September 2021 - ChimeraX-users - RBVI Mailing Lists

Turning off silhouettes to specific selection
by Abhilash Padvannil 17 Sep '21

17 Sep '21

Hi Is there a way to turn off the silhouettes on specific selections of a model? Thanks Abhilash.

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Remove older ChimeraX Linux
by Nebojsa Bogdanovic 16 Sep '21

16 Sep '21

Hello, I am trying to reinstall the new ChimeraX on the linux system, however my previous incomplete installations are creating problems. I am not sure how to get rid of them and start anew so I would appreciate your help. I can send more context in our next correspondence. Looking forward to hearing from you. Thank you and best regards. Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Interface residue selection - command line option?
by Vorländer,Matthias Kopano 15 Sep '21

15 Sep '21

Dear ChimeraX team, I am trying to selected interface residues using the “interface” tool. While doing this through the context menu of the interface plot works, I am analyzing a larger number of PDBs and am therefore looking for a way to achieve this through the command line (the contacting chains are displayed already in the log window. Essentially I wonder if it is possible to expand this to the contacting residues). Thanks a lot in advcance, Matthias

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how to save .pdb file of predicted fusion protein generated by chimerax and alphafold
by Ruby Pelingon 15 Sep '21

15 Sep '21

Hi, I tried using chimeraX and alphafold to predict my fusion protein. The result seems promising and generated a .pdb file. I would like to enquire how to save the .pdb file. I would like to open the .pdb file using pymol. Thank you. Kind Regards, Ruby Pelingon

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Re: [chimerax-users] [ChimeraX] #5218: surface color value on mouseover replaced by chain info in status line
by Elaine Meng 15 Sep '21

15 Sep '21

Hi Boaz, When a bug is reported as fixed, the next successful daily build should contain the fix. Occasionally the fixer might forget to do all the steps to get it in that day, but it is supposed to be in there. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 15, 2021, at 8:14 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi Tom, > Thanks a lot. Is this fix already implemented in the Chimerax daily build? > Cheers, > Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > > On 14 Sep 2021 17:26, ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: > #5218: surface color value on mouseover replaced by chain info in status line > ----------------------------------+------------------------- > Reporter: Elaine Meng | Owner: Tom Goddard > Type: defect | Status: closed > Priority: high | Milestone: > Component: UI | Version: > Resolution: fixed | Keywords: > Blocked By: | Blocking: > Notify when closed: | Platform: all > Project: ChimeraX | > ----------------------------------+------------------------- > Changes (by Tom Goddard): > > * status: assigned => closed > * resolution: => fixed > > > Comment: > > Fixed. > > Made surface value status message suppress chain description status > messages on mouse hover. > > -- > Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5218#comment:3> > ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> > ChimeraX Issue Tracker > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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Fwd: Display of actual values of APBS electrostatic potential projected on protein surface
by Boaz Shaanan 13 Sep '21

13 Sep '21

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel ---------- Forwarded message ---------- From: בעז שאנן <bshaanan(a)bgu.ac.il> Date: 9 Sep 2021 17:39 Subject: Display of actual values of APBS electrostatic potential projected on protein surface To: ChimeraX-users-request(a)cgl.ucsf.edu Cc: Hi, Is there a way in Chimerax to know the actual APBS electrostatic potential values in various points on the surface? Is there such feature already in Chimerax that I missed? Such feature is essential (I think) to monitor subtle changes in surface potential following mutations or other variations (pH, salt concentration etc.). If it's not there yet, could you please add it to the (enormous, I guess) to-do list? In Chimera this is done by moving the cursor to the various points of interest, a feature that I found most useful (and helpful in convincing color blind referees 😉). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

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Re: [chimerax-users] Problems with Measuring Angles in ChimeraX
by Elaine Meng 10 Sep '21

