- ChimeraX-users - RBVI Mailing Lists

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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ChimeraX Appreciation and Feature Suggestion (+ New #ChimeraX Tag on image.sc)
by José Jorge Ramírez Franco 16 Jul '25

16 Jul '25

Hi there, First of all, thank you for this outstanding piece of software. ChimeraX is truly invaluable and has become an essential tool in my workflow. As a microscopist working primarily with light microscopy (particularly confocal and light-sheet imaging) I’ve found ChimeraX’s rendering capabilities to be far superior to most tools currently available. I’ve even recommended its use several times on the image.sc forum <https://image.sc>, especially for rendering high-quality visualizations. In fact, I recently noticed that there was no #chimerax tag on the forum (surprisingly!) so I took the liberty of creating one. You can find the related post here: https://forum.image.sc/t/3d-multichannel-surface-rendering-from-z-stacks-na… While I have this opportunity, I’d like to *suggest a feature* that I believe would significantly enhance ChimeraX’s utility for large-scale light-sheet microscopy datasets: *support for .tiff files larger than 4 GB* . These large file sizes are quite common in light-sheet acquisitions, and the ability to open them natively in ChimeraX would be a substantial benefit to researchers in this field. Thank you once again for all the incredible work that goes into developing and maintaining ChimeraX. It’s deeply appreciated. Warm regards, J -- J. Jorge Ramírez-Franco PhD Institut de Neurosciences de la Timone, SpiCCI Team Faculté de Médecine 27, boulevard Jean Moulin 13005 Marseille, France

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Directed camera mouvement along cartoon chain
by Enrico Desperados 16 Jul '25

16 Jul '25

Dear ChimeraX users! I would like to create an artistic movie for an X-ray structure making an impression that I am running on the protein cartoon like on the serpentine road. I have tried the following trivial algorithm: view :1 clip false; zoom 0.6; wait 30 view :2 clip false; zoom 0.6; wait 30 view :3 clip false; zoom 0.6; wait 30 view :4 clip false; zoom 0.6; wait 30 ... view :200 clip false; zoom 0.6; wait 30 However, It just moved the camera focusing on each residue, without giving the impression of movement along the protein chain. Do we have a special orient option that could introduce such smooth movements ? Many thanks in advance! Enrico

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eachChain option for fitmap?
by Oliver Clarke 15 Jul '25

15 Jul '25

Hi, Fitmap has on option to fit each model sequentially (eachModel). Would it be possible in a future version to add an "eachChain" option to fit each polymer chain in a mult-chain model independently? This would be useful when quickly fitting oligomeric models to an EM map. Alternatively, is there another quick way to do this? I thought about using perframe, but that only take numerical ranges, not alphabetical Cheers Oli

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Inquiry About Training for ChimeraX Plugin Development
by Rafat Hasan Khan 14 Jul '25

14 Jul '25

Dear ChimeraX Team, I am part of a research group working with Dr. Amitava Roy (University of Montana). We plan to develop a plugin, but when we initially started using your documentation with version 1.9 (2024-12-11), we failed to make it work despite following the guides on "Bundle Example: Add a Qt-based Tool." Could you please let us know if there are any training programs, workshops, or additional resources available for developers? Any help or direction would be greatly appreciated. Thank you for your time. -- Best Rafat

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contacts
by mariela Urrutia 14 Jul '25

14 Jul '25

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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Map resolution range values
by Rayees Mattoo 10 Jul '25

10 Jul '25

Hi, How to extract Map resolution range values from a resmap.mrc file for the Table 1 validation (for publication) using chimeraX? Other suggestions, using different methods to extract the map res range values are also welcome. Best

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How to get just model name
by Alexandra Zahradnikova 09 Jul '25

09 Jul '25

Dear All I would like to extract just the model name (as a variable) from a model, to write into an output file with other data. However I am not able to find in the help how to do it - I can output all model information ("Model info") to the log but not to see just model name. Is that possible? Thanks in advance Best regards Sasha

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XYZ basis vectors
by Jan Hofmann 09 Jul '25

09 Jul '25

Hello, how can I show the XYZ basis vectors somewhere next to my structure in ChimeraX? I found the .bild datei but I don't want the arrows in my structure, rather outside, next to it, like in Crystalmaker. It would be really helpful to have the basis vectors to compare orientations with other images. Thanks a lot. Best, *Jan Hofmann, M.Sc.* *PhD Candidate, Department of Chemistry* *Chapman Group* Stony Brook University *jan.hofmann(a)stonybrook.edu <andrew.nicoll(a)stonybrook.edu>* Office: Room 577, Chemistry

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Changing bond color in Chimerax
by khaja faisal tarique 08 Jul '25

08 Jul '25

Hi I am trying to color different bonds with different colors in ChimeraX, but when I select one bond and change its color so it gets applied to all bonds. Is there any trick to do that ? What I am doing is the Cltr+Bond to select a bond then changing color to that selected bond. But I do not why the change is applied to all other bonds. Any help would be appreciated Faisal --

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Coloring an Isosurface Using a Second Cube File in ChimeraX
by mohyeddine.taleb 08 Jul '25

08 Jul '25

Hi, I would like to ask how to color a given isosurface (built with the commands open cube1.cube and volume #1 level 0.02 style surface) using the values from a second property stored in another cube file, cube2.cube. Please note that the two cube files describe exactly the same grid. I have also attached an example showing the interaction between two water molecules. Best regards, Mohyeddine Taleb

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Request to help in command panel in chimera X 1.10
by Singh, Prashant Kumar 08 Jul '25

08 Jul '25

Hi, I have recently downloaded Chimera x 1.10, in which I am trying to change the size of sticks and spheres in ball and stick model but the commands I am trying to were not working with error message "Expected a keyword" Here are the commands which I am using Style stick/sphere set stick/sphereRadius 0.3 setattr Radius 0.3 target #3 set stickRadius 0.3 target all size #1 ballScale 1.5 size #1 ballScale 1.5 size #1 ballScale 1.5 setattr m ballScale 0.5 style ligand ball vdw scale 0.8 set stickRadius #3 0.35 set stickRadius 0.3 target sel set stickRadius 0.3 target all set stickRadius 0.3 target all set stickRadius 0.3 target all Unfortunately none of them is working in my command line, will you guys plz help me to to change the size of sticks and sphere in ball & stick model. i am using iMac computer. Best regards Prashant

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Displaying atomic serial numbers
by Michael Patzschke 08 Jul '25

08 Jul '25

Hello, I have a seemingly trivial problem. I have a small molecule and I want to display the serial number of all atoms. Under “Action->Labels->Atoms->Name” I can get atom names, but these are not what I want. I want the atoms numbered as they appear in the .xyz file. Is this possible? Kind regards, Michael

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Unsescribe
by Felipe Munoz Gonzalez 04 Jul '25

04 Jul '25

Hello, I want to unsubscribe of this list thanks

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Boltz-1 data privacy
by Dario Passos 03 Jul '25

03 Jul '25

Dear ChimeraX team, I have a question regarding data privacy when using the Boltz-1 structure prediction tool within ChimeraX. Is the input or output data temporarily or permanently stored, logged, or shared in any way by UCSF, ColabFold, or any third-party services? Is there an option to ensure that all data remains strictly local and is not stored externally? Thank you, Dario

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Coot-like navigation?
by Murpholino Peligro 02 Jul '25

02 Jul '25

Can we navigate the protein model like in coot? spacebar jumps from residue i to residue i+1 shift-spacebar jumps from residue i to residue i-1 ctrl-g shows a tiny window where I can input 'a1' and the cofr goes to chain a residue 1 Can you point me in the right direction? Do I have to use aliases or is it something more complicated? Thanks

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rainbow separate color for each residue
by Rebecca Grace 02 Jul '25

02 Jul '25

Hello ChimeraX, Greetings! I've never asked a question, but I need to expedite solving this issue, so thought the time is now. :-) (I should also add, thank you for Chimera and then Chimera X, it has been so beneficial to my research and presentations!) Several months ago I used rainbow to color a range of residues on my structure. Now I am trying to recreate it on a different model and I can't seem to recapture the detail where every residue is delineated versus a continuous gradation across the selected region. I've searched and read several help emails etc, and maybe if I was a more expert user I would understand this from the usage/help entries about rainbow, but alas, I cannot recreate it. Please let me know how I did this?? Thanks for any help! Cheers, Bec Here is the past way that I want to recreate: *notice how each residue of tube helix has a separate color whereas the next image has no separations [image: image.png] And here is the way I can only seem to get the program to do today: [image: image.png]

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Model grouping and next/previous buttons
by Oliver Clarke 02 Jul '25

02 Jul '25

Hi, I use the next/previous buttons (sequential display controls) in the model panel quite a lot for quickly flicking between 3D classes - they are very handy for this! I would like to be able to use the same buttons for switching between model/map pairs, but there is no way to do this currently. I expected that if I grouped models by using the rename command to make (for example) the map a sub-model (e.g. model #1, map #1.1), then the next/prev buttons would switch between the model groupings, but this is not the case - it still treats the sub-models as independent models. Would it be possible to revisit this logic so that if a "base-level" model like #1 is selected, next/prev will switch between model groupings, while if a member of an ensemble is selected (say #1.1), it will cycle through members of the ensemble? Also, would it be possible at some point to add a GUI option for grouping models - perhaps a button in the model panel that allows for automatic grouping of the selected models? Cheers Oli

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Check waters with a full density map?
by Murpholino Peligro 01 Jul '25

01 Jul '25

Dear all I got a pdb and a mtz file (from phenix.maps) with: Number of columns: 11 label #valid %valid min max type H 23487 100.00% 0.00 56.00 H: index h,k,l K 23487 100.00% 0.00 39.00 H: index h,k,l L 23487 100.00% 0.00 26.00 H: index h,k,l 2FOFCWT 23337 99.36% 0.01 1113.30 F: amplitude PH2FOFCWT 23337 99.36% -180.00 180.00 P: phase angle in degrees 2FOFCWT_fill 23487 100.00% 0.01 1113.30 F: amplitude PH2FOFCWT_fill 23487 100.00% -180.00 180.00 P: phase angle in degrees FOFCWT 23337 99.36% 0.00 836.89 F: amplitude PHFOFCWT 23337 99.36% -180.00 180.00 P: phase angle in degrees ANOM 19860 84.56% 0.00 149.58 F: amplitude PHANOM 19860 84.56% -179.97 179.99 P: phase angle in degrees (as reported by phenix.mtz.dump) I open both in chimerax with open /home/murph/doc/pdbs/mol1/mol1.pdb open /home/murph/doc/pdbs/mol1/mol1_map_coeffs.mtz structureModel #1 (clipper already installed) If I do tools->structure analysis->check waters and choose the model (now id #1.2) and the 2fofc map (#1.1.1.2) I got a warning saying "Some (or all) atoms lie outside the volume, continue anyway?" If I continue anyway... some waters with density do have a 0 in the density column... This is, I think, because by default the density is not displayed around all atoms of the model (huge models would crash the computer, right?).. so maybe I just need to show the density around all the atoms in the model... How do I do that? (I thought that 'volume unzone' was the magic command but that only shows a bigger cube of density around the center of rotation, instead of the smaller sphere of density). Thanks

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BIOMT output
by Sui, Haixin (HEALTH) 01 Jul '25

01 Jul '25

Hello Is there a way to write out the BIOMT matrices associated with the input symmetry symbol in the output PDB file saved by Chimerax? Thank you Haixin -- Haixin Sui, Ph.D Pronouns: he, his, him (What's This<https://oer.ny.gov/system/files/documents/2023/11/personal-pronouns.pdf>?) Principal Investigator Wadsworth Center NY State Department of Health Biggs Lab C311, Empire State Plaza Albany, NY 12237 (518) 474-4235 (o) haixin.sui(a)health.ny.gov<mailto:haixin.sui@health.ny.gov> www.wadsworth.org/research/laboratories/sui-laboratory/sui-laboratory<http://www.wadsworth.org/research/laboratories/sui-laboratory/sui-laboratory>

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zone ID
by Denton, Jerod S 01 Jul '25

01 Jul '25

Hi, We are trying to see/export a list of amino acids that are within 5 angstroms of a docked ligand. Can you please tell me how to do this if possible? Thanks, Jerod Denton Vanderbilt

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Query for Volume viewer
by Akash Singh 01 Jul '25

01 Jul '25

Hi, I'm a researcher from India. I have been trying to make some EM fitting image with model protein. There is no Volume viewer option for Line smoothening, surface smoothening or square mesh to triangle mesh conversion. Also surface smoothening problem. I have been trying to execute through the command line, but it doesnt work . Can you help me regarding command line code for following Mesh Line smoothing Mesh surface smoothening Dim transparency The suite is ChimeraX or ChimeraX 1.9 Regards, Akash Singh

4 5

Filling gaps in selection
by Bruno Hay Mele 30 Jun '25

30 Jun '25

Hi all, I'm trying to evaluate salient differences within a specific topological domain across a set of protein structures. My workflow is as follows: I choose a reference structure, and use MatchMaker to align all other structures to it. Then, I use the Contacts tool with distance 0 and overlap 0 to select CAs of residues that are perfectly aligned to the reference selection (i.e. the topological domain). This approach works well in conserved regions, but it results in gaps where insertions or small variations occur. I've tried to use sel up to fill these gaps, but my attempts have failed miserably. Is there a way to fill in gaps within a discontinuous selectionbi.e., to make it continuousbwithout extending the selection outward beyond the domain of interest? Ideally, I'd like to interpolate or bridge only the missing parts, without picking up unrelated residues. cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118

3 4

rotating 2dlabels?
by coyote_v2002＠yahoo.com 30 Jun '25

30 Jun '25

Is there a way to rotate 2dlabels within ChimeraX? The only way I found to add such labels is in an external program like Inkscape. Vis

2 1

Re: interrupted beta-strands
by Elaine Meng 29 Jun '25

29 Jun '25

Hi Maria, For ChimeraX questions, it is better to use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here. The chimera-users address is for Chimera and we don't want people to get confused between the two. In ChimeraX: Probably you also need to set ss_id to indicate they are all in the same strand, instead of two consecutive strands, which would always be shown with a short connector instead of as a continuous strand. Please see <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue> ... and previous posts, such as these talking about helices but probably the same problem as your strands: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu…> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu…> I hope this helps, 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 Jun 29, 2025, at 8:02 AM, Maria Sola i Vilarrubias <maria.sola(a)ibmb.csic.es> wrote: > > Dear colleagues, > > I would like to know how to solve a problem that I encountered several times in ChimeraX , which is a disruption of beta strands. I attach a figure. This is a beta-hairpin of a model that ChimeraX showed as a coil, but previous data showed that this region corresponds to a beta-hairpin. I imposed a beta-strand fold for each of the corresponding segments with ChimeraX (setattr #3/a:40-52,59-66) res ss_type 0) but the strands appear interrupted between consecutive residues. I guess it's a problem of the polypeptide bond, but nevertheless Chimera can solve the problem. How can I solve this in ChimeraX? > > Thank you for your time and best regards, > Maria > > -- > Maria Solà > Dep. Structural Biology IBMB-CSIC > Barcelona Science Park (Helix Building) > Baldiri Reixac 15 > 08028 BARCELONA > Spain > Tel: (+34) 93 403 4950 >

