB driver package as a separate installer on NVIDIA.com moving forward - see Quadro Advance Options <https://www.nvidia.com/object/quadro-advance-options.html>. This will allow users to upgrade the graphics driver while continuing to use the standalone 3D Vision USB driver." If this statement from Nvidia is true then the 3D Vision emitter on your computer can only work if you have installed a separate 3D Vision USB driver. If the emitter does not work the screen will show a double image and stereo software like ChimeraX, Chimera and Coot will not complain but you will not see it in stereo through the glasses because the glasses cannot synchronize to the interleaved in time left and right eye images without the infrared emitter. It is possible that that separate 3D Vision USB driver does not work with a core OpenGL context. Kenneth Satyshur has several legacy Nvidia stereo systems and may know how to make ChimeraX work in stereo with 3D Vision. Ultimately, you are trying to use no longer supported hardware. Honestly Nvidia never supported 3D Vision well, and Windows is much more likely to work than Linux. It probably can be made to work with ChimeraX if enough hours are sunk into it, and will certainly be easier if you use old graphics software such as Chimera or Coot which was written based on the legacy OpenGL that 3D Vision originally worked with. Tom > On Jan 7, 2021, at 5:53 AM, Jean-Christophe HAESSIG <haessigj(a)igbmc.fr> wrote: > > Le mardi 05 janvier 2021 à 10:31 -0800, Tom Goddard a écrit : >> Hi Jean-Christophe, > Hi, > > That was a *very* insightful answer, thank you vey much. But at the > same time it's a bit saddening because it sounds like there will be no > way to use ChimeraX fully on this setup. > > My tests indicate that for the time being, 3D Vision still works with > the latest Nvidia driver on Linux. Despite nvidias decision to retire > 3D Vision, it only means they will stop producing shutter glasses. The > following FAQ entry makes that a little clearer : > https://nvidia.custhelp.com/app/answers/detail/a_id/4845 > Still, that doesn't explain how standard OpenGL calls would not be > supported on a recent driver. Maybe using 'Option "Stereo" "10"' in X > selects an alternate code path where only legacy contexts are > available. On the other hand, it seems this is the only way to get the > glasses to work. In fact, I tried every single stereo mode of the > nvidia driver, and all of them except one gave the same results : the > programs using the legacy contexts worked and ChimeraX crashed. > I also tried Chimera and indeed, it works as you suggested. > > In mode 14 (dubbed "Generic Stereo for DP") however, I couldn't get any > of the programs to work. Stereo is reported as disabled in nvidia- > settings but that could simply be beacuse there is no DP screen > attached. Anyway, it sounds more like this mode could support one of > the more recent GL calls. > > I guess I will keep the older 3D vision sets to run coot and chimera, > and seek more recent hardware for chimeraX. > > J.C. Haessig -- systems administrator, IGBMC > >

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