August 2025 - ChimeraX-users - RBVI Mailing Lists

Not opening
by Davis, Jamaine 11 Aug '25

11 Aug '25

Hello, We are attempting to install ChimeraX 1.10.1 on a PC. We can install it, but it will not open. Can you provide assistance? Best, JSD

2 1

Version of Boltz in updated ChimeraX
by Jacek Jagodzinski 11 Aug '25

11 Aug '25

Do I need to manually/separately update Boltz to ver2 from ver1 after updating to current ChimeraX 1.10.1 or is this handled while update is installed? Jacek

2 1

Tailoring Boltz-2 ChimeraX Output for AlphaBridge server Circos Plot Submission
by Arun Gupta 09 Aug '25

09 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

2 2

Re: Post-translational Modification in Boltz Prediction
by Tom Goddard 08 Aug '25

08 Aug '25

Hi Xicong, You need to run that boltz command from a terminal, not from the ChimeraX command-line. Since you are on Windows you could use Windows Command Prompt, or PowerShell. I use a cygwin bash shell. Any of those will work. You are directly running the Boltz executable instead of using ChimeraX to handle the modified residue. Tom > On Aug 8, 2025, at 1:54 PM, Xicong Wang <xicongwang(a)brandeis.edu> wrote: > > Hi Tom, > I tried to enter the command in the command line, but it says that it is unknown. Did I miss something? My YAML file with phosphothreonine and phosphotyrosine is p38alpha - 2p.yaml. > Best, > Xicong Wang > <image.png> > > On Thu, Aug 7, 2025 at 6:38 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Xicong, >> >> As Elaine said ChimeraX does not currently have a user interface to modify residues in Boltz predictions. I have not had time to add that yet. But you can pretty easily add the modification to input file for Boltz that ChimeraX creates and run it from a terminal. >> >> Here is an example of how to predicted a protein with a phosphoserine, I used PDB 2PIL as an example. I ran Boltz in ChimeraX with a standard serine. Here is the input YAML file ChimeraX produced ~/Desktop/2pil/2pil.yaml >> >> version: 1 >> sequences: >> - protein: >> id: [A] >> sequence: FTLIELMIVIAIVGILAAVALPAYQDYTARAQVSEAILLAEGQKSAVTEYYLNHGKWPENNTSAGVASPPSDIKGKYVKEVEVKNGVVTATMLSSGVNNEIKGKKLSLWARRENGSVKWFCGQPVTRTDDDTVADAKDGKEIDTKHLPSTCRDNFDAK >> >> I copied this 2pil.yaml file to 2pil_sep.yaml and added a few lines to say make serine 68 a phosphoserine (3-letter code SEP): >> >> version: 1 >> sequences: >> - protein: >> id: [A] >> sequence: FTLIELMIVIAIVGILAAVALPAYQDYTARAQVSEAILLAEGQKSAVTEYYLNHGKWPENNTSAGVASPPSDIKGKYVKEVEVKNGVVTATMLSSGVNNEIKGKKLSLWARRENGSVKWFCGQPVTRTDDDTVADAKDGKEIDTKHLPSTCRDNFDAK >> modifications: >> - position: 68 >> ccd: SEP >> >> Then I reran the boltz command that ChimeraX used from a terminal changing the 2pil.yaml input file to 2pil_sep.yaml. The command ChimeraX used is in the ~/Desktop/2pil/command file >> >> $ /Users/goddard/boltz/bin/boltz predict /Users/goddard/Desktop/boltz/boltz_2pil/2pil_sep.yaml --write_full_pae --use_msa_server --accelerator gpu --no_potentials >> >> When that ran it put the resulting predictions in >> >> boltz_results_2pil_sep/predictions/2pil_sep/2pil_sep_model_0.cif >> >> so I open that prediction in ChimeraX and aligned it to my original PDB using ChimeraX command "matchmaker #3 to #1". Result is shown in the image below. The Boltz documentation page shows other ways you can modify the input .yaml file for instance to add templates or constraints between atoms >> >> https://github.com/jwohlwend/boltz/blob/main/docs/prediction.md [github.com] <https://urldefense.com/v3/__https://github.com/jwohlwend/boltz/blob/main/do…> >> >> In the future I hope to provide ChimeraX user interfaces to allow those possibilities. >> >> Tom >> >> PDB 2PIL in tan, Boltz prediction with serine 68 in blue, Boltz prediction with phosposerine 68 in pink. >> >> <boltz_mod.png> >> >>> On Aug 7, 2025, at 8:36 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Sorry no, the ChimeraX tool to run Boltz does not have a way to define post-translational modifications. This issue is mentioned in the Limitations section: >>> >>> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/boltz.html#limitations [rbvi.ucsf.edu] <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/…>> >>> >>> Best regards, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Resource for Biocomputing, Visualization, and Informatics >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>>> On Aug 6, 2025, at 7:07 PM, Xicong Wang via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> 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 >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ [mail.cgl.ucsf.edu] <https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list…>

1 0

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

3 2

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

2 1

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>

3 2

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

3 5

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

2 2

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

2 3