1 0

How to run a python script in chimerax
by zg2234＠cumc.columbia.edu 27 Jun '25

27 Jun '25

Dear ChimeraX team, May I ask a basic question regarding running Python scripts in ChimeraX? I’m trying to execute a simple test script using the runscript command from the ChimeraX command window: runscript ~/Desktop/test_print.py Here is the content of test_print.py: def run(session, data=None): session.logger.info("✅ Successfully executed runscript_test.py!") from chimerax.core.commands import run as cxrun cxrun(session, "log clear") cxrun(session, "log info ✅ runscript_test.py is working") However, nothing seems to happen—there is no output in the log window, and it seems the script is not being executed at all. Ultimately, I would like to perform a coordinate transformation on a structure in ChimeraX using the equation: r = RM * r0 where: RM = [ 0.323, 0.9326, -0.1611], [-0.925, 0.2751, -0.2623], [-0.2003, 0.2337, 0.9515] But I am currently stuck at the first step: getting a Python script to run properly in ChimeraX. Any advice or suggestions would be greatly appreciated! Best regards, Zhen Gong

2 2

viewing mmcif reflection files with multiple blocks
by Kreitler, Dale 26 Jun '25

26 Jun '25

Hi, I'm working with mmcif files that contain multiple blocks of x-ray structure factors, such as those that arise from x-ray fragment screening campaign PDB group depositions. With the chimerax clipper plugin I'm able to open these mmcif files and associate the structure factors with the corresponding model, but this action only works for the first block in the file which contains the output of the refinement program. I'd like to access the other blocks which contain the binding event/evidence density maps. Would someone be able to point me in the right direction for accessing the additional blocks? Thank you, Dale ============================= Dale Kreitler AMX Beamline Scientist National Synchrotron Light Source II Building 745, Rm. 5L143 Upton, NY 11973 631-344-7318

2 1

ChimeraX version 1.10 has been released
by Elaine Meng 26 Jun '25

26 Jun '25

UCSF ChimeraX version 1.10 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.9 (December 2024) include: - Boltz machine-learning structure prediction of proteins, nucleic acids, and their complexes with ligands - Plotting measurements (distances, angles, SASA) across a trajectory - "aniso" command for displaying anisotropic B-factors as ellipsoids - Find Cavities GUI enhancements such as changing calculation parameters - Profile Grid condensed view for large sequence alignments - multiple sequence alignment server updated to MUSCLE v5 - structure superposition based on an existing sequence alignment - sequence-viewer region browser now includes UniProt feature info For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Ca-trace
by Das, Abhinaba 26 Jun '25

26 Jun '25

Dear community, Is there a way to show only the Ca backbone trace? Looks like this was a while ago in the forum (https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu…) so was wondering if it is now possible to do so in ChimeraX. Thanks, Abhi

2 2

Sponsorship Request: Samsung Odyssey 3D (G90XF) Monitor for ChimeraX Development
by Michaelis, Andre Clemens 25 Jun '25

25 Jun '25

Dear Samsung Sponsorship Team, I am writing to request consideration for a sponsorship in the form of a single Samsung Odyssey 3D (G90XF) monitor to support the continued development of ChimeraX, a powerful open-source visualization software used by scientists and researchers worldwide. About ChimeraX: ChimeraX is a state-of-the-art molecular visualization program developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco. This software is freely available for both academic and industrial use, serving thousands of researchers globally who work in fields such as: * Protein Design * Structural biology * Drug discovery and pharmaceutical research * Materials science * Biochemistry and molecular biology education The software specializes in rendering complex 3D molecular structures with exceptional clarity and detail, making it an essential tool for scientific research and education. Why the Samsung Odyssey 3D (G90XF) Monitor? The advanced 3D capabilities of your Odyssey 3D monitor would significantly enhance ChimeraX's development in the following ways: 1. Improved Spatial Visualization: The monitor's 3D technology would allow our developers to implement and test more realistic spatial rendering of molecular structures. 2. Enhanced User Experience: With proper support for your 3D technology, ChimeraX users worldwide would benefit from unprecedented depth perception when analyzing complex molecular structures. 3. Technical Innovation: The integration would enable new visualization features that are currently impossible with standard displays. Mutual Benefits This sponsorship opportunity offers several advantages for Samsung: * Exposure to Scientific Community: Your technology would be featured in a widely-used scientific application, showcasing its capabilities to companies, researchers and institutions globally. * Market Expansion: As ChimeraX adds support for your monitor's 3D capabilities, it would create a compelling reason for industry, laboratories, and research institutions worldwide to purchase the Samsung Odyssey 3D. * Technology Leadership: This partnership would demonstrate Samsung's commitment to supporting scientific advancement and innovation. Our Request We are requesting a single Samsung Odyssey 3D (G90XF) 27" monitor to integrate proper support for its 3D capabilities into ChimeraX. Once implemented, we could: * Acknowledge Samsung's contribution in our documentation and release notes * Provide regular updates on the implementation progress * Share user feedback and testimonials about the enhanced experience Thank you for considering this sponsorship opportunity. I believe this collaboration would be valuable for both Samsung and the global scientific community and industries that rely on ChimeraX. We look forward to discussing this proposal further and would be happy to provide any additional information you may require. Sincerely, André Michaelis, ChimeraX customer https://www.cgl.ucsf.edu/chimerax/ André Michaelis —————————————————— André Michaelis Max-Planck Institute of Biochemistry Dept. Proteomics and Signal Transduction Am Klopferspitz 18<x-apple-data-detectors://3/> D-82152 Martinsried<x-apple-data-detectors://3/>/Munich Phone: +49 89 8578 2213<tel:+49%2089%208578%202213> email: michaelis(a)biochem.mpg.de<mailto:michaelis@biochem.mpg.de> http://www.biochem.mpg.de/mann/<http://www.biochem.mpg.de/mann/>

1 0

Re: Glasses-free Samsung Odyssey 3D Monitor support
by Michaelis, Andre Clemens 25 Jun '25

25 Jun '25

Hi Tom and Greg, Thanks so much for the infos. I am torn between the 2 ‘normal’ displays from Samsung or Acer, which are also cheaper. Quite early I guess, but I notice some general excitement so future developments are not of the table i assume? About the SBS: I noticed that it is a little complicated to get there, but it is possible to get ChimeraX into full screen, SBS on and all menus and bars including command prompt hidden. Isn’t this view a perfect SBS picture that the Samsung monitor should be able to use? Only question in this case would be if fullscreen mode is recognized as such by the monitor. If yes, shortcut to get there would be nice. [IMG_0568.jpeg] About the openXR: I found the following about the Samsung monitor in a review online: ‘I want to take a moment to talk about XRGameBridge and VRto3D. This is a reshade plugin that you use to mod your Steam VR instance so that, along with VRto3D makes your SR display mimics a VR headset in a sense. With those tools alone you can launch steam VR games in 3D on your Spatial Reality (SR) display. What really excites me about this is that the developers managed to activate the monitors 3D mode without any special sdk from Samsung. I didn't realize this at the time but it seems like all SR displays like Acer spatial labs and Lenovo Thinkvision 3D seem to use basically the same SR sdk, which may be made my Leia (makes of the lume pad and their own SR displays). This means that it might be possible for any developer to make some tools or apps to help round out this monitor’ Wouldn’t that be a possibility to get VR working? A mode to just isolate the main window and drag it and full screen it to the 3D monitor would be helpful, but it sounded like hard to realize. Thanks again Best André Am 22.06.2025 um 19:21 schrieb Tom Goddard <goddard(a)sonic.net>: Hi Andre, We discussed the Samsung Odyssey 3D on the ChimeraX mailing list last month https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… The display manual does not mention OpenXR, only side-by-side stereo. https://downloadcenter.samsung.com/content/UM/202506/20250612182444761/BN81… does not support fullscreen side-by-side stereo so it won't work with this display. We might in the future add support. Tom On Jun 22, 2025, at 11:14 AM, Greg Pintilie via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: Hi Andre, I can pass some information since I’ve been looking into this with Tom Goddard a lot recently, not with the Samsung monitor, but with two others that have the same technology: Tom has the ChimeraX latest builds working with the "Sony 3D Spatial Reality Display” monitors. You just have to connect the monitor, run ChimeraX and then type “xr on” in the command line. We also tried the "Acer 3D SpatialLabs ViewPro 27”, but Tom found bugs in their openXR implementation, so the latest ChimeraX is not working with this yet, but likely there will be a fix very soon. Tom has a modified version of ChimeraX that works with this monitor, but it is not released yet. You can google the above names, I would put links but they seem to vary by region. I am a huge fan of both of the above two monitors. The 3D effect is great, very useful for modeling and viewing complex models and 3D maps. Also super easy to run, compared to previous technologies. There are still some quirks, like that you have to interact with the 3D view on your main monitor, not on the 3D monitor directly. There are no tests yet of ChimeraX with the Samsung monitor, that I know of. It looks really nice, but I didn’t find any info on whether it supports openXR or not, which is what ChimerX is using. We had some discussion on this list recently about whether it’s worth using the SBS mode, which it apparently supports, but that mode has even more quirks, so would not encourage. Greg P. On Jun 21, 2025, at 11:54 AM, Michaelis, Andre Clemens via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: Dear ChimeraX Team, I was wondering if you had experience with the glasses-free Samsung Odyssey 3D monitor or know if ChimeraX is supporting it? Maybe you got already feedback from some users, as this seems like the perfect solution to work with! <https://www.samsung.com/us/monitors/gaming/27-inch-odyssey-3d-g90xf-4k-165h…> <http://samsung-logo-1-1.jpg> Odyssey G9 27" 3D 4K Gaming Monitor with Speakers<https://www.samsung.com/us/monitors/gaming/27-inch-odyssey-3d-g90xf-4k-165h…> http://samsung.com<https://www.samsung.com/us/monitors/gaming/27-inch-odyssey-3d-g90xf-4k-165h…> Thank you Best, André —————————————————— André Michaelis Max-Planck Institute of Biochemistry Dept. Proteomics and Signal Transduction Am Klopferspitz 18 D-82152 Martinsried/Munich Phone: +49 89 8578 2213 email: michaelis(a)biochem.mpg.de<mailto:michaelis@biochem.mpg.de> http://www.biochem.mpg.de/mann/<http://www.biochem.mpg.de/mann/> _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

3 7

Request for Mathematical Details or Source Code for Helix Axis and Interhelical Distace/Angle Calculations in Chimera
by pupadhyay21 24 Jun '25

24 Jun '25

Respected Sir/Madam, My name is Prashant Upadhyay, and I am currently pursuing a Ph.D. in Bioinformatics and Molecular Dynamics Simulation at the Indian Institute of Technology Kanpur (IIT Kanpur), India. As part of my research, I am analyzing the structural dynamics of helical membrane proteins using molecular dynamics simulations. I have been using UCSF Chimera extensively for structural analysis. Specifically, I have been utilizing the Structure Analysis → Axes/Planes/Centroids tool to calculate the helix axes of selected helices in my protein of interest. When I select two helices, the Reply Log provides the interhelical distance and angle between the computed axes. This functionality has been incredibly useful for analyzing static structures. To extend this to a dynamic context, I am interested in applying the same axis and angle calculation to each frame of an MD trajectory. For this, I would greatly appreciate it if you could share the mathematical methodology or the relevant portion of the source code that Chimera uses to compute: 1)The helix axis from selected residues 2)The angle and the shortest distance between two helix axes My aim is to replicate this analysis programmatically over the entire simulation trajectory. Any guidance, reference, or code snippet you could provide would be immensely helpful. Thank you, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur (IIT Kanpur)

3 3

substitution conflicts between perframe subcommands and runscript arguments
by d＠wolf.gdn 24 Jun '25

24 Jun '25

Hey there So I'm invoking some rendering jobs like this: `cx --script "./a.cxc 2 3"` Inside a.cxc there's something like: ``` perframe "coordset #1 $1" frames 24 format %03d range $1,$2,1 showCommands true ``` Now the problem is that the script arguments in the script are all being replaced So $1 in the perframe subcommand becomes "2" just like in the range option I couldn't find documentation on a built-in escape mechanism yet I tried "\$1" and "$$1" w/o success tho Alternatives that I see are generating a list of script files that don't rely on substitution and have hard-coded frame offsets or ig I could also explore python scripting Wanted to ask if there's a way to do it with escaping tho Thanks!

3 2

How to save coordinates of a fit atomic model
by Tom Goddard 24 Jun '25

24 Jun '25

Hi Peter, To save an atomic model after you have moved it to fit into a map use menu File / Save..., file type mmCIF, uncheck "Use untransformed coordinates", and save. If you have multiple models open it won't show that option and instead will show "Save relative to model: <menu>" and choose to save relative to the map. Or if you want to use a command just use "save myfitmodel.cif". If you have multiple models open you have to specify in the command which to save "save myfitmodel.cif model #3". Please ask questions about how to use ChimeraX on the mailing list and not in bug reports. That way others can benefit from the answers. Tom > Hi Tom, > I’m having an issue in ChimeraX and would appreciate your help. > I aligned an atomic model with a cryo-EM map and would like to save the > atomic model in its aligned position, so that when I reopen both the map > and the model later, they appear properly aligned. > I tried using the GUI to save the transformed atomic model in different > formats, but when I reopened the files, the alignment was lost. > I also tried using the save command, but encountered the same issue — the > model was saved in its original, unaligned coordinates. > Finally, I attempted to save the session as a .cxs file and open it in > Chimera, but Chimera cannot open .cxs session files from ChimeraX. > Could you please tell me exactly what I need to do to save the atomic > model with its current (transformed) coordinates so that it stays aligned > with the map when reloaded? > Thank you very much for your help. > Wishing you a great day, > Peter

4 3

Adding chain description and Uniprot accession number to a pdb file
by Rayees Mattoo 23 Jun '25

23 Jun '25

Hi, I want to add chain description and Uniprot accession ID to my PDB file which contains many chains (chain IDs from A-M). Please suggest a way to add those details in chimeraX? Best

2 3

Get model chain color
by Walshe, James 23 Jun '25

23 Jun '25

Hi All, Is there an easy way to get the color code for a model? Or a specific chain of that model? Let’s say I really like the default colors a model is loaded with and I want to find the exact hexa color code for each chain? Thanks! Dr James Walshe | Postdoctoral Researcher | Cramer Group Department of Molecular Biology | Max Planck Institute for Multidisciplinary Sciences | Am Fassberg 11 37077 Göttingen, Germany T: +49 551 201-2807 | E: james.walshe(a)mpinat.mpg.de | https://www.mpinat.mpg.de/cramer

3 6

Selecting corresponding residue of different model
by Alexander Lee 22 Jun '25

22 Jun '25

Hello ChimeraX community, I have 2 pdb models of the same protein, but they don't have the same sequence numbering and length. After doing matchmaker, is there a command to select a selected residue's corresponding residue in the other model? Ex: After doing matchmaker, I selected #1/A:100 (HIS). I want a command to select #2 (HIS) in the same part of the sequence. That residue may be > 2 Angstroms from #1:100, but it's in the same position sequentially. Is there a way to do this preferably via command line? Regards, Alex

2 1

Glasses-free Samsung Odyssey 3D Monitor support
by Michaelis, Andre Clemens 22 Jun '25

22 Jun '25

Dear ChimeraX Team, I was wondering if you had experience with the glasses-free Samsung Odyssey 3D monitor or know if ChimeraX is supporting it? Maybe you got already feedback from some users, as this seems like the perfect solution to work with! <https://www.samsung.com/us/monitors/gaming/27-inch-odyssey-3d-g90xf-4k-165h…> [samsung-logo-1-1.jpg] Odyssey G9 27" 3D 4K Gaming Monitor with Speakers<https://www.samsung.com/us/monitors/gaming/27-inch-odyssey-3d-g90xf-4k-165h…> http://samsung.com<https://www.samsung.com/us/monitors/gaming/27-inch-odyssey-3d-g90xf-4k-165h…> Thank you Best, André —————————————————— André Michaelis Max-Planck Institute of Biochemistry Dept. Proteomics and Signal Transduction Am Klopferspitz 18 D-82152 Martinsried/Munich Phone: +49 89 8578 2213 email: michaelis(a)biochem.mpg.de<mailto:michaelis@biochem.mpg.de> http://www.biochem.mpg.de/mann/<http://www.biochem.mpg.de/mann/>

