- ChimeraX-users - RBVI Mailing Lists

Hardware for VR of volume data
by Tom Goddard 11 Jul '18

11 Jul '18

Hi Bernard, VR is not going to handle large volumes no matter what hardware you buy. To avoid causing nausea current VR headsets use 90 frames/second graphics updating. That is in two eyes, so the effective graphics frame rate needed is 180 frames/second. By comparison on a flat panel display it is routine to show a very large volume at 10 frames per second and this causes no problem. So VR requires about 20 times the rendering speed of visualization on a conventional display. So here are some ideas of what you can expect. Some recent 3d light microscopy I was looking at in VR is 4K by 2K by 31 z planes with 3 channels — and it rendered fast enough with VR on a GTX 1080 and also on a Quadro P6000. Comparing to your 2K cubed example my data was equivalent to about 2k x 2k x 186, or about 1/10th the size. I haven’t benchmarked volume rendering so I don’t actually know at what size graphics is too slow — I should test this. But I suspect this is close to the limit. For molecular structure display, 100,000 atoms with very coarsely triangulated spheres works in VR but is near the limit. For surface and triangle rendering the limit is about 2-5 million triangles depending on which high-end graphics card before frame drops start causing flicker. For molecules showing 2.4 million atoms of HIV capsid 3j3q is fine on a desktop display but is not going to work in VR. With that in mind I would recommend a GTX 1080 Ti graphics card with a high-end CPU, maybe 64 Gbytes of memory, definitely get a high-end SSD drive or two as the data transfer rates of about 3 Gbytes/second are very handy for large data compared to the 100 Mbytes/second of spinning drives — the whole system would be about $4-5k. You could spend more but you won’t get any better performance. The main VR performance bottleneck is going to be in the software if you use ChimeraX. Unfortunately it does color blending and mapping data values to colors and cropping on the CPU instead of the GPU which is painfully slow, tens of seconds to adjust brightness on the above-mentioned 3-channel light microscopy. I expect to put the blending and color lookup on the GPU in ChimeraX over the next 12 months. Tom > On Jul 10, 2018, at 12:48 PM, Heymann, Bernard (NIH/NIAMS) [E] wrote: > > Hi > > I'm interested in acquiring a PC with capabilities to use ChimeraX for 3D VR visualization of large volumes (2k cube). What is the best configuration (CPU, GPU, VR hardware) for around a $5-10k budget? > > Bernard > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

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pdb and map colors
by Andrey Feklistov 25 Jun '18

25 Jun '18

My question is about ChimeraX 0.6: is it possible to highlight different parts of a pdb (based on the protein sequence) with different colors and then color a corresponding map accordingly. I can't find an option 'Sequence' like in the old Chimera, is it possible to do this from a command line? Thanks!

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Re: [chimerax-users] [Chimera-users] ChimeraX won't start on Ubuntu 16.04
by Greg Couch 22 Jun '18

22 Jun '18

(This is really a question for the chimerax-users mailing list, not the chimera-users one.) If you can wait a week or so, I'll have a ChimeraX .deb package for Ubuntu 16.04 (and another for 18.04). But to answer your question, you do not need a system-wide replacement of Qt5. libQt5core.so.5 is in CHIMERAX/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Core.so.5, where CHIMERAX is where ChimeraX was installed. So add that directory to the LD_LIBRARY_PATH environment variable and rerun ldd on libqxcb.so. And please let me know what you find out so I can make sure the .deb package avoids that problem. Regards, Greg On 06/21/2018 10:34 AM, Petr Leiman wrote: > Dear ChimeraX users and Developers, > > ChimeraX v. 0.5 or 0.6 would not start on our stock Ubuntu 16.04 > machines. The error message is as follows: > > This application failed to start because it could not find or load the > Qt platform plugin "xcb" > in "". > > Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, > offscreen, vnc, xcb. > > Reinstalling the application may fix this problem. > Fatal Python error: Aborted > > Current thread 0x000014f406ce7740 (most recent call first): > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/chimerax/ui/gui.py", > line 93 in __init__ > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", > line 485 in init > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", > line 788 in <module> > File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line > 85 in _run_code > File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line > 193 in _run_module_as_main > Aborted (core dumped) > > A few more errors while checking for missing libraries (ldd) of > ChimeraX-supplied libqxcb.so, libqxcb-glx-integration.so > or libqxcb-egl-integration.so > /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.9' not found > /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5' not found > /usr/lib/x86_64-linux-gnu/libQt5XcbQpa.so.5: version > `Qt_5_PRIVATE_API' not found > /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5: version `Qt_5' not found > /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5 > > Do I need to do a system-wide replacement of Qt5 for a different > flavor (OpenGLES)? > > Thanks, > > Petr > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Questions about ChimeraX and problems re-downloading Chimera
by Steven Douglas Aird 21 Jun '18

