- 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

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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

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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

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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…>

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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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ChimeraX color fromcartoon error
by Prafful Sharma 25 Jul '25

25 Jul '25

* Dear ChimeraX Developer, I was recently trying to color a model in chimeraX based on a similar model with the same chain IDs and residues, and so I was using the command color fromcartoon #1 target #2 as specified in the documentation however I am receiving an error that says " Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword". I assume it is asking me to add a specific color name/code, but the other models have many different colors. I tried multiple turnarounds and even took help from different AI models, but still could not solve the error. I therefore think the functionality is not active, or there is some issue with I am not able to figure out. Can you please let me know if this functionality is working, or if there is any other way I can do this? Thank you for ChimeraX and your kind help! Prafful Sharma Ph.D candidate, TH lab | Structure, function, and regulation of protein synthesis Dept. of Developmental Biology and Genetics, Indian Institute of Science, Bangalore 560012

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Obtaining a list of residues that are solvent-accessible
by Gracia Mazuca, Luis Antonio 24 Jul '25

24 Jul '25

Hello, I am currently employing ChimeraX to study features of a molecule. I am studying ribosomal RNA (rRNA) in the E. coli ribosome using the PDB model 4YBB. We are interested in seeing what residues from the 23S rRNA are solvent-accessible using a probe radius of 3Å. We are wondering if you could give us some advice on how to achieve this. We have tried a few methods we have found online, but they all yield different results. I look forward to hearing from you. Thank you very much in advance. Best, [cid:25bde0d5-3803-4708-9790-94c965927e2c] Luis Antonio Gracia Mazuca Ph.D. Research Associate Department of Chemistry and Biochemistry The University of Texas at El Paso 500 W. University Ave. El Paso, TX 79968 Office: CCSB G.0512A utep.edu<http://utep.edu/>

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issue with ChimeraX 1.10 in snapdragon windows 11
by Erramilli, Satchal 24 Jul '25

24 Jul '25

Hello, I am reaching out to ask if there are any compatibility issues with ChimeraX 1.10 in Snapdragon Windows 11. The earlier version, 1.9, worked, but 1.10 doesn't. Is this a known issue with the Snapdragon architecture? Thanks, Satchal Erramilli ============================================================ This electronic message transmission and any attachments are confidential and/or proprietary and may constitute legally privileged information of Meso Scale Diagnostics, LLC. The information is intended for solely the use of "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu>. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or the taking of any action in reliance of this information is strictly prohibited. You are not authorized to retain it in any form nor to re-transmit it, and you should destroy this email immediately. If you have received this electronic transmission in error, please notify us by telephone (240-314-2600) or by electronic mail to the sender of this email, "Erramilli, Satchal" <SErramilli(a)meso-scale.com>, immediately. ===========================================================

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boltz latest version with ChimeraX1.10
by svle＠tiscali.it 23 Jul '25

23 Jul '25

Hi, it is possible to install the latest version ( 2.1.1 ) of boltz in ChimeraX 1.10 with the command boltz install? Thanks. Saverio

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Correlation Question
by Amin, M.A.A. 23 Jul '25

23 Jul '25

Hello, I'm trying to get the correlation between 2 maps. I used the command: measure correlation #2 in_map #1 I also saved the resampled map. Then, I wrote a very simple python code that calculates the correlation coefficient as following: def compute_correlation(map1, map2): threshold = np.percentile(map1.flatten(), 99) # top 1% value mask = (map1 >= threshold) #& (map2 != 0) values1 = map1[mask] values2 = map2[mask] corr = np.corrcoef(values1, values2)[0, 1] return corr Although it is considered masking as it is done in ChimeraX, I was never able to get the correlation value I got from ChimeraX. I got 0.1 from the python code and 0.68 in ChimeraX. Any suggestions? Thank you -- Muhamed Amin, Ph.D Assistant Professor of Physics University of Groningen, Groningen, Netherlands

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show only extra density
by maria l 23 Jul '25

23 Jul '25

Good Morning, I have a cryoEM map and a pdb, after fitting them i see an extra density i can´t explain with my model (pdb), is there an easy way, in chimera (old version), to show only that extra density? Thanks M

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Multiple alignment
by Marco Sette 23 Jul '25

23 Jul '25

Dear all, I have few pdb structure and I would like to build a multiple alignment of the sequences based on structural alignment. While in Chimera it was an easy task I'm find some problems with ChimeraX since it returns a series of pairwise alignments (structure A vs. B, A vs. C, A vs. D) rather than a multiple one (A vs. B vs. C. vs. D). Is it possible to do? Thanks Best Marco -- Dr Marco Sette, PhD Department of Chemical Sciences and Technology The University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Re: Addendum to Terms and Conditions - UCSF
by Francois-Xavier Campbell-Valois 23 Jul '25

