- ChimeraX-users - RBVI Mailing Lists

developing bundles autocompletion
by Daniel Esteban Palma Igor 05 Jun '20

05 Jun '20

Hi, normally I use spyder for writing python code, is there a way to have autocompletion of functions and modules when developing a bundle for ChimeraX? Any other tips for development is well received. Regards, Daniel Palma Igor

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2D and 3D objects
by Jazzar, Rodolphe 04 Jun '20

04 Jun '20

Hi, First of all, this is a great program, and I am barely using it to full extent of its possibilities. I am currently interested in combining a 3D object (a molecule.pdb) and a 2D object/plane/image (as a .png or any other). The idea being that I want to show a slice of an ELF plot, with the 3D molecule embedded through the 2D plot. Good news is that I can import both objects (.pdb and .png). However I face a size issue with the 2D object, which is considerably bigger than the 3D one. Would you know if I can size down a 2D object, or enlarge a 3D one respectively. All in all would you know if chimeraX can generate something like the picture attached by combining a 2D and a 3D object. Thanks for your time, Cheers, Rodolphe [cid:D31DAF51-91B8-4F78-94B3-4C0FCD9C860E] Dr. Rodolphe Jazzar, CNRS Research Associate - (French National Centre for Scientific Research) UCSD-UMI 3555 ORCID : 0000-0002-4156-7826 Office: (858)-534-5315 Mobile: 858-337-2228 University of California, San Diego, 5213 Pacific Hall, Department of Chemistry, 9500 Gilman Dr, # 0343, La Jolla, CA 92093-0343 http://bertrandgroup.ucsd.edu<http://bertrandgroup.ucsd.edu/> https://northamerica.cnrs.fr<https://northamerica.cnrs.fr/> http://www.cnrs.fr/en/cnrs [cid:image001.png@01CFDE12.00855770]

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Re: [chimerax-users] ChimeraX cross links
by Elaine Meng 04 Jun '20

04 Jun '20

> On Jun 4, 2020, at 1:25 AM, Dina Schneidman <duhovka(a)gmail.com> wrote: > > Hi, > We are getting addicted to the ChimeraX graphics, amazing! > I couldn't find how to add cross-links on top of the structure. What would be the best way to do this? > Also, is there a way to color different cross-link types in distinct colors? > Thanks and stay safe! > Dina Hi Dina, Glad you like it, and I certainly hope you and your family are staying safe too! As I understand it there are two ways for atomic structures with crosslinks to be shown in ChimeraX: (1) some integrative modeling structures include such crosslinks. If you download the "cif" from the PDB IHM site <https://pdb-dev.wwpdb.org/> and then change its filename suffix to "ihm" instead, then you can open it in ChimeraX. If the IHM model has crosslinks, they should show up somewhere in the model hierarchy of that data, which you can explore in the Models panel. An example of one with crosslinks is the BBSome: <https://pdb-dev.wwpdb.org/entry.html?PDBDEV_00000018> (2) or if you just have any atomic structure already in ChimeraX and you want to add crosslinks, you can read in pseudobond file (filename.pb), which is just a series of atom-pair specifications in plain text. You can also include color, radius, number of dashes. The file description is the bottom section of this page: <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html> Also, you can change colors, number of dashes, and radius of any pseudobonds already in the structure or previously added, just using the commands "color" "style" and "size"; see the links in the top section of the pseudobonds page. There is a chimerax mailing list CC-d here for questions (unless they contain private data). 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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Installation of ChimeraX in Centos 7
by Gaya Yadav 01 Jun '20

01 Jun '20

?Dear Sir/Madam, I am trying to install Chimera X in the Centos 7 in my local directory. I installed it by converting it chimerax-rc.cpio?. But I cannot launch it, it was showing error about the openGL. Is that because of the openGL or it is not installed properly? Here is the error: WARNING: QXcbConnection: XCB error: 145 (Unknown), sequence: 178, resource id: 0, major code: 139 (Unknown), minor code: 20 NOTE: available bundle cache has not been initialized yet ERROR: ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4 Try updating your graphics driver. WARNING: The X11 connection broke: No error (code 0) XIO: fatal IO error 0 (Success) on X server "localhost:12.0" after 668 requests (668 known processed) with 0 events remaining. ? Thanks Gaya

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Source Code
by Dario Eltzner 29 May '20

29 May '20

Hello, I was interested in reading the ChimeraX source code but found only this site https://www.cgl.ucsf.edu/chimerax/docs/devel/conventions.html which references a git repo that is password protected. Is the source code not freely available? Best Wishes Dario Eltzner

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Re: [chimerax-users] 3D stereo lighting is not the same as mono
by Tom Goddard 27 May '20