10 Sep '21

> On Sep 10, 2021, at 11:41 AM, liangb2 <liangb2(a)rpi.edu> wrote: > > Hi Elaine: > I'm new to ChimeraX for Cryo-EM data. Currently, I imported my tomogram (.mrc file) into ChimeraX and acquired a density map of it. I was able to get the x,y,z coordinates of the three points of interest. However, I was not able to find ways to measure the angle among the three points on the tomogram density map. I have looked up tutorials, but all of those I have found are for proteins. > > Can you please provide some help on how I can measure the angle among three points on the density map? I would really appreciate your help. > Thank you for your time! > Best, > Biqing Liang Hi Biqing, Welcome to ChimeraX! We recommend using the chimerax-users(a)cgl.ucsf.edu address for asking questions (CC'd here so you don't need to do anything). Depending on the question, other people might want to see the answer, or give better answers than mine, or I might not know the answer at all. I don't know how you got the X,Y,Z coordinates for those three points. The way I know how to do it: You can put several "markers" (balls, fake atoms) at points on the surface, and/or at peaks in the density values. Then you can select any 3 of the markers (Shift-Ctrl-click on them) and then use the "angle" command: angle sel <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html> The way to put markers on interactively is first to go to the Markers toolbar across the top of the ChimeraX window. The different icons assign different ways of adding markers by mouse click. For example, clicking the third from left icon in the Markers toolbar assigns the right mouse button (= trackpad + Alt on Windows, trackpad + command key on Mac) to adding markers on the surface. See the following for what the different icons mean and explanation of markers: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markers.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html> 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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Question.
by Yunsik Kang 10 Sep '21

10 Sep '21

Hello, My name is Yunsik Kang, and I am a postdoc in Marc Freeman's lab at the Vollum Institute. I would love to use ChimeraX to predict the structure of my protein of interest. I watched all the YouTube videos and tried to run the program. Unfortunately, my protein is 5005 amino acids in humans and 2958 aa in yeast. I get a message "Please use the full AlphaFold system for long sequences." My question is what is the best way to approach this problem? Should I cut the protein in half and run the program? In one of the videos, it mentions after 700 aa it will have problems. Will it work if I get Colab-Pro? Or would the server crash no matter what. I am not a structural biologist, but I hope the structure can help be predict me with my research. Thank you, Yunsik

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Help with Volume Series
by Ioannis Skalidis 10 Sep '21

10 Sep '21

Greetings to all! I am trying to play a volume series data in ChimeraX (daily build). I open the multiple .mrc frames and they are automatically grouped, but then, when I use the vseries play command, I get an error message that I have not specified a volume series. What am I doing wrong? Should I open the frames differently? I also tried to open them with the open command, a wildcard character for the frame names and vseries true modifier but even then, it only opens the first frame, which I found very strange as well. Could somebody offer some advice? It would be greatly appreciated! Cheers, Yiannis. -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/

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Re: [chimerax-users] [ChimeraX] #5198: Transparent background not transparent when selection outline shown
by Zhao, Bingchun (NIH/VRC) [F] 10 Sep '21

10 Sep '21

Hi, Tom, I received this below email reported that this bug has been fixed. Do I need to download the latest version and re-install the ChimeraX? Thank you very much! Best, Bingchun On 9/9/21, 9:35 PM, "ChimeraX" <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: #5198: Transparent background not transparent when selection outline shown --------------------------------------+------------------------- Reporter: bingchun.zhao@… | Owner: Tom Goddard Type: defect | Status: closed Priority: normal | Milestone: Component: Graphics | Version: Resolution: fixed | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | --------------------------------------+------------------------- Changes (by Tom Goddard): * status: assigned => closed * resolution: => fixed Comment: Fixed. Offscreen rendering was making a framebuffer with no alpha channel, even though for image save it already had an offscreen framebuffer with alpha channel. Made offscreen check and not create a new framebuffer if we are already using an offscreen framebuffer. -- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5198#comment:3> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> ChimeraX Issue Tracker

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ChimeraX-users September 2021