3 2

Request for Mathematical Details or Source Code for Helix Axis and Interhelical Distace/Angle Calculations in Chimera
by pupadhyay21 22 Jun '25

22 Jun '25

Respected Sir/Madam, My name is Prashant Upadhyay, and I am currently pursuing a Ph.D. in Bioinformatics and Molecular Dynamics Simulation at the Indian Institute of Technology Kanpur (IIT Kanpur), India. As part of my research, I am analyzing the structural dynamics of helical membrane proteins using molecular dynamics simulations. I have been using UCSF Chimera extensively for structural analysis. Specifically, I have been utilizing the Structure Analysis → Axes/Planes/Centroids tool to calculate the helix axes of selected helices in my protein of interest. When I select two helices, the Reply Log provides the interhelical distance and angle between the computed axes. This functionality has been incredibly useful for analyzing static structures. To extend this to a dynamic context, I am interested in applying the same axis and angle calculation to each frame of an MD trajectory. For this, I would greatly appreciate it if you could share the mathematical methodology or the relevant portion of the source code that Chimera uses to compute: 1)The helix axis from selected residues 2)The angle and the shortest distance between two helix axes My aim is to replicate this analysis programmatically over the entire simulation trajectory. Any guidance, reference, or code snippet you could provide would be immensely helpful. Thank you, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur (IIT Kanpur)

1 0

Help with ChimeraX Boltz Structure Prediction Command for Multi-Component Systems
by Arun Gupta 20 Jun '25

20 Jun '25

Dear ChimeraX Team, I'm currently working with the Boltz structure prediction tool in ChimeraX GUI (ChimeraX 1.10 Release Candidate (15 June 2025) ) and would appreciate your guidance on the correct command syntax—particularly when specifying the single or multiple protein components via the ChimeraX GUI command line. I would like to run Boltz predictions with the following specific parameters: * nstruct: 5 (Default is 1) * recycles: 10 (Default is 3) * seed: 42 (Random numbers of seed (integer), Fixed seed value ensures reproducible results) * steering: true (enables or disables the steering potential) I tried running the following command in the command line, "boltz predict protein sequences "MKALTQRPLD... (your protein sequence)" nstruct 5 recycles 10 steering true" but it doesn't work. Could you please provide an example of the correct command format for: 1. A single molecular component (e.g., one protein sequence). 2. A multi-component system (e.g., protein + peptide or multiple protein chains). Additionally, if there are any special considerations or formatting requirements for specifying multiple sequences or components in the GUI , I’d be grateful for your advice. Thank you for your time and support. 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

3 3

Determining Chirality
by steffen＠sthomas.de 20 Jun '25

20 Jun '25

4 5

ChimeraX documentation as file download
by Michaelis, Andre Clemens 20 Jun '25

20 Jun '25

Dear ChimeraX team, Fantastic software! Since you have a great documentation and turials online, I was wondering if you could provide those also in file format (txt, pdf etc)? Would be extremely helpful for the use with chat bots! Having an assistant next to you helping you with exact commands for individual applications. Thanks a lot best André —————————————————— André Michaelis Max-Planck Institute of Biochemistry Dept. Proteomics and Signal Transduction Am Klopferspitz 18<x-apple-data-detectors://3/> D-82152 Martinsried<x-apple-data-detectors://3/>/Munich Phone: +49 89 8578 2213<tel:+49%2089%208578%202213> email: michaelis(a)biochem.mpg.de<mailto:michaelis@biochem.mpg.de> http://www.biochem.mpg.de/mann/<http://www.biochem.mpg.de/mann/>

2 2

Structural predictions of autocatalytically cleaved proteins and visualizing a homotetramer of heterodimers
by Jernej Turnsek 19 Jun '25

19 Jun '25

Hi All, I am working on a bifunctional enzyme with these two hypothesized features: - it is first autocatalytically cleaved to form a heterodimer; - it then forms a homotetramer of heterodimers. These two events would lead to a protein assembly with 2 active sites for catalytic activity A and 1 active site for catalytic activity B. I have two questions: 1. I have modelled the initial heterodimer by "cleaving" the preprotein at the predicted autocatalytic cleavage site and feeding the resulting two aa sequences to the AlphaFold Server. Is there a better way to predict heterodimerization of such proteins using AlphaFold? 2. Is there a way to tetramerize the resulting AlphaFold heterodimer from 1. in ChimeraX? Thank you and best wishes, Jernej -- Jernej Turnšek, PhD (hear my name <https://www.name-coach.com/1b5bbbb9-5b8c-46bc-8678-a30c25e11bc3>) Postdoctoral Scientist Department of Plant and Microbial Biology University of California, Berkeley Personal Website <https://plantandmicrobiology.berkeley.edu/users/jernej-turnsek>

3 3

query 2fo-fc map
by mariela Urrutia 19 Jun '25

19 Jun '25

HelloCould you tell me how can I see the 2fo-fc map in a particular residue?Thanks you in advance.Mariela

2 4

Method of calculation of SASA
by komatireddy.nikhita＠gmail.com 18 Jun '25

18 Jun '25

Dear Sir/Madam, I am Nikhita, an undergraduate student working on a research project and I am considering to use ChimeraX to calculate solvent accessibility surface area (SASA) for some residues of a protein. However, since I would like to calculate relative solvent accessibility surface area manually, I am using the reference maximum SASA values from Tien et. al. (2013) which mentions that using softwares that calculate SASA using the Lee & Richards method are preferable. As such, I would like to ask if ChimeraX uses the Lee & Richards method to calculate SASA as I could not find much about this on the ChimeraX website. Thank you! Warm regards, Nikhita

4 8

Re: [Chimera-users] query
by Eric Pettersen 18 Jun '25

18 Jun '25

Hi Mariela, I don’t really know what a “superior menu” is. Maybe you could clarify? If you mean a popup menu, you get that by clicking the right button on your mouse (or the equivalent on a trackpad). Since this is a ChimeraX question, I have cc’ed the chimerax-users list and directed replies there. Chimera and ChimeraX are separate programs and have separate mailing lists. --Eric Eric Pettersen UCSF Computer Graphics Lab > On Jun 12, 2025, at 9:23 AM, Mariela Urrutia via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, > Could you give me direction to add the superior menu in ChimeraX 1.9 (2025-3-6)? > Thanks you in advance! > Mariela > > Dra. Mariela Urrutia > Investigadora > Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” (CEDIE) > CONICET – FEI – División de Endocrinología, Hospital de Niños Ricardo Gutiérrez > > Gallo 1330 – C1425EFD Buenos Aires – Argentina > Tel. (+54-11) 4963-5931 int 290 > murrutia(a)cedie.org.ar <mailto:murrutia@cedie.org.ar> 🌎 www.cedie.org.ar <https://cedie.conicet.gov.ar/> 👥 Facebook <https://www.facebook.com/CEDIE-Centro-de-Investigaciones-Endocrinol%C3%B3gi…> Instagram <https://www.instagram.com/cedie.conicet/> > > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

4 4

Cross section visual of map model fit
by Das, Abhinaba 18 Jun '25

18 Jun '25

Dear community, How do we go about creating an image like this where the density around the model is quite sharp, that is, there is almost no interference from the top or the bottom density? Tried clipping volume and volume zone; both didn’t seem to give quite the same effect. Thanks, Abhi [cid:image001.png@01DBDFC6.1AD09EC0]

3 3

cartoon selection by color
by Михаил Егорочкин 18 Jun '25

18 Jun '25

Hi, my name is Mike and I placed some atomic (cif) models in my chimera session. Also I performed manual coloring of some protein domains (watch the picture). Now I have realized that I want to change uncolored parts (#d2b48c). So manually it will take a lot of time (i have a lot of these models), is there any way to select by cartoon color. I imagine this as some command or script like: "sel by color #d2b48c" and after that i go action color and choose my desired color. Please help me.

2 1

Model loops with MODELER in ChimeraX
by Alexandra Zahradnikova 16 Jun '25

16 Jun '25

Hello, I have recently watched a Youtube video (https://www.youtube.com/watch?v=GV6jHhxR5T4) about completing loops with Modeller in ChimeraX. However, the structure I want to model is only a part of the actual molecule, and I want to replace one unresolved segment (300 residues long) with 11 glycines. When I upload both, the FASTA file with the sequence as it should look after completion of the loops, and the PDB file of the incomplete structure, I am not able to align them together in order to perform the modelling. - If I use the original PDB file containing the SEQRES part, the association is performed but produces mismatches after the start of the unresolved sequence. - If I use the PDB file without the SEQRES part, I am not able to perform the association. Can anybody help me? Thanks in advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796

3 6

cysteine palmitoylation with ISOLDE?
by Alexis Rohou 16 Jun '25

16 Jun '25

Hi ISOLDE users & Tristan, Has anyone got experience building a palmitoylated cysteine residue? I'd appreciate any pointers you may have. Based on how glycosylations can be built (see thread <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu…>) I was thinking to start with isolde add ligand PLM but that fails with "ValueError: No template for residue type PLM" Are we in covalent ligand (unsupported) territory here? Cheers, Alexis

4 3

Parallel capabilities of ChimeraX
by Alexandra Zahradnikova 16 Jun '25

16 Jun '25

Dear All, In the ChimeraX article (doi: 10.1002/pro.3235) it is written: "ChimeraX is built using standard software toolkits that utilize advanced Graphics Processing Unit (GPU) capabilities and the parallel computing capabilities of modern hardware. " However, when I run ChimeraX on Windows10, Windows11, or Linux, it only grabs one thread and does not use the GPU at all (neither the built-in one not the NVIDIA one). Am I doing something wrong? Best regards Sasha

3 2

Method of calculation of SASA
by komatireddy.nikhita＠gmail.com 15 Jun '25

15 Jun '25

Dear Sir/Madam, I am Nikhita, an undergraduate student working on a research project and I am considering to use ChimeraX to calculate solvent accessibility surface area (SASA) for some residues of a protein. However, since I would like to calculate relative solvent accessibility surface area manually, I am using the reference maximum SASA values from Tien et. al. (2013) which mentions that using softwares that calculate SASA using the Lee & Richards method are preferable. As such, I would like to ask if ChimeraX uses the Lee & Richards method to calculate SASA as I could not find much about this on the ChimeraX website. Thank you! Warm regards, Nikhita

1 0

Docstring/help for aliases?
by Oliver Clarke 13 Jun '25

13 Jun '25

Hi, I use a lot of custom aliases, some quite complicated. It would be useful when creating an alias to have the option to provide a docstring, which could be printed to the log when either executing the alias or listing aliases in the Log (using "alias list"). E.g. I quite like this alias: ``` alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; close sel; show $2 ``` Which fits models or maps to a spherical zone in a target map around the center of rotation - useful for aligning maps locally after 3D classification to look for bound ligands etc - but often I forget the usage pattern (local_fitmap #models_to_fit #target_map radius), so it would be very handy to optionally have this printed to the log when running the alias. Cheers Oli

2 9

Labeling chains in MD simulation trajectories of a multimer
by Alexandra Zahradnikova 13 Jun '25

13 Jun '25

Hi All, I am interested in MD simulations of homomultimeric ion channels, which I do in GROMACS. I would like to analyze my output files with ChimeraX but I run into the following problem: The .gro output of the simulation consists of a single chain named /? in ChimeraX. When I open the file in old Chimera, it shows every chain of the original protein separately but with the same name ()

3 9

'scene' functionality in ChimeraX
by Maria Voigt 12 Jun '25

12 Jun '25

Good afternoon, I've started using ChimeraX recently after long time using the old Chimera. I've been teaching myself the command line animation lately. One thing I don't seem to be able to find is whether there is something in Chimera X that is equivalent to the old 'add Scene' from Utilities > Animation. This feature saves the position, the shades, whether assets are shown or hidden. Please let me know, Greetings, Maria -- *MARIA VOIGT* Senior Outreach Coordinator, RCSB Protein Data Bank Research Associate, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848-445-4987 | E: maria(a)rcsb.rutgers.edu rcsb.org <https://www.rcsb.org/> | iqb.rutgers.edu <https://iqb.rutgers.edu/> | facebook <https://www.facebook.com/RCSBPDB> | twitter <https://twitter.com/buildmodels> | youtube <https://www.youtube.com/user/RCSBProteinDataBank>

2 2

How to measure and visualize the distance between two benzene rings in ChimeraX?
by Nan Zhang 11 Jun '25

11 Jun '25

Dear ChimeraX Developers, I am working with a protein-ligand complex where there seems to be a π-stacking interaction. I would like to measure the distance between the benzene ring of an amino acid residue in the protein and the benzene ring of the small molecule ligand. Could you please advise on the specific steps within ChimeraX to perform this measurement and also visualize it (e.g., showing the distance label)? Looking forward to your answer, thank you! Best regards, Nan Nan Zhang zhangnan(a)nankai.edu.cn

2 1

Hiding Centroid markers while keeping distance measurement visible in ChimeraX
by Nan Zhang 11 Jun '25

11 Jun '25

Dear ChimeraX Developers, I'm working on visualizing a protein-ligand complex with potential π-stacking interactions. To measure the distance between the centroids of two benzene rings (one in the protein residue, one in the ligand), I used the following workflow: define centroid1 define centroid2 distance centroid1 centroid2 (to measure and show the distance between the centroids)My issue: When I try to hide centroid1 centroid2 to generate a cleaner image showing only the distance measurement (the dashed line and label), hiding the centroid points also automatically hides the distance object. Question: How can I hide only the centroid markers (points) while keeping the distance measurement (the dashed line and its label) visible for visualization? Is there a specific command or GUI manipulation to separate these visual elements? I'd appreciate any guidance on resolving this. Thank you for your help and your excellent tool. Best regards, Nan Nan Zhang zhangnan(a)nankai.edu.cn

2 1

Eachmodel option for volume?
by Oliver Clarke 10 Jun '25

10 Jun '25

Hi, Fitmap has a handy "eachmodel true" option, which allows one to fit a bunch of maps or models to a single target map. It would be useful I think to have a similar option in the "volume" command, to allow one to quickly multiply a bunch of maps (e.g. from 3D classification) by a single mask. Cheers Oli

2 2

suggestion: let user specify id of coordset generated by morph command
by Alexis Rohou 10 Jun '25

10 Jun '25

Hi team, For convenience, especially when scripting, it would be good if the morph command would accept an "id" argument (much like the open command has "id" or combine has "modelId"). This would let the user specify the model id of the coordset created by morph. Current behavior is that the first available (lowest numerical) id is used, which is not easy to keep track of when scripting. Cheers, Alexis

2 2

Edit right mouse labels?
by Oliver Clarke 10 Jun '25

10 Jun '25

Hi, There is probably an easy way to do this but I could not find it in the GUI. Is there a way to edit labels placed with the right mouse? Currently they only give the residue type and number, there doesn't seem to be a way to edit or configure them in the same way as one can do using the global per-residue labels in Actions>Labels. If it doesn't exist, perhaps a right mouse mode "Edit label" would be useful to complement Label and Move Label? This would be helpful when making a quick movie to show density quality, and would allow one to easily add custom labels without needing to use the CLI. Cheers Oli

