- ChimeraX-users - RBVI Mailing Lists

Tailoring Boltz-2 ChimeraX Output for AlphaBridge server Circos Plot Submission
by Arun Gupta 08 Aug '25

08 Aug '25

Dear ChimeraX Team, I am currently working on visualizing interface residues using Circos plots via the Alphabridge web server, and I’m exploring ways to tailor the Boltz-2 ChimeraX output folder to serve as a compatible input format for Alphabridge web server (https://alpha-bridge.eu/) similar to the AF-3 output zipped folder. AlphaBridge<https://alpha-bridge.eu/> Zip file containing the AlphaFold resultSubmit job alpha-bridge.eu Despite successfully generating Boltz-2 outputs in ChimeraX daily build, I’m facing challenges in aligning the output folder with what Alphabridge web server expects for Circos plot generation. Could you kindly advise on: * Whether there is a recommended way to export or reformat Boltz-2 ChimeraX outputs for Alphabridge webserver compatibility? * Any scripts or workflows that facilitate this integration? Any advice on post-output work flow steps would be immensely helpful, as I aim to produce publication-quality Circos plot visualizations of interface residue networks similar to those demonstrated by recent AlphaBridge pre-print publication (DOI: https://doi.org/10.1101/2024.10.23.619601) Thank you very much for your support and for the fantastic tool you continue to develop for structural biology community. I look forward to your recommendations. Best regards, Arun Arun Gupta PhD, MRSC Sr. Post Doctoral Research Assistant Gillespie/McMichael Group Nuffield Dept. of Clinical Medicine, University of Oxford, Centre for Immuno-Oncology Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ Tel: + 44 (0)1865 2612913

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Post-translational Modification in Boltz Prediction
by Xicong Wang 07 Aug '25

07 Aug '25

Dear ChimeraX developers, I'm trying to predict a structure with two phosphorylated residues using Boltz. Is there an option for me to do that in ChimeraX? I didn't find any options to let me do any post-translational modification on the protein sequence I entered. Best regards, Xicong Wang

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How to measure and visualize the distance between two benzene rings in ChimeraX?
by Nan Zhang 06 Aug '25

06 Aug '25

Dear ChimeraX Developers, I want to create a video using ChimeraX. I plan to use the Morph command to make the structure change. At the same time, I also want this conformational change to occur while the structure moves to another position. Can this be achieved in ChimeraX? Looking forward to your answer, thank you! Best regards, Nan Nan Zhang zhangnan(a)nankai.edu.cn

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Save a surface
by Zhou, Tongqing (NIH/VRC) [E] 06 Aug '25

06 Aug '25

Dear ChimeraX, Is there a way to save a surface created by the “surface” command in the PDB or cif format? Best regards, Tongqing Tongqing Zhou, Ph.D. Principal Investigator and Chief Structural Virology and Vaccinology Section Structural Biology and Structural Bioinformatics Cores Vaccine Research Center (VRC), NIAID National Institutes of Health Building T40, Room 117 (Office) Building 40, Room 4609B (Lab, shipping) Office: (301) 761-7068 Cell: (240) 695-0536 https://www.niaid.nih.gov/research/tongqing-zhou-phd tzhou(a)nih.gov<mailto:tzhou@nih.gov>

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feature request: add bring option to the align command
by Alexis Rohou 05 Aug '25

05 Aug '25

Hello, I really love (and depend on) the "bring" option to the "matchmaker" command. Occasionally though, I have to fall back on "align" when I need to specify atoms that should be superposed. Would you please consider adding a "bring" option to the "align" command? Cheers, Alexis

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ChimeraX displaying hydrophobicity
by Roy Chowdhury, Shatabdi 04 Aug '25

04 Aug '25

Hi, I'm trying to display the hydrophobic parts of a molecule, and I'm trying this command "mlp #1 map true key true palette lipophilicity range -5,5 transparency 100" When I use various values for the lipophilicity range, it does not affect the colors of the potential. They also do not have the gradients like the molecule display -> hydrophobic tab. Is there a way to make this happen? Thanks, Shatabdi Roy-Chowdhury, PhD. Postdoctoral Research Scholar, Cardiovascular Research Institute University of California, San Francisco

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Studying the structure at the positions of the mutations
by Richard melzack 04 Aug '25

04 Aug '25

Hello I have started using your excellent Chimera X 1.10.1 visualisation platform and have uploaded a protein and mutated protein onto the matchmaker screen. The RMSD is low so the general appearance is very similar. However, I was wondering (the mutated protein has a 6bp insertion and a nonsynonymous SNP) how to examine the details around the exact points of the mutations (both are on the same exon). I have tried a number of ideas. The command line doesn't like sequence or sequence #1 #2. I would be grateful for your assistance. Thank you Dr Richard Melzack

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saving submodels as separate pdbs
by Alexandra Zahradnikova 30 Jul '25

30 Jul '25

Hi All, I have a trajectory (xtc) from which I can read selected frames into ChimeraX. I can then write all frames as one pdb with many submodels. But I am not able to find out how to open the frames as separate models, or save the trajectory as separate models. I will appreciate your help. Best Sasha Zahradnikova

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ViewDock Feedback and Feature Requests
by Andrii Kyrylchuk 29 Jul '25

29 Jul '25

Hi ChimeraX team! I would like to thank you for all the magnificent work you’re doing! My work would be much harder if Chimera and ChimeraX wouldn’t exist! After testing the new ViewDock (not ViewDockX), I have a few suggestions: 1. The rating system is still a bit inconvenient to use. A quick “OK/Bad” checkmark and fixed buttons to score the current ligand (as in classic Chimera) would speed up triaging. Dragging to each cell now slows review. 2. It would be great to have a possibility to rearrange columns. Now their order seems fixed. 3. It’s impossible to select and copy text in the lower part of the window. It would be very helpful in case I want to look into a specific ligand, e.g. copy its SMILES and visualize the 2D structure. 4. The window width follows the longest data field, leaving wide blank areas (see the screenshot). Could you allow arbitrary window sizes? Thanks for considering these ideas, and for all your ongoing work on ChimeraX. Sincerely, Andrii 

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How to replace ss_id for a secondary structure region?
by Rayees Mattoo 25 Jul '25

25 Jul '25

Hi, I have a region in my structure (res 208-229) which is displayed as a discontinuous helix when I am certain it is a continuous helix. I want to modify the pdb file to consider it as a continuous helix using chimeraX. I used the following commanlines: settatr #1/K:208-229 res ss_type 1 setattr #1/K:208-229 res ss_id 999 It works. However, I believe the command assigns the same region with a new unique ss_id (999), leaving the original ss_id intact. If I want to replace the the original ss_id with a new sequence range (res 208-229) how would I do that? Also, is there a way to directly text edit pdb file secondary structure list in ChimeraX? Best Rayees

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