27 May '20

Try "camera sbs" and see if shadows look right. If they do look ok, but stereo does not then it will require some debugging with a stereo system that reproduces the problem and I am not able to test that until quarantine is over. Tom > On May 26, 2020, at 10:01 AM, Kenneth Satyshur <kenneth.satyshur(a)wisc.edu> wrote: > > Thanks. I will check out the versions as they come out. Hopefully this can be fixed. I can try a VR and see what is up with the display if anything. > kas > > > Kenneth A. Satyshur, M.S., Ph.D. > Senior Scientist, > Department of Bacteriology: College of Ag and Life Sciences; > Departments of Bio Molecular Chemistry, > Neuroscience, Oncology, and Carbone Cancer Center: > School of Medicine and Public Health; > and the School of Pharmacy > University of Wisconsin-Madison > Madison, Wisconsin, 53706 > 608-215-5207 > From: Tom Goddard <goddard(a)sonic.net> > Sent: Tuesday, May 26, 2020 11:48 AM > To: Kenneth Satyshur <kenneth.satyshur(a)wisc.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] 3D stereo lighting is not the same as mono > > I made a bug report for this > > https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3315 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3315> > > I am not able to test stereo, don't have a computer that can do it. For me other two eye modes like VR and SBS (side-by-side) have correct shadows. The problem may be a graphics driver bug effecting shadow calculation. Or it might be a bug in ChimeraX in how OpenGL quad-buffering are used. > > Tom > > >> On May 23, 2020, at 4:39 PM, Kenneth Satyshur <kenneth.satyshur(a)wisc.edu <mailto:kenneth.satyshur@wisc.edu>> wrote: >> >> I am using version 1.0 in Centos7 with Nvidia 3D glasses and K4000 video card. I do all my work in 3D stereo. Especially density fitting. I noticed that the lighting is different in mono vs stereo mode. When i go to stereo mode with >> >> camera stereo >> >> the image is in stereo but the "full" lighting is on and the image is very dark with shadows. If I switch to 'simple' it is bright and has weak shadowing. Switching to 'soft' the image is flat black and can only be seen with white background but contains no atoms. I think this is a bug. >> But a Great improvement in rendering of images. >> thanks >> kas >> p.s. old chimera does stereo very well on my system >> Linux kenworkathome 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux >> >> >> Kenneth A. Satyshur, M.S., Ph.D. >> Senior Scientist, >> Department of Bacteriology: College of Ag and Life Sciences; >> Departments of Bio Molecular Chemistry, >> Neuroscience, Oncology, and Carbone Cancer Center: >> School of Medicine and Public Health; >> and the School of Pharmacy >> University of Wisconsin-Madison >> Madison, Wisconsin, 53706 >> 608-215-5207 >> _______________________________________________ >> 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://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

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3D stereo lighting is not the same as mono
by Kenneth Satyshur 26 May '20

26 May '20

I am using version 1.0 in Centos7 with Nvidia 3D glasses and K4000 video card. I do all my work in 3D stereo. Especially density fitting. I noticed that the lighting is different in mono vs stereo mode. When i go to stereo mode with camera stereo the image is in stereo but the "full" lighting is on and the image is very dark with shadows. If I switch to 'simple' it is bright and has weak shadowing. Switching to 'soft' the image is flat black and can only be seen with white background but contains no atoms. I think this is a bug. But a Great improvement in rendering of images. thanks kas p.s. old chimera does stereo very well on my system Linux kenworkathome 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, Department of Bacteriology: College of Ag and Life Sciences; Departments of Bio Molecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center: School of Medicine and Public Health; and the School of Pharmacy University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207

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Recreating views
by Martin Montgomery 22 May '20

22 May '20

Hi, I have a session file that contains everything I need to make figures for a paper. With pymol, I saved the get_view matrix in a text file for each view which meant that with one session file I could easily recreate the views if I needed to go back and tweak a figure. In ChimeraX, the closest way that I found to replicate this was to use named views. Am happy to supply a session file if it helps also happy to be educated if there is a better way of doing this, especially as now the ChimeraX session files can get rather large. Cheers MGM Martin G Montgomery Senior Scientist ATP Synthase Group MRC Mitochondrial Biology Unit University of Cambridge The Keith Peters Building Cambridge Biomedical Campus Hills Road Cambridge Great Britain CB2 0XY www.mrc-mbu.cam.ac.uk <http://www.mrc-mbu.cam.ac.uk/>

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Save/restore scene?
by Oliver Clarke 20 May '20

20 May '20

Hi ChimeraX-ers, Is there currently an equivalent of the "scene" command from Chimera? It was super helpful to be able to quickly switch between different (and often complex) representations of a molecule. I know the view command for saving and restoring orientations, and the "name" command for saving selections, but I can't find an equivalent of scene. I'm guessing it's not yet implemented, but count me as one vote for porting it over after 1.0 is out the door, it was super helpful in Chimera! Cheers Oli

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Feature suggestion - show color code in picker?
by Oliver Clarke 19 May '20

19 May '20

Hi, I love the color editor in ChimeraX, it is much nicer than the one in Chimera and is super useful! One minor suggestion - would it be possible to add a dynamically updated label showing in the editor the current color code? This sometimes shows up in the log but not always, and it is useful to have easily copy-able for use in scripts and aliases. Cheers Oli

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