2 2

Boltz-2
by Lynne Howell 10 Jun '25

10 Jun '25

I’m sure it already on your radar – but would love to see Boltz-2 and its ability to predict binding affinity integrated into ChimeraX – as you did for Boltz-1. Thanks L P. Lynne Howell Canada Research Chair (2006-2020) Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children Professor, Department of Biochemistry, University of Toronto Office and Mailing address: Room 20-9-715 Peter Gilgan Centre for Research and Learning (PGCRL) 686 Bay St. Toronto ON M5G 0A4 Phone: 416-813-5378 (Internal 305378) Web page: https://lab.research.sickkids.ca/howell/ ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

3 6

Re: Robust way to setup scene and save image such that zoom and resolution are always the same across different monitors
by Daniel Larsson 09 Jun '25

09 Jun '25

I think what throws you off is the aspect ratio of the ChimeraX window. Add a command to set the size of the window into your workflow. For example: windowsize 800 800 Regards, Daniel From: Samuel Haysom via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Reply to: Samuel Haysom <Samuel.Haysom(a)Nxera.life> Date: Monday, 9 June 2025 at 17:10 To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Robust way to setup scene and save image such that zoom and resolution are always the same across different monitors Hello, Is there a recommended set of commands to setup a particular view of a molecule and then save an image of that view such that the size of the molecule within the image, the resolution of the image, and the position of the clipping planes will always be the same regardless of what monitor size/resolution it is taken on? Currently I setup an image using the following commands: e.g. view matrix camera 0.98237,-0.066404,-0.17474,86.421,0.014131,-0.90572,0.42363,190.37,-0.1864,-0.41863,-0.88882,-48.082 clip near -10 far 10 position /R:LIG zoom pixel 0.0348 I then save it using: e.g. save 'dir_path/image.png' width 2000 height 2000 supersample 10 transparentBackground False I often will come back to the same cxc script and want to re-render with e.g. a modified pdb file but still want to get exactly the same view. I can then substitute this picture into a figure I've created in e.g. Inkscape without having to resize the image. However I've noticed that often the new image will not have the same zoom (so the model will be bigger and smaller within the total FOV) which means I have to then manually resize it to match what I already have. I've also noticed that if I render on e.g. my laptop rather than my desktop monitors this effects both the zoom as previously mentioned but also the final resolution of the image as this seems tied to the screen resolution. Is there a way to make it so the image will always look the same regardless of hardware etc.? KR, Sam Samuel Haysom<mailto:Samuel.Haysom@nxera.life> Senior Scientist • Protein Sciences Nxera Pharma UK<https://nxera.life/> Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom [cid:image001.png@01DBD963.DEF37B10] The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989. VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

1 0

Robust way to setup scene and save image such that zoom and resolution are always the same across different monitors
by Samuel Haysom 09 Jun '25

09 Jun '25

Hello, Is there a recommended set of commands to setup a particular view of a molecule and then save an image of that view such that the size of the molecule within the image, the resolution of the image, and the position of the clipping planes will always be the same regardless of what monitor size/resolution it is taken on? Currently I setup an image using the following commands: e.g. view matrix camera 0.98237,-0.066404,-0.17474,86.421,0.014131,-0.90572,0.42363,190.37,-0.1864,-0.41863,-0.88882,-48.082 clip near -10 far 10 position /R:LIG zoom pixel 0.0348 I then save it using: e.g. save 'dir_path/image.png' width 2000 height 2000 supersample 10 transparentBackground False I often will come back to the same cxc script and want to re-render with e.g. a modified pdb file but still want to get exactly the same view. I can then substitute this picture into a figure I've created in e.g. Inkscape without having to resize the image. However I've noticed that often the new image will not have the same zoom (so the model will be bigger and smaller within the total FOV) which means I have to then manually resize it to match what I already have. I've also noticed that if I render on e.g. my laptop rather than my desktop monitors this effects both the zoom as previously mentioned but also the final resolution of the image as this seems tied to the screen resolution. Is there a way to make it so the image will always look the same regardless of hardware etc.? KR, Sam Samuel Haysom Senior Scientist • Protein Sciences Nxera Pharma UK Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

1 0

ChimeraX adjacent question about AF2 vs AF3
by David S. Fay 09 Jun '25

09 Jun '25

Greetings, I am curious if others have found AlphaFold3 to be slightly worse or less consistent at predicting protein-protein interactions than AlphaFold2. From the AF3 paper it appeared that they were roughly equivalent, with AF3 perhaps having a slight edge. Certainly when it comes to speed and the handling of large proteins, AF3 is far superior. But over time I’ve found a number of cases where AF2 did a better job based on experimentally supported evidence from our lab. Admittedly, this observation is entirely anecdotal and likely prone to bias. And I get that AF2 may predict some interactions better than AF3 and vice versa. But it’s still makes me wonder and I was curious if others had noticed this pattern or had thoughts on the matter. Thanks in advance. David

2 1

copy from Chimera
by Sherwood Casjens 06 Jun '25

06 Jun '25

Sirs: I recently got a new MacBook Pro computer that is running system Sequoia 15.4.1. We loaded ChimeraX version 1.8 (2024-06-10). It seems to work OK except there is no “copy” command in the edit menu and command-C does not copy sequence in the sequence window of Chimera. Any idea what my problem is? Sherwood Casjens Univeristy of Utah

2 2

Q-Score not shown in output file
by Thu Nguyen 05 Jun '25

05 Jun '25

Hi, I am trying to calculate the Q-score of this density map and structure pair using the Q-Score plugin <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxqscore> in ChimeraX and save the score to the output file. I loaded the 2 files to ChimeraX and used this command "qscore #2 toVolume #1 useGui false pointsPerShell 8 shellRadiusStep 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false outputFile /Desktop/q_score.txt" However, the output file is empty and I got the error message in ChimeraX. When I removed the outputFile option, it worked as normal and gave me the average score of .32. Do you know why it happened like this and what I should do to fix it? Thank you very much. Best regards, Thu

2 1

Select all truncated amino acids in model (though ISOLDE?)
by Vorländer,Matthias Kopano 05 Jun '25

05 Jun '25

Hi everyone, Is it possible to create a selector or python script to identify/match all truncated amino acids in a model? If not possible directly in ChimeraX, could ISOLDE offer a solution through matching to residue template “TRUNC_CB”? Thanks in advance, Matthias

3 3

Using measure area command
by jillian.baker＠som.umaryland.edu 04 Jun '25

04 Jun '25

Dear ChimeraX community, I am trying to use the 'measure area' command to measure the area using three atoms (essentially trying to calculate the area of a triangle). I have come up with the script of "measure area #2/b:44@o,97@ca,57@hz3" with 2 being model ID, b being the chain, and then the numbers being residues and the atoms are followed by the "@" symbol. I don't quite get an error here, but I get back "No surfaces specified." I can't seem to figure out away to specify a surface or use a different command to calculate the between these three points. Any help with this would be greatly appreciated. Thanks, Jill

2 1

Align molecule to axes
by Alexander Lee 03 Jun '25

03 Jun '25

Dear ChimeraX community, I have an optimized benzene ring that's floating in space. Is there a way to align that ring to one of the axes' planes so that 2 of the 3 cartesian coordinates read 0,0? Ex: C1 0.00 0.00 z1 C2 0.00 0.00 z2 C3 0.00 0.00 z3 etc Regards, Alex

2 1

Shading from N-terminus to C-terminus?
by Nick Matzke 02 Jun '25

02 Jun '25

Dear ChimeraX list, Thanks so much for this amazing software! I have a kind of obscure question for which I could not find an answer on Google. I've got the FliPQR-FlhB structure, from here: https://www.rcsb.org/structure/6S3L This has 5 copies FliP 1 copy FliR 4 copies FliQ 1 copy FlhB I opened it and am using ribbon view. I've colored the chains by protein type with these commands: color /a,b,c,d,e purple color /f red color /g,h,i,j green color /k yellow Now, I'd like to have each chain shaded from N-terminus to C-terminus, e.g. dark red to light red, or something like that. (I see the rainbow option, but this creates a very complex view if all 11 chains are each an roygbiv rainbow.) Almost as good, is there a way to easily label the N-terminus and C-terminus of each chain? Any suggestions! Thanks so much, Cheers, Nick

2 2

ChimeraX support: Alphafold contacts
by Anthony Newcombe 02 Jun '25

02 Jun '25

Hello I have a commercial license of ChimeraX, I have a question you may be able to help with I have used Structure prediction > Alphafold to predict structures and interactions between 2 proteins and this returned the best_model.pdb But I would like to identify contacts within 8 angstroms, as shown in the Youtube video: https://www.youtube.com/watch?v=TMcjEecFHaI&list=WL&index=26'm typing the command: alphafold contacts /A to /B distance 8 But receive the error: 'Structure best_model.pdb #1 does not have PAE data opened' Do I need to open something? If you can help that would be much appreciated Many thanks Tony Anthony Newcombe PhD Applied Biopharm Consulting Ltd Cork, Ireland http://www.appliedbiopharm.com<http://www.appliedbiopharm.com/> IE: +353 (0)87 3634486 [cid:image001.png@01DBD2E1.AD97E890] Applied Biopharm Consulting Limited is a company located in the Republic of Ireland Reg. No: 747251, VAT No: IE4188817RH. Registered office: Brook Lodge, Lisnacunna, Ballinascarthy, Clonakilty, Cork, Ireland P85 C832. This message is confidential and intended solely for the recipient(s). If you are not the intended recipient, any use, disclosure, copying or distribution of this message or its attachments is strictly prohibited. Please notify the sender immediately by replying to this email and delete the message, its attachments and any copies.

3 2

Comparing Maps
by Abhilash Padavannil 02 Jun '25

02 Jun '25

Hello, I have five different cryoEM maps coming from similar samples. The maps are at different resolutions. I want to compare the density at the region of interest across these maps. How do I normalize the maps say to the first map to make accurate analysis. I know I could scale them using vop scale, but I am wondering which of the parameters I should use. Thanks in advance for your suggestions. Abhilash.

3 4

How to create singlke protein from assembly of 5 individual chains
by Jacek Jagodzinski 29 May '25

29 May '25

Hi, I am medicinal chemist. I used ChimeraX to model missing parts/loops of the protein for which I had cryo-EM structure. It is transmembrane protein consisting of 5 individual chains. I managed to reconstruct missing parts using as a template known sequences of publicly available X-ray structures of proteins and known sequences. I have now a nice assembly of five individual “repaired” proteins perfectly aligned with parts of my cryo-EM structure. However the PDB file of those FIVE individual proteins is not recognized as ONE protein with five separate chains by my other programs. I suppose there is a way to get the result I need, but I cannot find the solution by myself. Can you help? Jacek Jagodzinski, PhD

2 4

Use minimization in chimerax using command line
by TUSHAR GUPTA 29 May '25

29 May '25

Good morning I would like to appreciate your work and efforts in developing and maintaining ChimeraX, it has always been so useful tool in my research. I was initially using Chimera that had excellent feature of using amber force field for energy minimization of structure and making movie using topology and coordinate file. I am working on inducing mutation in nucleic acid and protein structures. I wish to incorporate the minimization step in my research using Chimerax. I will be highly grateful if you could guide me how can I use minimization steps in Chimerax using command line codes. Thank you Tushar Gupta PhD biotechnology Bennett University Greater Noida India "He that can have patience can have what he will." - Benjamin Franklin _____________________________________________ Vineet Jain (Chancellor) Inspiration

2 4

Issue in using vop maximum to make composite map
by Dr. Heng Zhou 29 May '25

29 May '25

Dear ChimeraX developers, I have an issue when using vop maximum command to combine two local maps. Map A and Map B have an overlapping area with each other. The hinge point of structural flexibility is at the center of the overlapping area. Therefore, the left part of Map A and the right part of Map B have a better local density quality, which I want to keep in the composite map. But vop maximum did it on the opposite, resulting in a worse local resolution at the edges of the overlapping area (e.g., Region 1 and 2). Technically, this is not an issue of vop maximium itself. In Region 1, Map A has a better local density quality, while Map B has higher values in some voxels. So the composite map has more voxels derived from Map B in Region 1. Vice versa for Region 2. The only solution in my mind is to split both Map A and B at the hinge point, then do vop maximum for only the left part of Map A and the right part of Map B. But this is time-consuming since I have many local maps to combine. I wonder if you have a better solution? I would appreciate it if you could give advices. Thanks! Best regards, Heng Heng Zhou, PhD | Postdoctoral research fellow Stefan Raunser lab | Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11, 44227 Dortmund, Germany Phone: +49 231-133-2326

5 7

Disulfide bridges
by Pascal Rochaix 28 May '25

28 May '25

Hello, I am a long time user of PyMOL and I am testing ChimeraX for the first time. Is there a simple command to show the disulfide bridges ? It is easy in PyMOL but I don't find it in ChimeraX... Thanks in advance, Pascal Rochaix Protein Scientist www.metafora-biosystems.com<http://www.metafora-biosystems.com> [Logo mail]Pépinière Paris Biotech Santé 29 rue du Faubourg Saint Jacques | 75014 Paris | France

3 4

Working with c-beta truncated models in ISOLDE
by Vorländer,Matthias Kopano 28 May '25

28 May '25

Hi everyone, Is there a way to work with c-beta truncated models in ISOLDE? For truncated residues, Isolde brings up the unparameterized residues dialog, and matches as a possible template the ligand “TRUNC_CB”, which seems reasonable. Since the model also contains complete sidechains, I would not want to rebuild all residues to template, and doing it residue-by-residue is impractical, too. Can the “rebuild to template for all residues of this name” be limited to a selection? Thanks a lot, Matthias

2 2

swapna command extremely slow for large structures
by Vorländer,Matthias Kopano 27 May '25

27 May '25

Dear ChimeraX team, I have noticed that on some structure I am working with, the swapna command is extremely slow, making it almost unusable for structure manipulation. For a single nucleotide substitution, ChimeraX froze for >5 minutes before finishing the operation (that particular structure had ~300 000 atoms). When I however first delete all proteins from the structure, the operation is very fast. What is the rate limiting step in the swapna command? Does it invoke renumbering of all atoms in the PDB file? Without having quantified it, I experienced similar behavior for the build replace command. Would be fantastic if there would be a way to speed this up to increase its usability! Many thanks in advance, Matthias

2 1

Taking control of the string displayed in a pbond associated tooltip
by svle＠tiscali.it 27 May '25

27 May '25

Hi, I have specified some pseudobonds using pbond. It is possible to add a string, conveying other related informations , to that displayed in the tooltip when hovering the mouse on the pseudobond? Also, it is possible to take the complete control of what is displayed in the tooltip? Thanks. Saverio

5 4

How do I get Modeller structure if there was a connection timeout error on ChimeraX?
by Andy Liwang 23 May '25

23 May '25

Dear ChimeraX, I used “Model Loops” on a large protein and even though ChimeraX indicated “Modeller Webservice: 1 of 1 models generated”, it also gave the following error message: modeller refine<help:user/commands/modeller.html#refine> 1:1:all-missing 1/A:1:all-missing numModels 1 fast false adjacentFlexible 1 protocol standard Webservices job id: RO5U9U0YU7YY6TM5 2025-05-23 15:51:56,220 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<urllib3.connection.HTTPConnection object at 0x32f0aa350>, 'Connection to webservices.rbvi.ucsf.edu timed out. (connect timeout=None)')': /cxservices/api/v1/chimerax/jobs/RO5U9U0YU7YY6TM5/files Am I able to retrieve the model from webservices.rbvi.ucsf.edu<http://webservices.rbvi.ucsf.edu/>? Sincerely yours, Andy LiWang Professor of Chemistry & Biochemistry University of California Merced, CA 95343

2 3

Problem using pbond
by svle＠tiscali.it 23 May '25

23 May '25

Hi, I would like to use pbond with a pair of atoms. For one of these it is available the model number , the chain ID and the atom serial number. How it is possible to give the atom specification ,having the previous three information, for using it in pbond? Thanks. Saverio

