July 2023 - ChimeraX-users - RBVI Mailing Lists

Regarding Usage of ChimeraX for PDB file creation
by Protya, Satirtha 21 Jul '23

21 Jul '23

Hello, Hope this email finds you well. I am Satirtha Saha, an undergrad research assistant at UIUC. Currently, I am using ChimeraX for one of my research projects. I need to build structures and download the PDB files. I can do that for all L amino acid containing peptides, but I don’t know how to use ChimeraX for D amino acid containing peptides. For example, I have a sequence NWF. Now it is available in this standard L format and also in NdWF format. As ChimeraX is not case sensitive, I don’t know how I should give the command to build the structure with D amino acid containing peptide. Secondly, I have some peptides that have Amidation or NH2 at the C terminus. I don’t know how to add this to my structure. Please let me know how to solve this to issues. That will be really helpful for me. Have a great day. -- Yours sincerely Satirtha Saha He/Him/His Beloit College | Class of 2025 Triple Major | Biochemistry, Cognitive Science and Data Analytics Research Assistant | Sweedler Lab | UIUC Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615<tel:+16084736615> Schedule an Appointment<https://admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_med…> sahass(a)beloit.edu<mailto:sahass@beloit.edu> [Image][cid:image002.png@01D9BB19.9CD8CA10]

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Matching ChimeraX color with the Adobe illustrator colors?
by Rayees Mattoo 20 Jul '23

20 Jul '23

Dear ChimeraX users, I am trying to match the colors of ChimeraX model to the Adobe illustrator drawing. I used Web safe colors to color my model in chimeraX and then used the same hex codes in the illustrator, but the colors did not match. Any thoughts or workarounds would be appreciated. Best Rayees

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Re: Opening MTZ Files
by Elaine Meng 20 Jul '23

20 Jul '23

Hi Natalie, Everything I know on this topic is written in the documentation linked below, and yes, as it says therein, you do need to have Clipper installed. Then title of the section is "Open/Save Options from Clipper": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper> I can't think of anything else to say without getting more details from you. What is the problem? Which part are you confused about? What did you try? What happened? Did you follow the instructions in the link? Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 6, 2023, at 9:14 AM, Natalie Walsh <natalie.walsh(a)slu.edu> wrote: > > Hello, I previously asked a question (sent to the wrong email, oops!) about not being able to use MTZ maps in Chimera X (I was using 1.17.1, I just installed 1.17.2 today and still have the same issues). These were the instructions previously provided: > > "The instructions of how to open MTZ files with ChimeraX are here: > > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/comman… > > > "Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc." > > I read through the like and am still confused. I have also installed the Clipper Plugin (although I am unsure if it was installed correctly) since I saw somewhere that might be needed. > > Thanks, > Natalie Walsh

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Running ChimeraX in batch mode on Mac OSX
by Enrico Martinez 20 Jul '23

20 Jul '23

Hello Greg, In addition to my previous message regarding running Chimera-X on Ubuntu, I have a similar question regarding MacOSX. In fact I have a macbook pro equipped with the Mojave (10,14.16) which I used with ChimeraX-1.3 that worked well in no-gui mode (without any additional flags like --offscreen). I've tried more recent releases of Chimera-X and found that it has not worked with Mojave. Anyway, if I do an update would it be possible to use the latest ChimeraX on Mac without gui ? Many thanks in advance Enrico

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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 19 Jul '23

19 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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