21 Jun '18

Dear Elaine, Is there a way in ChimeraX to specify colors for individual species of amino acids? I would like to color cysteine residues to illustrate disulfide bonds. There appears to be no ‘byresidue' or ‘byaminoacid’ command. Since I had formerly done this in Chimera, I sought to re-download that from: https://www.cgl.ucsf.edu/chimera/download.html This page has been unresponsive for hours and the download cannot be completed. Thanks for your help, as always. Sincerely yours, Steve Aird Steven D. Aird Technical Editor Faculty Affairs Office Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp<mailto:steven.aird@oist.jp>

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Color clip plane
by Reza Khayat 15 Jun '18

15 Jun '18

Hi, I'm coloring a cryo-EM image reconstruction based on its local resolution. Thus, the image reconstruction will contain multiple colors. Is it possible to color the clipping plane the same as the underlying image reconstruction? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070

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Deactivate model
by Reza Khayat 12 Jun '18

12 Jun '18

?Hi, Is it possible to deactivate a model like in Chimera? I wan to manually align a cryo-EM image reconstruction to another before using the fit command. The orientations are too different for fit to work. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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naming chain ids
by Andrew Macrae 06 Jun '18

06 Jun '18

To whom it concerns I am wondering if it is possible to change the names of the models in chimera X in a similar manner that was possible in chimera. When I split a large complex such as the ribosome it is nice to rename them so I don't need to memorize or reference the PDB what all the numbers and or letters mean. Thanks Cheers, Andrew MacRae

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can now bundle user documentation with ChimeraX bundles
by Greg Couch 30 May '18

30 May '18

Starting with the next daily build, it is possible to have documentation for the tools and commands in the bundle automatically integrated into the User's Manual index. In the bundle_info.xml file, add the documentation to the DataFiles section, e.g.: <DataFiles> <DataFile>docs/user/commands/tutorial.html</DataFile> <DataFile>docs/user/tools/Tutorial_GUI.html</DataFile> </DataFiles> As you can see above, the documentation is in a directory hierarchy that matches the hierarchy of the builtin documentation. The file name for the tool should be the tool's name with underscore's replacing any spaces followed by .html. The file name for commands should be the the first word in the command name followed by .html. If help is asked for a subcommand, then a named reference is made to the subcommand, i.e., /command/.html#/subcommand/. -- Greg

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Re: [chimerax-users] Question about Space navigator and ChimeraX
by Tom Goddard 29 May '18

29 May '18

Hi Rod, I just tried SpaceNavigator with the May 29, 2018 ChimeraX build on macOS 10.13.4 and it worked. Are you still getting the error that it cannot load _spacenavigator? Are you trying to use it on Mac or Windows or Linux? And does space navigator work with Chimera on that same machine? Tom > On May 29, 2018, at 12:17 PM, Tweten, Rodney K. (HSC) wrote: > > Hi Tom, > I downloaded the latest ChimeraX daily build (2018-05-29 02:45:16 PDT), but the space navigator still does not appear not work. Was it included in this build? Thanks! > > From: Tom Goddard <goddard(a)sonic.net> > Date: Friday, May 25, 2018 at 4:33 PM > To: "Tweten, Rodney K. (HSC)" <Rodney-Tweten(a)ouhsc.edu> > Cc: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> > Subject: [EXTERNAL] Re: [chimerax-users] Question about Space navigator and ChimeraX > > Hi Rod, > > Our Mac ChimeraX build machine did not have the Space Navigator library installed so it did not compile the module to use Space Navigator with ChimeraX. I've installed it on the build machine so hopefully tonight's build will have Space Navigator support. It works on my development machine. Thanks for reporting the problem. > > Tom > > > >> On May 25, 2018, at 11:02 AM, Tweten, Rodney K. (HSC) wrote: >> >> I have been using Chimera for some time and like it very much so I thought I would try ChimeraX, which has an undo button! However, I am unable to get the Space navigator to work with chimeraX. I keep getting that it can’t load space navigator (see attached screenshot). Can you tell me if I am doing something wrong here (likely) or if the use of the Space Navigator is not implemented yet. Thanks! >> >> <image001.png> >> >> Cheers, >> Rod Tweten, Ph.D. >> George Lynn Cross Professor >> "It's a great life if you don't weaken" >> >> Microbiology & Immunology >> BMSB-1053 >> 940 Stanton L. Young Blvd. >> The University of Oklahoma Health Sciences Center >> Oklahoma City OK 73104 >> USA >> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mail…>

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Question about Space navigator and ChimeraX
by Tweten, Rodney K. (HSC) 25 May '18

25 May '18

I have been using Chimera for some time and like it very much so I thought I would try ChimeraX, which has an undo button! However, I am unable to get the Space navigator to work with chimeraX. I keep getting that it can’t load space navigator (see attached screenshot). Can you tell me if I am doing something wrong here (likely) or if the use of the Space Navigator is not implemented yet. Thanks! [cid:image001.png@01D3F428.99CAA4A0] Cheers, Rod Tweten, Ph.D. George Lynn Cross Professor "It's a great life if you don't weaken" Microbiology & Immunology BMSB-1053 940 Stanton L. Young Blvd. The University of Oklahoma Health Sciences Center Oklahoma City OK 73104 USA Work phone: 405 271-1205 FAX: 405 271-3117 Skype: toxlab1 Email: rod-tweten(a)ouhsc.edu

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