3 5

remotecontrol observations and suggestions
by Roden Deng Luo 23 May '25

23 May '25

Hi, This is to share my observations and practices mainly with people using `remotecontrol xmlrpc`, likely developers. `xmlrpc` has a very high overhead, `remotecontrol rest` with "multipart/form-data" header POST requests should be a better option. First, the REST method can also be used programmatically in scripts or applications fairly easily. I have been sending GET requests using the REST method. Then, I hit "Request-URI Too Long" as I am sending decent sized json data (17KB). Then I tried XML-RPC and realized the frame rate dropped from 58 to 8. The frame rate can be displayed at the status line via `graphics rate true`. Then GPT guided me to try POST with "application/x-www-form-urlencoded" as Content-Type. I got stuck here for a while and found _parse_post <https://github.com/RBVI/ChimeraX/blob/3233aaaf01623ca24bccff7196410401872ce…> returns "fields" in binary and the program could not parse args["command"] <https://github.com/RBVI/ChimeraX/blob/3233aaaf01623ca24bccff7196410401872ce…> as what's inside is b"command". Then I refactored my client to POST with "multipart/form-data" and it worked. More details in my conversations with bots: URL too long: https://chatgpt.com/share/682c856c-174c-8003-bfc9-96fa7e2db0c3 Frame rate cmd: https://chatgpt.com/share/682c8589-2da0-8003-8c14-a59b75927c6b XML-RPC overhead: https://chatgpt.com/share/682c85a7-5f40-8003-8615-095e0a28fccd POST: https://chatgpt.com/share/682c85ca-9938-8003-bb0b-1fb7dd7938ef Best, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Commercial vs personal use
by Smith, Timothy 22 May '25

22 May '25

Hello, I previously used ChimeraX for my academic work during my PhD and would like to continue using it for personal use. I do work for a biotech company and while I don't use ChimeraX for work related to my job, I do only have a work issued computer where IT needs to install software. My question is would I still need a commercial license even if I only use it for personal use on my work computer? Thanks, Tim

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1.10 Release Candidates Available Now
by Zach Pearson 21 May '25

21 May '25

Hello ChimeraX users, The first release candidate of ChimeraX 1.10 is available for download today. — Zach

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request help about chimeraX
by Pietro Rizza 21 May '25

21 May '25

hi, thank you for your reply...I hope to explain clearly my problem In attached you will see the file saved with CHIMERA X and I' d like to open my data, in particular SCORE, ENERGY OF POSES in the Biovia Studio DIscover Visualizer....... If you see the second attached.....are reported the several energy of poses (indicated by red arrow) probably I save my data in CHIMERAX IN NOT CORRECT WAY? Why do I not open the energy of poses in Biovia Studio Discover Visualizer? thank you again sincerely Pietro -- ------------------------------------------------------------------------------------------------------------------ Il banner è generato automaticamente dal servizio di posta elettronica dell'Università della Calabria <https://www.unical.it/5x1000>

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Re: request your help about ChimeraX
by Elaine Meng 21 May '25

21 May '25

> On May 21, 2025, at 7:19 AM, Pietro Rizza <pietro.rizza(a)unical.it> wrote: > > Hi Dr Meng > Please you could help me, how do you save the data in CHIMERAX? > How can I save the energy of different poses? > Thanks in advance > Sincerely > Pietro > Hi Pietro, It is better to send questions to the chimerax-users(a)cgl.ucsf.edu address (CC'd here so you don't have to send it again), unless you are including private data. If you send only to me, it may not get answered. I removed your attachment in case it was private, but I see you are using ViewDockX. Of course, the energies and other descriptors of each pose are read from your original input file, so they are already "saved" there, but maybe you are trying to save as a spreadsheet format like CSV? It was not clear from your question. The ViewDockX "Save" button will just save another file that has all of the coordinates as well as the scores (like your original input file). There is no option to save a CSV file from the table, sorry. The only similar possibility is to convert the ViewDockX columns into a model attribute with this recipe <https://rbvi.github.io/chimerax-recipes/vdx_attrs/vdx_attrs.html> ... and then use the "save" command to save an attribute file <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> ... but in my opinion it would be MUCH easier just to process these values from your original input file (the one output by the docking program). You just can't do it with ChimeraX, sorry. 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

1 0

Questions about alphafold interfaces output discrepancies
by Bruno Hay Mele 20 May '25

20 May '25

Hi! I am dabbling with the alphafold interfaces command, and I cannot make sense of the data. In my user case, the table synthesis produced by the command says: Models Confident pairs #Res1 #Res2 4 23 12 12 opening the best model produces these relevant lines in the log 200 atoms, 188 bonds, 24 residues, 1 model selected alphafold contacts last-opened & /A toAtoms last-opened & /B distance 4.0 maxPae 5.0 Found 14 residue or atom pairs within distance 4 with pae <= 5 in the csv, the same model has these relevant columns: distance, max_pae, num_res1, num_res2, num_interface_res1, 4, 5, 246, 246, 20, num_interface_res2, num_interface_res_pairs, num_confident_pairs, 20, 42, 23, interface_res_num1, interface_res_num2 12 values 12 values I am struggling a bit to reconcile all these numbers. The 24 residues selected by chimera after opening are not anywhere else. I suppose these are #Res1 + #Res2 of the synthesis (and interface_res_num1 + interface_res_num2 in the csv)? Both the log synthesis and the csv report 23 as number of confident pairs, but the log message after opening best model says 14 residues (I assume these are those within the distance/pae constraint?) Why Confident pairs is not #Res1 + #Res2? I am also a little bit puzzled by the csv where I read num_interface_res_pairs = 42 and num_interface_res1, num_interface_res2 20 ( I was expecting either 21,21 for num_interface_res or 40 for num_interface_res_pairs. I attach the prediction I was using for diagnosing the problem. cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118

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Smooth MD script vs morph movie
by Alexander Lee 19 May '25

19 May '25

Dear ChimeraX developers, I have been wondering about the pros/cons between the 2 methods to smoothen a trajectory. If I provide a pdb and an nc trajectory file, I can use the smooth_md python script. If the trajectory originally has 100 frames , there will still be 100 frames after using the script. If I exported my trajectory into separate pdb models and morph between each of them, with the default of 50 frames created between each trajectory frame, there will be 5,001 frames after using the command. While importing many pdb's and morphing them takes longer than importing a trajectory and smoothing it, are there any benefits to using either one over the other? I remember seeing some post-production artifacts in smooth_md python script method like the hydrogens of a lysine being in an odd geometry briefly throughout the smoothed trajectory and am unsure if morph command would do the same. Regards, Alex

4 5

Foldseek
by Lynne Howell 15 May '25

15 May '25

Hi Is there an easy way to export the list of similar PDB structures, the % sequence ID, E-value etc that can be found using FOLDSEEK to an excel file. Thanks in advance L __________________________________________________________________________ P. Lynne Howell Canada Research Chair (2006-2020) Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children Professor, Department of Biochemistry, University of Toronto Office and Mailing address: Room 20-9-715 Peter Gilgan Centre for Research and Learning (PGCRL) 686 Bay St. Toronto ON M5G 0A4 Phone: 416-813-5378 (Internal 305378) Web page: https://lab.research.sickkids.ca/howell/ ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

3 2

Issues with the 1.9 release on macOS
by Zach Pearson 15 May '25

15 May '25

Hello everyone, I just came across a bug report on our ticket tracker regarding a missing SciPy symbol in the 1.9 release. The basic problem is that scipy has two macOS arm64 wheels up, and one is targeting a higher MACOSX_DEPLOYMENT_TARGET than the other. I think pip ignores this environment variable when selecting packages, so without qualifying that we need the lower deployment target version, pip selects the higher one on our build machines. I fixed this issue a few weeks ago for the 1.10 daily builds, before release candidates went out, so neither of those versions are affected. If you have an ARM Mac and your macOS is less than 14, you should use a daily build or release candidate. You can check your version of macOS by clicking on the Apple logo in the top left, then clicking “About This Mac”. Because we are so close to the 1.10 release, we do not plan to make a 1.9.1 release at this time. Our website will be updated to reflect this information shortly, along with a BlueSky announcement. Thank you, — Zach

1 0

Search in Command History
by Roden Deng Luo 15 May '25

15 May '25

Dear ChimeraX team, Not sure if there is one already, would be great to have a search box in the "Command History" window. Best, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

3 8

Atoms on the other side of the box
by Alexandra Zahradnikova 15 May '25

15 May '25

Dear all, I am trying to minimize the volume of my Gromacs simulation box and therefore in some frames of the trajectory, the atoms appear on the other side of the box. Is there a way to correct this problem in ChimeraX or do I need to resolve it in Gromacs? Best Sasha

2 2

Re: error with trying to open a saved chimera .cxs session
by arangarajan＠initialtx.com 14 May '25

14 May '25

i am trying to open a saved chimerax session saved with version 1.10.dev202504020144 (2025-04-02) using a newly installation of daily build dated 2022-12-30 and i am getting this error : unable to restore session : need to update bundle To restore session: update atomic bundle to ver 1.60.5 or newer ( have 1.43.4) please let me know how to fix this, thanks amith

1 1

Creating a virtual atom n Chimerax
by svle＠tiscali.it 14 May '25

14 May '25

HI, I want to draw a pseudobond between a real atom and the centroid of six carbon atoms. How it is possible define a virtual or pseudo atom with the coordinates of the centroid as one of the ends of the psudobond? Thanks. Saverio

2 2

Re: cif file from pdb-ihm, the integrative structure
by Yaowang Li 13 May '25

13 May '25

Agreed, but has information on proteins and AAs yaowang From: Tom Goddard <goddard(a)sonic.net> Sent: Wednesday, May 14, 2025 9:37 AM To: Yaowang Li <liyaowang2911(a)163.com> Subject: Re: [chimerax-users] cif file from pdb-ihm, the integrative structure Molstar is showing a tube through the beads of the coarse grain model. Tom On May 13, 2025, at 6:28 PM, Yaowang Li <liyaowang2911(a)163.com <mailto:liyaowang2911@163.com> > wrote: Hi Tom The chimerax indeed can open the file, and I succeeded in opening it yesterday, same as you showed. Although the molstar program displays the atomic model, it is hard to analyze. Yaowang <image001.png> From: Tom Goddard < <mailto:goddard@sonic.net> goddard(a)sonic.net> Sent: Wednesday, May 14, 2025 9:17 AM To: Yaowang Li < <mailto:liyaowang2911@163.com> liyaowang2911(a)163.com> Cc: Ben Webb < <mailto:ben@salilab.org> ben(a)salilab.org>; ChimeraX Users Help < <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] cif file from pdb-ihm, the integrative structure Hi Yaowang, You can open the 8zza IHM model in ChimeraX using open 8zza from pdbdev If you get tomorrow's ChimeraX 1.10 release candidate or daily build you could also use open 8zza from pdbihm I just added the database name "pdbihm" because pdbdev was the development name of the IHM repository and is being phased out. As Ben said 8zza is a coarse grain model. Although you will see spheres in the model they do not represent individual atoms. The may represent whole residues or large subunits. Tom IHM 8zza shown in ChimeraX: <image003.jpg> On May 13, 2025, at 6:08 PM, Yaowang Li < <mailto:liyaowang2911@163.com> liyaowang2911(a)163.com> wrote: Hi, Ben and Tom Thank you for your help. “Real structural model” is not the right expression; I mean an atomic model. There should be an atomic model that was generated from the coarse-grained model, and the molstar program on the IHM website can display its atomic model. So it will be perfect that I can open it in Chimerax for viewing this complex structure. In short, I just want to get the atomic model, not the coarse-grained model. Best wishes, Yaowang From: <mailto:chimerax-users-bounces+liyaowang2911=163.com@cgl.ucsf.edu> chimerax-users-bounces+liyaowang2911=163.com(a)cgl.ucsf.edu < <mailto:chimerax-users-bounces+liyaowang2911=163.com@cgl.ucsf.edu> chimerax-users-bounces+liyaowang2911=163.com(a)cgl.ucsf.edu> On Behalf Of Tom Goddard via ChimeraX-users Sent: Wednesday, May 14, 2025 2:01 AM To: <mailto:liyaowang2911@163.com> liyaowang2911(a)163.com Cc: <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users(a)cgl.ucsf.edu Subject: [chimerax-users] Re: cif file from pdb-ihm, the integrative structure Hi Yaowang, As Ben points out 8zza is an integrative hybrid model (IHM). Unfortunately the PDB gives ChimeraX a file with suffix ".cif" for 8zza that does not use the atomic model mmcif dictionary. ChimeraX would need to look at the contents of the file to decide that it is using the IHM dictionary. Currently ChimeraX identifies file types using the file suffix ".cif". That is why it says "No mmCIF models found" when you open this file. I've made a ChimeraX bug report to see if we can improve this <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17661> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17661 ChimeraX is able to read the IHM files. So if you download the 8zza.cif file and open it in ChimeraX with "open ~/Downloads/8zza.cif format ihm" it will show you the coarse grain model. Tom On May 13, 2025, at 8:58 AM, Ben Webb via ChimeraX-users < <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users(a)cgl.ucsf.edu> wrote: On 5/13/25 7:33 AM, Yaowang Li via ChimeraX-users wrote: I am trying to analyze the structures that were deposited in the <https://pdb-ihm.org/> https://pdb-ihm.org< <https://pdb-ihm.org/> https://pdb-ihm.org> Such as the entry: 8zza [...] which is a coarse-grained model, instead of a real structural model consisting of atom coordinates. Could anyone help me figure it out? 8zza is a model of the yeast nuclear pore complex. As you have observed, it is a coarse-grained model, not atomic. I'm not sure what you mean by "real structural model" but the resolution of the data in 2018 was such that only a coarse-grained structure was possible. That's what was deposited and that's what ChimeraX will show you. What are you trying to do? Ben -- <mailto:ben@salilab.org> ben(a)salilab.org <https://salilab.org/~ben/> https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle _______________________________________________ ChimeraX-users mailing list -- <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to <mailto:chimerax-users-leave@cgl.ucsf.edu> chimerax-users-leave(a)cgl.ucsf.edu Archives: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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Re: cif file from pdb-ihm, the integrative structure
by Tom Goddard 13 May '25

