July 2023 - ChimeraX-users - RBVI Mailing Lists

colour palette of multiple models
by Enrico Martinez 20 Jul '23

20 Jul '23

Dear Chimera-X users ! I am performing visualisation of multi domain protein loaded in the Chimera-X as different pdbs. In the model panel each pdb coloured differently according to the model ID and everythings is OK for the first 11 models, while starting from the 12th all of them are colored in green (please see the screen-shot). Would it be possible to quickly change the auto-colouring of the multiple pdbs when I load all of them directly using chimerax workdir/*.pdb ? Many thanks in advance Enrico

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Running ChimeraX in batch mode in the Ubuntu terminal
by Enrico Martinez 20 Jul '23

20 Jul '23

Dear ChimeraX users ! I have a quick technical question. Typically I run ChimeraX with a batch script in order to perform some manipulation with input pdb and print the output image / save chimera-X session. In my Ubuntu terminal I run it using: chimerax script.cxc where the script could be something like : ### open input.pdb # do some manipulation like view, orient etc save image.png exit ## It works OK but, while running from linux terminal I have a quickly open-closed Chimera-X window which is not very practical when I put this script in loop etc. Is there any possibility to fully suppress the Chimera-X gui when I run my script in batch mode from the terminal? Many thanks in advance Enrico

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Feature request: support for MRC mode 12 (float16)
by Ricardo Righetto 20 Jul '23

20 Jul '23

Dear ChimeraX team, It seems that ChimeraX (tested version 1.6.1) does not yet support MRC data mode 12, corresponding to half-precision floating point (float16). This data mode is now supported in RELION-4 and IMOD, and is interesting to save storage in cryo-ET and subtomogram averaging workflows. Would it be possible to implement support for reading and writing this MRC data mode in ChimeraX? Thank you! Best wishes, -- Ricardo Diogo Righetto

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Q3 Score Calculation Tool ChimeraX that is similar to MapQ Plugin in Chimera
by Thu Nguyen 20 Jul '23

20 Jul '23

Good afternoon, I am calculating the Q-Scores in cryo-EM density maps and found the MapQ Plugin <https://github.com/gregdp/mapq> in Chimera that does Q3-score calculation and visualization. I wonder if we have a similar plugin in ChimeraX that does Q-score calculation? Thank you very much. Best regards, Thu

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Autodock Vina at ChimeraX
by ODA Natsuki 19 Jul '23

19 Jul '23

Dear all, Thank you for providing the license for ChimeraX. I have a question about ChimeraX for using Autodock Vina. Is it possible to use Autodock Vina at ChimeraX? I used to use Autodock Vina at Chimera before version of ChimeraX. I want to use Autodock Vina, so would you ask me the methods? Sincerely you. Natsuki ------------------------------------------------------------------ Name: Natsuki Oda Affiliation: Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University Student ID: number 1234521019 E-mail: oda.natsuki.i0(a)s.gifu-u.ac.jp ------------------------------------------------------------------

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Question about energy minimization
by Luca Massaccesi 18 Jul '23

18 Jul '23

Dear Chimera team, Can you please tell me if it’s possible to do energy minimization with Chimera X as I used to in previous Chimera? I looked for it on the Chimera X page and in many tutorials but it looks like this tool was cut out of the software. Thank you very much for your help, Luca

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view command to re-orient scene
by Enrico Martinez 17 Jul '23

17 Jul '23

Dear Chimera-X users! I would like to perform visualisation of the pre-oriented objects from a set of PDB filles. Briefly I load 20 pbs in chimera-x and the scene what I see, is depicted on the "initial.png" image attached to the mail. Then I need to orient it automatically in order that the scene would be perfectly parallel to the screen plane, as shown in the second enclosed image. What options for view command could be used to orient the object in the same way ? Many thanks in advance Enrico

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mcopy command
by Matzov Donna 17 Jul '23

17 Jul '23

Hello, I'm trying to use the mcopy command (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mcopy.html) as such: mcopy #1 toAtoms #2 settings a However, I get the following error message: Unknown command: mcopy #1 #2 settings a Am I using the wrong syntax? I am using the latest chimerax release. Thanks, Donna Matzov, PhD Department of Structural Biology Weizmann Institute of Science The Shalev-Benami Lab<https://www.weizmann.ac.il/Structural_Biology/Shalev-Benami/home>

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Slowing down a movie
by Leyre Marin Arraiza 17 Jul '23

17 Jul '23

Dear ChimeraX, I want to make a movie using ChimeraX, in which I can see the map of my protein complex rotating 360 degrees, plus a full rotation of the same map after zooming in. I managed to do so with the following command: movie record ; turn y 2 180 ; wait 180 ; zoom 1.5 ; turn y 2 180 ; wait 180 ; movie encode However, in the final .mp4 file I get, the rotation is quite fast. I would like to create the same movie, but with slower rotation. I have tried figuring it out reading through the guide and trying different commands, but I am not successful. Could you help me with this issue? Thanks in advance Best regards, Leyre Leyre Marin Arraiza PhD fellow University of Copenhagen Novo Nordisk Foundation Center for Protein Research Taylor Group Blegdamsvej 3B, Building 6, 6-1-10 2200 København N leyre.arraiza(a)cpr.ku.dk<mailto:leyre.arraiza@cpr.ku.dk> [CvwfJbQuv4S75bEAAAAASUVORK5CYII=] How we protect personal data<https://informationssikkerhed.ku.dk/english/protection-of-information-priva…>

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bond: merging two models within new model
by Enrico Martinez 17 Jul '23

17 Jul '23

Dear Chimera-X users ! I need to fuse two models in the entire construction. Precisely having a water soluble domain with a linker in the first model #1 as well as transmembrane alpha helix segment in the #2 I load the both in chimera-x and then use the bond command with the aim to create a peptide bond between the last residue of the #1 and the first residue of the #2. Here is my command: # select the last residue from the core and the first residue from the TM helix; build join peptide #1:182@C #2:1@N move large The problem is that on the text step I will need to add the membrane in the TM part, but the orientation of the created construction is not optimal. How could I easily modify the mutual orientation between #1 and #2 ? I join the both initial pdbs to this message, in order that my model could be checked :-) Many thanks in advance Enrico

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ChimeraX-users July 2023