May 2020 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] color by zone in chimeraX
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Pranav, I’m Cc'ing the chimerax-users(a)cgl.ucsf.edu list (recommended for ChimeraX questions). I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding. If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Hi Elaine and Co., > > I am trying to color a virus map with the relevant pdb file, the > series of commands I am running are as follows, > open virus.mrc > open virus.pdb > color /A plum target c > color /B lightgreen target c > color /C dodger blue target c > color zone #1 near #2 dist 3 > However, the resultant surface is rendered in splotches of red and > blue, which leads me to think the it is coloring the surface using > atom type. Could you tell me how I can get Chimera X to color the > surface using the colors of the chains only? FYI, color by zone works > flawlessly in chimera. > > Cheers, > Pranav

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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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Cartoon smooth loops chimX
by Dominik Hrebík 19 May '20

19 May '20

Hi all! Is there any possibility to smooth loops in cartoon representation in ChimeraX? I can't find it in the user guide. Something similar to pymol's cartoon_smooth_loops,1: https://pymolwiki.org/index.php/Cartoon_smooth_loops Best, Dominik -- ################################## Dominik Hrebik Laboratory of Structural Virology CEITEC, Masaryk University Kamenice 5 / A35 Brno, 625 00, Czech Republic Phone: +420 549 49 7764 <%2B420%20549%2049%207756> ##################################

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Focus in ChimeraX
by Luca Pellegrini 18 May '20

18 May '20

Hi, What is the ChimeraX equivalent to the Focus command in Chimera? I have selected a portion of a structure, and would like to bring it into focus without dragging it into view. Also Focus would automatically set the selection as the pivot point. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA lp212(a)cam.ac.uk

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Turntable rotation
by Scott, Brandon L. 16 May '20

16 May '20

I would like to create an animation where the camera is spun around at a constant azimuthal angle so the object appears to spin on a tabletop. Currently, when I use roll, when it spins to the backside I see underneath the model rather than remaining on top. Any help is greatly appreciated. -Brandon ____________________ Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor SDSMT, Nanoscience and Nanoengineering

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ChimeraX-users May 2020