13 May '25

Hi Yaowang, You can open the 8zza IHM model in ChimeraX using open 8zza from pdbdev If you get tomorrow's ChimeraX 1.10 release candidate or daily build you could also use open 8zza from pdbihm I just added the database name "pdbihm" because pdbdev was the development name of the IHM repository and is being phased out. As Ben said 8zza is a coarse grain model. Although you will see spheres in the model they do not represent individual atoms. The may represent whole residues or large subunits. Tom IHM 8zza shown in ChimeraX: > On May 13, 2025, at 6:08 PM, Yaowang Li <liyaowang2911(a)163.com> wrote: > > Hi, Ben and Tom > > Thank you for your help. > > “Real structural model” is not the right expression; I mean an atomic model. There should be an atomic model that was generated from the coarse-grained model, and the molstar program on the IHM website can display its atomic model. So it will be perfect that I can open it in Chimerax for viewing this complex structure. > In short, I just want to get the atomic model, not the coarse-grained model. > > > Best wishes, > > Yaowang > > > > > From: chimerax-users-bounces+liyaowang2911=163.com(a)cgl.ucsf.edu <chimerax-users-bounces+liyaowang2911=163.com(a)cgl.ucsf.edu> On Behalf Of Tom Goddard via ChimeraX-users > Sent: Wednesday, May 14, 2025 2:01 AM > To: liyaowang2911(a)163.com > Cc: chimerax-users(a)cgl.ucsf.edu > Subject: [chimerax-users] Re: cif file from pdb-ihm, the integrative structure > > Hi Yaowang, > > As Ben points out 8zza is an integrative hybrid model (IHM). Unfortunately the PDB gives ChimeraX a file with suffix ".cif" for 8zza that does not use the atomic model mmcif dictionary. ChimeraX would need to look at the contents of the file to decide that it is using the IHM dictionary. Currently ChimeraX identifies file types using the file suffix ".cif". That is why it says "No mmCIF models found" when you open this file. I've made a ChimeraX bug report to see if we can improve this > > https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17661 > > ChimeraX is able to read the IHM files. So if you download the 8zza.cif file and open it in ChimeraX with "open ~/Downloads/8zza.cif format ihm" it will show you the coarse grain model. > > Tom > > > > >> On May 13, 2025, at 8:58 AM, Ben Webb via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> On 5/13/25 7:33 AM, Yaowang Li via ChimeraX-users wrote: >> >>> I am trying to analyze the structures that were deposited in the https://pdb-ihm.org <https://pdb-ihm.org/><https://pdb-ihm.org <https://pdb-ihm.org/>> >>> Such as the entry: 8zza [...] which is a coarse-grained model, >>> instead of a real structural model consisting of atom coordinates. >>> Could anyone help me figure it out? >> >> 8zza is a model of the yeast nuclear pore complex. As you have observed, >> it is a coarse-grained model, not atomic. I'm not sure what you mean by >> "real structural model" but the resolution of the data in 2018 was such >> that only a coarse-grained structure was possible. That's what was >> deposited and that's what ChimeraX will show you. What are you trying to do? >> >> Ben >> -- >> ben(a)salilab.org <mailto:ben@salilab.org> https://salilab.org/~ben/ >> "It is a capital mistake to theorize before one has data." >> - Sir Arthur Conan Doyle >> >> _______________________________________________ >> 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/ >>

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cif file from pdb-ihm, the integrative structure
by Yaowang Li 13 May '25

13 May '25

Dear all, I am trying to analyze the structures that were deposited in the https://pdb-ihm.org Such as the entry: 8zza The chimeraX (version 1.7 to 1.10) cannot read the CIF file with warning information warning No mmCIF models found. While it succeeded in opening it after adding the option format ihm. But they are the start model, restraints, and results, which is a coarse-grained model, instead of a real structural model consisting of atom coordinates. Could anyone help me figure it out? Best wishes

3 2

Re: Samsung 27" Odyssey 3D G90XF 4K 165Hz Monitor
by Tom Goddard 12 May '25

12 May '25

Hi Gökhan, The Samsung web page you referenced says the monitor is $3000, the same price as the Acer 27", and the Samsung also uses eye-tracking so it will probably only work for one person. The Sony and Acer displays both use OpenXR and eye tracking. This is good and bad. The good part is as you move your head to the side you see the side of the rendered objects. The bad is that most 3D applications do not support OpenXR unless they are VR applications. In contrast the Samsung uses side-by-side video input. That allows it to work with any 3D application that supports that common 3D format. Here's a description on Reddit talking about side-by-side input with the Samsung. (Unfortunately the Samsung manual does not say much.) https://www.reddit.com/r/Monitors/comments/1k8wnqa/samsung_odyssey_3d_g90xf… The drawback of the Samsung approach is that the monitor has no way to tell the application (e.g. ChimeraX) that your head has moved to the side (that is what OpenXR does). So when you move your head to the side you just see the same view direction of the 3D object only skewed. It's not a disaster, you can rotate the molecule if you want to see it from the side. The Samsung manual says only Windows is supported since they include some crappy software that runs on your Windows machine. I'm not sure if it is needed to handle side-by-side input. I'd love to see the Samsung display. It uses a 4K panel like the Sony and Acer. Like those displays it must be using a lenticular grating to send some pixels to your left eye and some to your right eye so the actual resolution in 3D is more like HD (2K). Still that is pretty good. (With old technology LCD shutter glasses you would get full 4K resolution since the two eye images use all screen pixels and just alternate in time.) If I had one of these displays I think I could make ChimeraX render full-screen side-by-side. Since you can't drag the ChimeraX graphics into a separate window I would try to add code to create a separate window and render to it as an option. My lab does not have money to spare to buy such a display (NIH funding problems), so don't expect to work on this. Tom > On May 7, 2025, at 11:19 PM, <tolung.bio(a)gmail.com> <tolung.bio(a)gmail.com> wrote: > > Hi Tom, > > This Samsung is less than half the price (27” for 2K USD) compared to the SONY in the review. > > Let me know if you can score one of these to test/develop for :) > > Cheers, > > Gökhan > > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, 8 May 2025 8:45 AM > To: tolung.bio(a)gmail.com > Cc: chimerax-users(a)cgl.ucsf.edu > Subject: Re: [chimerax-users] Samsung 27" Odyssey 3D G90XF 4K 165Hz Monitor > > Hi Gökhan, > > There is no ChimeraX capability to make the graphics pane full screen, so it will not work with a 3D display that wants full-screen side-by-side stereo format. The graphics pane is not a docked panel like the other ChimeraX tools. The ChimeraX main window is a Qt QMainWindow which treats that center area specially and it cannot be detached into a floating window. I'm not sure how hard it would be to allow that. > > We are also working on glasses-free eye-tracked 3D displays such as the Sony Spatial Reality and Acer SpatialLabs displays. They use OpenXR and only work on Windows and only with 1 person viewing, and costly $3000-5000, so they have some limitations. Here's a description of trying the Sony 3D display with ChimeraX > > https://www.rbvi.ucsf.edu/chimerax/data/sony3d-mar2025/sony3d.html > > Tom > > > >> On May 7, 2025, at 12:24 AM, Gokhan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hello ChimeraX team and users, >> >> Does ChimeraX support this monitor? >> >> https://www.samsung.com/au/monitors/gaming/odyssey-3d-g90xf-27-inch-165hz-u… >> >> I read a very positive review about this monitor and may consider buying one if it works with ChimeraX. >> >> The review says that this monitor needs a full-screen side-by-side output. Just as many of the sub-windows of ChimeraX can be docked and undocked (e.g., log, Models, etc.), is there way to ‘undock’ the main graphics window to make it full screen? Or, is there a way to display the graphics window on a secondary monitor as a full-screen output? >> >> Thanks, >> >> Gökhan >> >> _______________________________________________ >> 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/

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Samsung 27" Odyssey 3D G90XF 4K 165Hz Monitor
by tolung.bio＠gmail.com 07 May '25

07 May '25

Hello ChimeraX team and users, Does ChimeraX support this monitor? https://www.samsung.com/au/monitors/gaming/odyssey-3d-g90xf-27-inch-165hz-uh d-ls27fg900xexxy/?srsltid=AfmBOopLIkVAywsvNylPGVRL3wUoUJuBvUOPOz0metBjwLM2Nn xgmQVf I read a very positive review about this monitor and may consider buying one if it works with ChimeraX. The review says that this monitor needs a full-screen side-by-side output. Just as many of the sub-windows of ChimeraX can be docked and undocked (e.g., log, Models, etc.), is there way to undock the main graphics window to make it full screen? Or, is there a way to display the graphics window on a secondary monitor as a full-screen output? Thanks, Gökhan

2 1

including HET atoms in kvfinder calculations from ChimeraX
by Elaine Meng 07 May '25

07 May '25

> On May 7, 2025, at 2:01 AM, Mühleip, Alexander <alexander.muhleip(a)helsinki.fi> wrote: > > Hi Elaine, > > I am checking out the new kvfinder tool in ChimeraX. I was wondering if there is some way to prevent it from disregarding heteroatoms in the cavity search (in my eyes, e.g. excluding hemes is not helpful). I tried changing the selection syntax, but I think the pruning is taking place internally in kvfinder. > > Is there some way to interfere with it or make an ignore option (like the isolde implementation in chimerax has)? > > Best wishes, > Alex > > Alexander Mühleip > group leader > HiLIFE-Institute of Biotechnology > University of Helsinki > Finland > +358503282167 Hi Alex, Generally it's better to ask on the chimerax-users list, since as the resident non-programmer I often don't know implementation details. I CC'd the list in case others may also be interested in this topic. After consultation with the programmer who implemented this tool, we could not think of any current workaround. It uses the "main" category of atoms (definition in link below) which is automatically assigned cannot be manually overwritten. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#surfcats> However, we can consider this a request for enhancement that might be added in the future. Best wishes, 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

1 0

Options to align two models and calculate per-residue RMSD
by christian.steinmetzger＠imbim.uu.se 07 May '25

07 May '25

Dear ChimeraX users, I'm working with some different ribosome structures which I first want to align to a reference structure (as rigid bodies) and then calculate RMSD values with respect to the reference. The number of chains are the same between my structures and the reference, and the chain names + residue numbers are congruent as well. However, some of my chains have residues missing or added at the ends, have a small number of insertions (using insertion codes in the pdb file) or point mutations. What I have tried so far is: "matchmaker #2 to #1 pairing ss show true" "save file.defattr #2 attrName r:seq_rmsd modelIds false" (to store the resulting RMSD values for later use) which aligns based on CA for protein chains and C4' for RNA. I haven't given any explicit chain specification (each model has 56 chains). Am I correct to think that the RMSD values I get are based on a whole-structure rigid-body alignment that takes all chains into account simultaneously? Or does it align each chain in #2 to its matching chain in #1 individually? For the proteins I think per-residue CA-RMSD values are suitable for what I need, but for the RNA chains I would like to get per-residue all-atom RMSDs, not just C4'. Can this be achieved with matchmaker? I have also tried to use the align command like this: "align #2 toAtoms #1 each structure matchChainIds true matchNumbering true" which, to my understanding, would do the alignment not just based on CA/C4', but for all atoms. Is that correct? With this, what would be the best way to extract per-residue RMSD values? The "rmsd" command rightfully complains about unequal numbers of atoms between #1 and #2. Is there a way to implicitly select only the atoms that are congruent between #1 and #2? Kind regards, Christian

2 2

RMSD for all frames in a trajectory
by Alexandra Zahradnikova 07 May '25

07 May '25

Dear All, I am working with a trajectory of a tetramer. I would like to align the A chains in all frame of the trajectory and then calculate the rmsd of all chains in all frames relative to the respective chain of the first frame (i.e., align only chains A but calculate for all chains), and write the results to a text file. Is that possible? I can do a similar calculation with a script in old Chimera but don’t know how to do it in ChimeraX. I attach the zipped script for old Chimera. Best regards Sasha

2 6

Re: [Chimera-users] Add sequence logo to view
by Elaine Meng 05 May '25

05 May '25

Hi Alex, Sorry no we do not have a feature like that currently. (P.S. It may be better to use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here for ChimeraX questions.) In ChimeraX: The most similar thing I can thihk of is that for deep mutational scanning results it is possible to show labels with the scores of each residue type shown in a color-coded grid, but the "rub" is that you would have to open the data from a specific format we are using for these kinds of results: mutation scores format: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/mutationcsv.html> I could imagine that instead the sequence alignment profile at each position could be shown as a similar label. ChimeraX has a new profile-grid viewer for sequence alignments as an optional alternative to the standard viewer, <https://rbvi.ucsf.edu/chimerax/docs/user/tools/profilegrid.html> .... so such a label could essentially be the profile column rearranged into a squarish grid, as in the mutational scanning labels image above. However, that has not yet been discussed (nor implemented, of course). We do not have any sequence logo type of display. 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 May 5, 2025, at 7:35 AM, Alexander Lee via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear ChimeraX community, > > I have a consensus sequence + logo done in an outside program. Is there a way to superimpose this onto a crystal structure? When hovering my mouse over a residue in the structure viewer (or sequence viewer), I would like the logo to come up. Is there a similar feature available? > > Regards, > Alex > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

1 0

How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified?
by 1025049892＠qq.com 04 May '25

04 May '25

Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match? Thank you for your attention. I'm looking forward to your reply.

4 5

Morphing of structures with different chain numbers
by Enrico Martinez 01 May '25

01 May '25

Dear ChimeraX Users, I am trying to perform a morphing between two cryo-EM structures of the same complex, where one structure has twice the number of chains as the other (PDBs 3J9K and 8Y6Q). However, the larger structure causes an error during morphing. I have attempted to write a script that aligns the two structures and deletes the unmatched chains from the larger structure. Unfortunately, the script is not working as expected. from chimerax.core.commands import run def delete_unmatched_chains(session): # Get models #1 and #2 m1 = next((m for m in session.models if m.id == (1,)), None) m2 = next((m for m in session.models if m.id == (2,)), None) if m1 is None or m2 is None: session.logger.info("Model #1 or #2 not found.") return chains1 = {chain.chain_id for chain in m1.chains} chains2 = {chain.chain_id for chain in m2.chains} unmatched = chains1 - chains2 if unmatched: chain_ids = ",".join(unmatched) # Deleting unmatched chains run(session, f"delete /{chain_ids}") session.logger.info(f"Deleted chains: {', '.join(unmatched)}") else: session.logger.info("No unmatched chains found.") Could you please help me or alternatively propose another solution? Any suggestions would be greatly appreciated. Thank you in advance ! Enrico

3 6

Saving Images with Specific Dimensions and DPI in ChimeraX
by svle＠tiscali.it 30 Apr '25

30 Apr '25

Hi, In Chimera, when saving an image, it's possible to specify the output size in centimeters and the resolution in DPI. This feature is very useful for preparing figures for theses and publications. Is it possible to do the same in ChimeraX? I've read the documentation for the save command, but it's not entirely clear to me how to achieve this. Do you have any suggestions? Best regards, Saverio

2 3

Reproducing the Chimera Preset Publication 5 ( flat ribbon ) in ChimeraX
by svle＠tiscali.it 29 Apr '25

29 Apr '25

Hi, it is possible to reproduce the Chimera Preset Publication 5 ( flat ribbon ) in ChimeraX? What are the commands to use in order to have this type of preset in ChimeraX? This is a very nice preset. Thanks. Saverio

2 2

How to apply symmetry I to generate an icosahedron model
by 唐延婷 29 Apr '25

29 Apr '25

Hi doctor, when I open a map (ID 1) and a model (ID 2), the map is the whole icosahedron while the model is the protomer of the icosahedron. I want to apply symmetry I to generate an icosahedron model. I have rotated and translated the model into a reasonable position inside the map and then done a “fit in map” to get the initial placement for sym. Then I enter a command ''measure center #1''，center of mass xyz coordinates for map_sharp.mrc = (238.08, 238.08, 238.08)，enter another command ''sym #2 I,222 center 238.08, 238.08, 238.08'' I can see an icosahedron model fit in map. But when I save the icosahedron model.pdb, I found the icosahedron model actually is the model of the protomer. How can I apply symmetry I to generate a true icosahedron model, used for subsequent model refine in coot and real_space_refine in Phenix. Thank you very much. Best wishes! yanting 延婷 yanting.tang(a)mail.nankai.edu.cn

2 2

Issues with find cavities tool
by Marino, Claudia 28 Apr '25

28 Apr '25

Greetings, I am not sure why I recently cannot longer use the tool “find cavities”. My ChimeraX version is 1.9 and my MacOS is Sequoia 15.4. Please, find below the screenshot of the Error message. [cid:image001.png@01DBA7F0.57B85750] Thank you very much in advance for your help. Sincerely, Claudia.