23 Jul '25

Hello, I approve this agreement to use UCSF ChimeraX License. Best regards, François-Xavier Campbell-Valois, PhD Professeur agrégé | Associate Professor Université d’Ottawa | University of Ottawa Department of Chemistry and Biomolecular Sciences D’Iorio Hall 10 Marie-Curie Private Ottawa ON K1N 6N5 CANADA Office: DRO 403 Lab: MRN 214C https://fxcampbellvalois.org<https://fxcampbellvalois.org/> https://www.researchgate.net/profile/Francois_Xavier_Campbell-Valois https://ca.linkedin.com/in/fxcampbellvaloishostpathogen -- De : mscontracting Med School Contracting via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Date : mardi, 22 juillet 2025 à 16:17 À : chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> Objet : [chimerax-users] Addendum to Terms and Conditions - UCSF Attention : courriel externe | external email Hello, I work for the Regents of the University of Minnesota and its Medical School. I am requesting signature on our standard supplier addendum to your UCSF ChimeraX License Agreement, both attached here. Please follow the instructions below: 1. If you are in agreement with the language on the addendum DO NOT SIGN. 2. Reply to this email that you are in agreement then I will send the addendum for signature via Adobe-Sign. 3. If you will not be the signatory please supply their email address. 4. Finally, a fully executed addendum will be returned. Please reach out with any questions or concerns. Thank you, Mequila Stevenson University of Minnesota Medical School Contracting Team Office Hours Zoom Link<https://umn-private.zoom.us/j/98326567540> Contract Routing Form<https://app.smartsheet.com/b/form/a4575a3938724cc68881868255b69dbb> Request Status Dashboard<https://app.smartsheet.com/dashboards/p7w62cJR57Qp3W9m56XhjX7w72xCcjr54hXvw…> (will need to request access)

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Intersurf and Surfnet in ChimeraX
by mlopez＠ibv.csic.es 23 Jul '25

23 Jul '25

Good afternoon, Does anyone know where are the Intersuf and the Surfnet options in ChimeraX?. Thanks a lot.

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Request: Complete ChimeraX User Manual in PDF Format
by 王雪 22 Jul '25

22 Jul '25

Dear UCSF RBVI Team, My name is Wang Xue, and I am a graduate student at South China Agricultural University. I have been learning to use UCSF ChimeraX to build the icosahedral capsid model of viral proteins. In the course of my studies, I discovered that the ChimeraX documentation and User Manual are provided as a collection of HTML files. While these are extremely helpful, I find that having a single, paginated PDF version would greatly facilitate offline review, bookmarking, and printing of the chapters I most frequently consult. Would it be possible for you to share the complete ChimeraX User Manual in PDF format? If such a version is already available, I would be grateful if you could direct me to its download link. Otherwise, I would very much appreciate your assistance in providing a consolidated PDF. Thank you for your help and for all the work you do in maintaining this valuable resource. I look forward to continuing to explore ChimeraX’s powerful features. Sincerely, Wang Xue South China Agricultural University July 20, 2025

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Issue with lighting and silhouettes
by Alessio Nocentini 20 Jul '25

20 Jul '25

Hello, I need your support again for another issue I am meeting in using ChimeraX. Unlike Chimera, I cannot find the lighting panel, which was very useful to adjust lights. Moreover, when I have a protein surface, the silhouettes are not complete in ChimeraX (black square in figure). I attach the same figure done with the 2 softwares. In chimera X I cannot increase the lighting in the active site. Can you help? Thank you Best regards Alessio [image: Chimera.png] [image: ChimeraX.png] -- Dr. Alessio Nocentini <https://cercachi.unifi.it/p-doc2-0-0-A-3f2b3c29372831.html> *Ricercatore Legge 240/10 a tempo determinato - Tipo B* *UNIVERSITÀ DEGLI STUDI DI FIRENZE* Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) *ECCELLENZA 2023-2027* Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685

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help
by mariela Urrutia 17 Jul '25

17 Jul '25

I want to unsubscribe .Thanks you.Mariela On Monday, July 14, 2025 at 04:00:15 PM GMT-3, chimerax-users-request(a)cgl.ucsf.edu <chimerax-users-request(a)cgl.ucsf.edu> wrote: Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. contacts (mariela Urrutia) 2. Re: contacts (Elaine Meng) 3. Re: Inquiry About Training for ChimeraX Plugin Development (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Mon, 14 Jul 2025 13:08:40 +0000 (UTC) From: mariela Urrutia <urrugada(a)yahoo.com> Subject: [chimerax-users] contacts To: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> Message-ID: <1518652022.1318836.1752498520245(a)mail.yahoo.com> Content-Type: multipart/alternative; boundary="----=_Part_1318835_1564174829.1752498520244" Hello, Could you tell me please how to get the contacts of a residue in a list and in the molecule representation?Thanks you in advance.Mariela

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