3 11

reduce gridpoints on the cryoEM map (640 x 640 x 640 ) to ( 320 x 320 x 320)
by arangarajan＠initialtx.com 28 Apr '25

28 Apr '25

hi, i need to reduce the grid points to make the map work with MOE. I am not sure if this is possible in chimerax and i would appreciate some suggestions for creating a mrc file with reduced grid points. please let me know your thoughts. best amith

2 2

VR on ubuntu workstation
by arangarajan＠initialtx.com 24 Apr '25

24 Apr '25

Hi, i got steam VR installed but later found out that Oculus does not support linux. Is there a work around for using chimerax VR on latest ubuntu machine with oculus rift s headset? i can get other headset also if it will fit this purpose. thanks in advance, best amith

2 3

Effect of clearing ChimeraX cache from Mac?
by Radford, Katelyn M. (Kate) 23 Apr '25

23 Apr '25

Hi there! I'm in the throes of a memory-expensive project and my computer is running out of space. A little bit of googling led me to conclude that it would probably make sense for me to clear my system's cache, as my system files take up about a third of my disk space. ChimeraX cache files account for a substantial portion of that memory usage. As I make figures, I save .cxs files of each figure so that it's easy to go back and edit things that need to be changed. My ChimeraX also has a bunch of plug-ins installed (e.g. ISOLDE). I'm wondering: how much damage will I do to my installation and to my .cxs files if I delete the ChimeraX cache? System and software details: ChimeraX version: 1.9 MacOS: Ventura 13.0 Chip: Apple M2 Max Thank you all so much for the excellent work you do, Best wishes, Kate Kate Radford (she/they) PhD candidate, Biochemistry and Molecular Biophysics California Institute of Technology 1200 E California Blvd Pasadena, CA 91125

3 2

Re: cartoon not displaying in ChimeraX despite complete backbone
by amith ranga 22 Apr '25

22 Apr '25

Dear ChimeraX users, I'm unable to display the cartoon representation for pdb file in ChimeraX, even though the residues and atoms appear complete. The structure contains standard RNA residues (A, G, U) , Each residue includes all expected backbone atoms (P, O5', C5', C4', C3', O3', C1', O4', etc.) as well as complete base atoms and hydrogens. The file was written out from MOE software and I am not sure if this is an issue. Some tips on how to edit the pdb file would be helpful Thanks, amith

4 3

[ISOLDE] Handling Lys-Asp iso-peptide bonds and D-amino acids
by Yang Lee 22 Apr '25

22 Apr '25

Addressing this to Tristan, in all likelihood. Is there a way of parameterising KD isopeptide bonds and D-amino acids? Perhaps a secret three letter code I can rename the residues to make them play nice? Unfortunately, I'm trying to model a peptide that has both of these exotic elements. Cheers, Yang

3 15

Color of unrolled density maps
by Sen, Anindito 21 Apr '25

21 Apr '25

Dear ChimeraX Team, Is there a way we can keep/restore the color of the unrolled helical density maps ? Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

2 1

Re: Regarding peptide bond formation using chimeraX
by Tom Goddard 21 Apr '25

21 Apr '25

Hi Harpreet, I'm not sure how you deleted the bond. If you deleted a peptide bond with delete bonds /A:102@C /A:103@N or the equivalent menu Actions / Atoms and Bonds / delete then you could just recreate it with bond /A:102@C /A:103@N I'm not sure why you would do that since there is no need to delete a bond to move the two pieces of the structure. Instead maybe you split the protein into two separate models. In that case you can't simply add a bond between different models, instead you have to combine the models (e.g. command "combine #1,2"). You might get better answers on the ChimeraX mailing list, so I have CC'ed that list. Tom > On Apr 21, 2025, at 4:06 PM, Singh, Harpreet <harpreet.singh2(a)ucsf.edu> wrote: > > Dear Professor Goddard, > > I hope you are doing well. > > I am a Postdoctoral scholar from the Robert M. Stroud lab. I recently deleted a peptide bond from our protein structure to adjust the model for cryo-electron microscopy (cryo-EM) mapping. I am now attempting to reconstruct the peptide bond using the Build Structure tool. However, I am encountering an error message indicating that there are no chain-terminal carbons in the atoms. > > I would appreciate your assistance in resolving this issue. > > Thank you for your time and consideration. > > Best regards, > Harpreet Singh > Postdoctoral Fellow, Stroud lab > Department of Biochemistry and Biophysics > UCSF

1 0

Color of unrolled density maps
by Eric Pettersen 21 Apr '25

21 Apr '25

The original was sent to the wrong address (chimerax-users-bounces)… Dear ChimeraX Team, Is there a way we can keep/restore the color of the unrolled helical density maps ? Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

1 0

Quality of sphere representation
by Enrico Martinez 21 Apr '25

21 Apr '25

Dear ChimeraX users! I wonder if there is a special option which would allow me to increase the quality of sphere representation (which are displayed by default for big cryo-em protein complexes loaded in chimeraX) in the same way as it can be done for surfaces using gridSpacing ? Many thanks in advance Enrico

2 1

Concatenating trajectories in ChimeraX
by Alexandra Zahradnikova 20 Apr '25

20 Apr '25

Dear All, I am new in molecular simulation and not very much experienced with ChimeraX. I did not find an easy way to concatenate trajectories (in my case, .xtc files from gromacs). Any suggestions would be welcome. Thanks in advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796

4 4

seeking help
by 张可依 20 Apr '25

20 Apr '25

Dear chimerax, hello, I would like to know if chimerax can draw protein secondary structure topology maps, and if so, can you tell me how to do the drawing?Something like the picture below Your help is of great importance to me and I, with my most sincere hope, look forward to your reply. All the best keyi [cid:494273c0-4f59-4f19-bd4d-5ac989d92136]

2 1

Question about morphing trajectory
by Enrico Martinez 20 Apr '25

20 Apr '25

Dear ChimeraX users ! Using the following command, I generated a 200-frame trajectory that morphs through three selected conformations: morph #2,3,4 core 0.1 frames 200 wrap f rate linear Would it be possible to have the morphing trajectory end on the starting structure (so the full transition path ends on the first snapshot in the morphin trajectory), so that I can create a smoothly looped GIF animation? Many thanks in advance ! Enrico

2 3

Combine PDBs in models instead of changing chainId ?
by Vincent CHAPTAL 17 Apr '25

17 Apr '25

Hi, using "combine #1-3" with 3 models having chain A only, it changes the chain Id to B and C for models #2-3, as described in the doc. Is it possible to combine PDBs as a multimodel PDB, seperated by MODEL keywords in the PDB file? Thank you. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

2 2

Request for Academic Use Confirmation Document – ChimeraX Demonstration Class
by Coordenação Farmácia_ 17 Apr '25

17 Apr '25

Dear UCSF ChimeraX Team, My name is Emanuell Santos, I am a pharmacist, Ph.D. in Drug Development Technology, and the coordinator of the Pharmacy program at a private Brazilian college. I also teach Medicinal Chemistry for both Pharmacy and Medical students. I am reaching out to respectfully request your support in including UCSF ChimeraX in a practical session of my Medicinal Chemistry course. The goal is to introduce students to molecular modeling approaches through a demonstrative class where they can also explore some of the software’s functionalities directly. This initiative is aligned with national educational guidelines from our Ministry of Education, which emphasize the inclusion of innovative and technological methodologies in undergraduate teaching. I plan to use the free academic version of ChimeraX solely for educational purposes and without any commercial intent. I kindly ask whether it would be possible to obtain a brief statement or document from UCSF (even if generic) confirming that such use falls within the allowed academic scope. This would be helpful in documenting compliance with institutional and governmental regulations. I greatly appreciate your attention and support, and I look forward to your response. Warm regards, Emanuell Santos Coordinator – Pharmacy Program FACENE/RN -- Prof. Dr. Emanuell dos Santos Silva *Coordenação de Farmácia - FACENE/RN* Por favor, confirmar o recebimento deste e-mail.

2 2

Re: Unable to display GLY in Chimera
by Elaine Meng 15 Apr '25

15 Apr '25

Hello Qiang, I guess you are talking about ChimeraX, not Chimera. They are two different programs. You can just hide all the other glycine atoms. This is not a bug. The suppressBackboneDisplay *allows* you to show both cartoon and backbone atoms at the same time, but you can still hide all the atoms you don't want to show. cartoon suppress false hide :gly show :93 I hope this helps, 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 Apr 15, 2025, at 9:16 AM, Qiang Liu <liu01301(a)umn.edu> wrote: > > Hi Chimera > > I am a Chimera user and unable to display single GLY as stick and cartoon. I found commend "suppressBackboneDisplay", however this command makes all the GLYs displayed as stick and cartoon. I only want to display GLY93 as stick and cartoon and could you please let me know how to make it happen? Thank you. > > Qiang. > > -- > Qiang Liu, Aldrich Lab > Medicinal Chemistry, College of Pharmacy > University of Minnesota > > 8-115 Weaver-Densford Hall > 308 Harvard St SE > Minneapolis, MN 55455

1 0

How to save the PAE plot as an image in ChimeraX using command line ?
by picasa1983＠gmail.com 14 Apr '25

14 Apr '25

Hi, I am using ChimeraX to visualize AlphaFold models and display the PAE plot with: alphafold pae #1 /path/to/confidences.json I would like to save only the PAE plot (not the 3D structure view) as a .png or .pdf file. What is the correct command to save the PAE plot image in ChimeraX? Thanks a lot!

4 5

B-strand arrowheads
by Lee Bardwell 13 Apr '25

13 Apr '25

Hi Elaine and team, I’ve noticed an issue that sometimes happens when I change some residues to a beta strand, e.g. setattr /A:149-151 res ss_type 1. Sometimes an arrowhead is not placed at the end of the strand. Am I doing something wrong? Or is there a way to force an arrowhead? Thank you! _________________________________ Lee Bardwell, Ph.D. Professor and Vice-Chair, Dept. of Developmental & Cell Biology Charlie Dunlop School of Biological Sciences University of California, Irvine __________________________________

2 1

Removing distance label from distance monitor
by Elaine Meng 13 Apr '25

13 Apr '25

> On Apr 12, 2025, at 2:01 AM, Yu GUO 郭宇 <guoyu60(a)westlake.edu.cn> wrote: > > Dear UCSF Chimera(X) team, > > I am using ChimeraX 1.9. As shown in the picture below, I labelled the atomic distance 1.52 A. I want to retain the dashed line but to remove the number "1.52". How can I realize this? > > Thank you! Next time, please send your questions to chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd here) --- if you send it to me only it may not get answered. I changed the subject line to describe the current topic. If you have distance monitors displayed there are several ways to hide the number labels. One way is command ~label pseudobonds If you just wanted to draw dashed lines and not show any distances, it may be a waste of time to use the "distance" command or Distances tool. Instead you can just use command "pbond" available in ChimeraX 1.8 or later, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/pbond.html> I hope this helps, 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

1 0

SwissDock dock4 in ChimeraX not recognized
by Nadia Elghobashi-Meinhardt 12 Apr '25

12 Apr '25

Dear all, When I try to open a SwissDock .dock4 file in ChimeraX, the swissdock format is not recognized. The chimeraX forum advises using "format swissdock" when opening the file, but I am getting 'invalid "format" argument'. Does anybody have a solution to this problem? Many thanks, Nadia -- Dr. Nadia Elghobashi-Meinhardt <https://people.ucd.ie/nadia.elghobashi-meinhardt> Assistant Professor (Ad Astra Fellow) School of Chemistry University College Dublin Belfield, Dublin 4, Ireland Tel: +353 1 716 2044

2 2

Features of Chimera X
by Ogbuehi, Ulochukwu 09 Apr '25

09 Apr '25

Greetings, I had a couple questions about the usability of ChimeraX. 1. Is there a way I can insert a variant sequence, and it produce the structure that I would like modelled. Or would I have to strictly use a generated PDB file of my variant for ChimeraX to model the structure. 1. I was able to upload and model my WT protein structure in ChimeraX from the AlphaFold WT PDB file I downloaded; however, I am not able to generate a PDB file for my variants and would like to know if there is a feature that allows me to insert my aa sequence into ChimeraX to model the variant structure? Or maybe even a feature that allows you to generate a PDB file using an aa sequence. 1. Would I need the WT PDB file to be uploaded and modelled in ChimeraX first prior to adding in my aa sequence, granted that I am even able to insert an aa sequence directly into ChimeraX? Kindest Regards, Bethel Ogbuehi

2 1

Refinement in ISOLDE failing
by Firdous Tarique 09 Apr '25

09 Apr '25

Dear everyone I am trying to refine my protein using ISOLDE in ChimeraX which is failing with the following error. "At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been parameterised. Launching the unparameterised residue widget to help sort this out." The protein contains two heme molecules and Ca ions which obviously is the reason why it is failing. Once these molecules are deleted it runs fine. My question is how to add that specific MD force field for these molecules in order to run the ISOLDE in ChimeraX. Any input would be appreciated. Firdous

1 1

Re: issues with writing models as pdb files
by arangarajan＠initialtx.com 08 Apr '25

08 Apr '25

Hi everyone, I noticed that sometimes when i write pdb of one model or a selection , it does not open in other programs.( MOE,Pymol). One of the errors i noticed recently was that th pdb file was written as a multi model pdb file ( each of the 70 residues in the protein were separate models) , i cleaned it using notepad++ by removing the model lines and it was opening correctly. i was told that it might be related to using split command. i use split often and it might be the case. can some one please explain how using split can lead to this? and if so what is best way to fix it? should i perhaps run some version of combine command on the model prior to writing it out as pdb file. thanks again, best amith

3 4

Can't open ChimeraX on my Win11
by kangkang042＠126.com 07 Apr '25

07 Apr '25

About 2 weeks ago, it worked fine. Today when I click the ChimeraX startup, nothing happened. I reinstalled the lastest version v1.9, nothing changed. Run ChimeraX-console.exe in cmd, it shows these information: NOTE: Traceback (most recent call last): File "<frozen runpy>", line 198, in _run_module_as_main File "<frozen runpy>", line 88, in _run_code File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\core\\__main__.py", line 1217, in <module> exit_code = init(sys.argv) ^^^^^^^^^^^^^^ File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\core\\__main__.py", line 653, in init sess = session.Session( ^^^^^^^^^^^^^^^^ File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\core\session.py", line 551, in __init__ from chimerax.graphics.gsession import register_graphics_session_save File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\graphics\\__init__.py", line 37, in <module> import chimerax.arrays File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\arrays\\__init__.py", line 24, in <module> from ._pyarrays import get_lib, get_include, load_libarrays File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\arrays\\_pyarrays.py", line 40, in <module> from . import _arrays ImportError: DLL load failed while importing _arrays: 找不到指定的模块。 BUG: ImportError: DLL load failed while importing _arrays: 找不到指定的模块。 File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\arrays\\_pyarrays.py", line 40, in from . import _arrays _See log for complete Python traceback._ My PC: Win11 Pro Workstation 26100.3624

2 3

How to browse inspect ligands?
by Guillaume Gaullier 04 Apr '25

04 Apr '25

Hello ChimeraX team, These days I look a lot a structures of photosystems, which contain large numbers of ligands: chlorophylls, carotenoids, etc. each by the dozens, adding up easily to more than 100 ligands. Is there any tool to browse through all ligands systematically? Ideally something similar to the sequence viewer, but for ligands. Or a way to generate a list with chain IDs and "residue" numbers reported, and clicking rows in the list would select the corresponding ligand. I looked for something like this, but couldn't find anything. Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

4 5

saving cloned structures on chimerax inquiry
by Joel Gallardo 03 Apr '25

03 Apr '25

to whom it may concern, i have mapped out a mol2file onto a structure found in a .mrc file. and then i ran this command to multiply the mol2 structure: sym #2 h,0.357979,132.83196,72,-40 coord #1 center 119.04,119.04,119.04 it multiplied it as intended which is good but now i want to save those multiplied mol2 files into a sperate mol2 files. i tried this command: save multiplied_structures.mol2 format mol2 models #2 but this only saves a single mol2 structure into the new mol2 file. i want all 72 molecules in one mol2 file. can you give me some advice as to how i may be able to do this? my ultimate goal is to take that mol2 file and do an md simulation. Best, Joel Gallardo (Graduate student in chemistry)

2 3

Keeping track of H-bonds in trajectories
by Alexandra Zahradnikova 02 Apr '25

02 Apr '25

Hello, I am new in molecular simulation and not very much experienced with ChimeraX. Is there a way to keep track of H-bonds between two specific residues (they can form one or more H-bonds) during the course of the trajectories (in my case, .xtc files from gromacs)? Thanks in advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796

2 2

Create new attributes
by javisanchezdelrio＠gmail.com 31 Mar '25

31 Mar '25

Hello! I am trying to create a new attribute in a cif file called align_rmsd. For the example, assume I want all atoms to have this attribute equal to 5. For this, I am opening the file in ChimeraX and applying the following command: setattr atoms align_rmsd 5.0 create true type float With the following result: Assigning align_rmsd attribute to 145 items However, when I do "save new.cif" I don't see any new attribute in the loop _atom_site.align_rmsd nor any value equal to 5. How can I store this values in a new cif file so that I see the values equal to 5? Thank you in advance! Javier

3 2

Downloading ISOLDE
by Ashley Gutierrez 28 Mar '25

28 Mar '25

Hi there, I am having a bit trouble downloading the ISOLDE bundle. While I can download the .whl to my computer, it will not open in ChimeraX. Please let me know if I am missing some commands in between, I am new to this system. Thank you (:

2 1

Ligand flying movie in chimeraX
by Matzov Donna 26 Mar '25

26 Mar '25

Hello, I'm trying to create a movie in Chimerax similar to the "Ligand flying into unbound conformation" that was in the old Chimera movie tutorials (https://www.cgl.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html) I tried using the "reset" command, but it seems like it doesn't exist in ChimeraX. Is there a command that replaces it? Alternatively, I would be happy for any suggestion for how to get an effect similar to the flying ligand in ChimeraX. Thanks, Donna 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>

2 2

Change location of .cache/ChimeraX ?
by James Vincent 24 Mar '25

24 Mar '25

Hello ChimeraX Devs/Users, Is there a way to specify the location of the .cache/ChimeraX directory? As far as I can tell it is always $HOME/.cache/ChimeraX (on Linux machines). I see no options or configs to change this. We are installing ChimeraX on a multiuser system and would like to add a plugin/ bundle to be available for all users ( ChimeraX_ScipionExtensions 1.3). Perhaps I missed this in the documentation, but is there a standard way to add plugins so that they are available for all users? Thanks, Jim

2 1

Force display of helix with setattr
by Kevin M Jude 24 Mar '25

24 Mar '25

For some reason the selected residues in this image are not displayed as a helix in ChimeraX. I think the command to force it woud be ‘setattr sel res ss_type 1’, but nothing changes (the log says “Assigning ss_type attribute to 2 items”). Same result if I try ‘setattr sel res is_helix 1’. Can anybody please set me straight (and my cartoons helical)? Using ChimeraX 1.9 for OS X. Thanks for any help. [cid:image001.png@01DB9CD2.E2CD6B60] -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

2 2

Inactivate models
by Burgers, Peter 24 Mar '25

24 Mar '25

Dear team, Classic Chimera had a command to turn off specific models, allowing manipulation of the other model(s). What is the command for that in ChimeraX? ChatGPT gave as answer “model toggle off #1” but that appears to be wrong. Thank you, Peter ---------------------------------- Peter M.J. Burgers Marvin Brennecke Professor of Biological Chemistry Department of Biochemistry and Molecular Biophysics Washington University School of Medicine BOX 8231 660 South Euclid Saint Louis, MO 63110 E-Mail: burgers(a)wustl.edu<applewebdata://1B940EF6-0122-4328-902B-DCB358A99492/burgers@biochem.wustl.edu> PH (314) 362-3872 (office) 286-2554 (lab) FAX (314) 362-7183 http://biochem.wustl.edu/~burgersw3/ ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 5

Problem with setting up Modeller
by Miloslav Radoslavov 24 Mar '25

24 Mar '25

Greetings, I encountered an issue when attempting to utilize the "Model Loops" option. After installing Modeller and specifying the path to it, Chimera X did not prompt me to input my activation key. Instead, it indicated that no Modeller key was provided. Also the console command "modeller licenseKey ...." does not seem to work. Could someone please assist me in resolving this issue? Is there an alternative method to input my key? Thank you in advance, M. Radoslavov

2 1

Error using matchmaker
by javisanchezdelrio＠gmail.com 23 Mar '25

23 Mar '25

Hello, I am trying to use matchmaker command (matchmaker #1 to #2 showAlignment true) with two cif files I've obtained from Kihara and Modelangelo. The problem is that, once I try to use the matchmaker command, I obtain the following error: "No matrix compatible with both reference structure and all match structures" and I don't know what is failing. Is it because the two structures are too different from each other? I hope I can get more information about this error message Thank you in advance, Javier

4 5

ChimeraX 1.9 dark theme
by jinlun_kylian zhang 22 Mar '25

22 Mar '25

Hi chimeraX developers, I've used chimeraX for a long time and today I upgraded it to 1.9, But i can't help to notice the chimeraX's theme has been set to dark rather light/white theme in 1.8. Can you please assist me to modify this dark theme back to white? I am more used to that. [image: image.png] Best, kylian

2 1

Switch Dark theme of chimeraX1.9 back to white theme
by hytxnt123＠gmail.com 22 Mar '25

22 Mar '25

Hi, I just upgrade my chimeraX to v1.9 but I dont really fit in the dark theme. Can anyone help me to switch back to the white theme just like v1.8?

2 1

Advice on Meeting settings
by Edwin Kyi 20 Mar '25

20 Mar '25

Hello, We have been experimenting with the Meeting command in VR and are seeing some real uses for guided teaching sessions. We're looking for ways to finesse set up for these sessions and I wonder if you could help with some technical questions we have: 1. What main optimisations of the settings would you recommend for smoother running in VR? 2. Is there an easy way to toggle off all people's interactions with the model with one command except the host? 3. Same as Q2, is there an easier way to toggle off people's hands unless they are the ones asking a question? 4. Can the VR ava VR be resized ie. smaller? Kind regards Edd Edwin Kyi Multimedia Learning Experiences Developer (CTL) Join the VR Society, see: https://www.guildofstudents.com/organisation/ubvr/ +44 121 415 9049 University of Birmingham Collaborative Teaching Laboratory (CTL) Edgbaston Birmingham B15 2TT www.birmingham.ac.uk<http://www.birmingham.ac.uk/> Twitter<https://twitter.com/unibirmingham> / Instagram<https://www.instagram.com/unibirmingham/> / Facebook<https://www.facebook.com/unibirmingham> / LinkedIn<https://www.linkedin.com/school/university-of-birmingham/> [University of Birmingham logo.]<https://www.birmingham.ac.uk/index.aspx> For the most up-to-date-information, visit: www.birmingham.ac.uk<http://www.birmingham.ac.uk/>

3 2

ChimeraX not communicating with GPU
by #TAN YONG JUN EDDIE# 20 Mar '25

20 Mar '25

Dear Developers, Hope this email finds you well. I have encounter an issue regarding the GPU driver usage for chimeraX. The issue is that the model and density movement is very choppy at step size 1, with a box size of 400. Here are some information on the software that I am using. Downloaded Software: Ubuntu 22.04 (Linux) ucsf-chimerax_1.9ubuntu22.04_amd64.deb<https://www.cgl.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?file=1.9/u…> This is my current nvidia driver and cuda version: NVIDIA-SMI 560.35.05 Driver Version: 560.35.05 CUDA Version: 12.6 It came to my attention that it is not utilising GPU upon running "graphics driver" on chimeraX, which outputs: graphics driver OpenGL version: 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3 OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits) OpenGL vendor: Mesa additionally, it is not showing up under nvidia-smi when I am running the program. Is there any solutions to this issue? Thank you in advance. Regards, Eddie

2 1

Protein-Protein Interaction Prediction
by Charity Conlin 19 Mar '25

19 Mar '25

Hello, I am trying to use ChimeraX to predict the interaction of 2 proteins using alphafold: Beta-Lactoglobulin and Lactoferrin. I have plugged the 2 protein sequences into the alphafold tool to try to predict the interaction, but I get a failure code in google colab. I am wondering how I can get around this? I think it is because the wrong versions of numpy and colab are installed during the program. Thanks, Charity [cid:b73a7660-3878-48cf-87d5-ddcd6ab388c2]

2 4

Poor performance on Ubuntu w/ discrete graphics vs basic b laptop
by ben 19 Mar '25

19 Mar '25

I'm looking for trouble shooting tips on poor graphics performance on linux. I have read through the FAQ's and done a basic search of the chimera list. Observed: Symptom: Prohibitively slow rendering when just rotating a map, especially if a model is loaded as well. When using Isolde (and presumably anything with clipper) performance is more "normal" as only a small portion of the map is displayed. System: This is observed on Ubuntu distros (both 20.04 22.04) with their respective Chimerax packages, tested versions 1.6.1 and 1.9. Nvidia drivers installed via the cuda toolkit (535.183.01 CUDA Version: 12.2 ) GPUs are either rtx 3090 or 4090s Point of reference: Performance is compared to my relatively very underpowered Windows thinkpad w/o discreet graphics. Thanks for any pointers to resources! Ben Sent with [Proton Mail](https://proton.me/mail/home) secure email.

2 3

Issue with crashing after mac upgrade to Sequoia
by Lee, Juliet A. 19 Mar '25

19 Mar '25

Hello! I recently updated my Mac (M2) to Sequoia 15.3.2, and I have had a specific issue in ChimeraX since then (though I cannot be 100% positive the two things are linked). Basically - whenever I try to save (anything) in ChimeraX, the application stops responding and I have to quit it. I downloaded the newest version 1.9 of ChimeraX as well as the daily build version - but this problem persists. I read about issues with the graphics driver - but these seem to be limited to Intel chips... Hoping you might have some insight as to why this is occurring, thank you!!! Sincerely, Juliet

3 7

secondary structures
by Bajaj, Ruchika 18 Mar '25

18 Mar '25

Hi I want to determine helices and betasheet and their ranges in a structure. Could you please let me know which command and its usage I can use to get it. Please let me know. Thanks !! Regards Ruchika

2 2

Request for Review of Figure 12 instructions
by Zeenat Bashir 18 Mar '25

18 Mar '25

Dear ChimeraX Developers, I hope this email finds you well! I am developing a hands-on module for students using ChimeraX, and I want to express my appreciation for this powerful and beautifully designed tool. I would like to request a review of the instructions on page 11 for generating Figure 12. I have successfully generated this figure before and am now attempting to do so using ChimeraX. However, I would appreciate your guidance to ensure the accuracy and clarity of the instructions (I have highlighted it in red) Thank you for your time and support! I look forward to your feedback. Best Regards, Zeenat -- *Dr. Zeenat Bashir* *Senior Lecturer* *Biotechnology Lab Coordinator* *Department of Chemical and Biomolecular Engineering* *University of Pennsylvania* *310 Towne Building* *220 S. 33rd Street* *Philadelphia, 19104 -6393* bashirz(a)seas.upenn.edu

1 1

sybyl vs amber atom types in ChimeraX
by laurene.jacquot 17 Mar '25

17 Mar '25

Dear ChimeraX community, I hope this message finds you well. I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein. Chimera does not manage to parametrize my protein at all, which is why I switched to ChimeraX. ChimeraX does manage to generate a mol2 file, but it writes sybyl atom types. Despite looking on forums, I have not found a feature like in Chimera to write amber atom types instead. I was wondering if such a feature exists in ChimeraX ? Thanks in advance, Best, Laurène Jacquot PSL University, ChimieParisTech

4 3

Automating the process of data generation via ChimeraX
by mishra.ananya.163＠gmail.com 17 Mar '25

17 Mar '25

Dear Sir/Madam, I am an undergraduate student working on a project and I am trying to generate values for the solvent accessible surface area, mean molecular lipophilicity potential and mean surface electrostatic potential for a dataset involving protein 3D structures (in pdb format). We also plan to introduce point mutations via ChimeraX using the swapaa command and measure the same values for the mutated proteins. As such, we were wondering if there is a way to automate this process of generating the values for each protein, without having to manually do it. We tried to test out some code to see if it is possible to run a python file in ChimeraX. This was the code we wrote: import chimerax import csv import os from chimerax.core.commands import run run(session, "open" + r'C:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb') run(session, "color red") run("surf") However, we received this error message: openC:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb Traceback (most recent call last): File "C:\Users\anany\Downloads\Research\Test_PDB_Passenger\test_import.py", line 6, in <module> run(session, "open" + r'C:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb') File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3156, in run raise UserError(self._error) chimerax.core.errors.UserError: Unknown command: openC:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb Error opening python file C:\Users\anany\Downloads\Research\Test_PDB_Passenger\test_import.py We would appreciate your kind assistance! Thank you!

4 6

Feature request alphafold: return selection when dragging in PAE plot
by Vorländer,Matthias Kopano 17 Mar '25

17 Mar '25

Dear ChimeraX team, I love the alphafold tools in ChimeraX, and have a small suggestion to make it even better. Currently, when associating a PAE plot from a JSON file, you can drag the mouse in the PAE plot to color the corresponding residues (magenta and lime), but the residues do not become selected (although the color command gets printed in the log). I think it would be helpful if there was an option (or default behavior) to return a selection in addition, so that the selected region could be saved as a named selection, the display style changed ect… Or am I missing anything? Many thanks in advance, Matthias

2 1

Fwd: Re: coloring surfaces by electrostatic potential from different atoms
by Boaz Shaanan 16 Mar '25

16 Mar '25

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel ---------- Forwarded message ---------- From: Boaz Shaanan <bshaanan(a)bgu.ac.il> Date: Mar 16, 2025 18:32 Subject: Re: coloring surfaces by electrostatic potential from different atoms To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Cc: Hi Elaine, Thank you so much for the prompt an informative reply. The points about the offset and dielectric are very relevant. In fact, in a quick test that I ran before posing the question I noticed that the coloring of the electrostatic potential on the cofactor was quie dim, probably because of those parameters. I'll also look into the MOLE and pseudo atom coloring. Thanks again. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Mar 16, 2025 17:50, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: Hi Boaz, I changed the subject line to try to describe this topic. We aren't the APBS experts but my understanding is that yes, it will generate potential at all points in the rectangular grid, based on the input atoms charges and locations. There will of course be potential values even at grid points where there are no atoms, since electrostatics are fairly long-range interactions. However, the magnitude will depend on what dielectric parameters you have given the calculation. Whether it makes sense: that is somewhat up to your scientific judgement. In my opinion, yes, it makes sense, but you have to think carefully about the "offset" you use to color the cofactor surface. Normally when the surface is on the same atoms that produced the charge, you use a positive offset (default 1.4) to color by values projected that distance outward from the surface, to represent what other outside atoms might "see". If you are coloring a surface of the cofactor atoms to try to understand the potential from the protein that the cofactor "sees," you should consider instead using a negative (say -1.4) or zero offset. The offset is adjustable in the Surface Color dialog options and the "color electrostatic" command: <https://protect.checkpoint.com/v2/r02/___https://rbvi.ucsf.edu/chimerax/doc…> <https://protect.checkpoint.com/v2/r02/___https://rbvi.ucsf.edu/chimerax/doc…> Note that an analogous procedure could be done in ChimeraX with the Coulombic electrostatic potential. For example, see the MOLE channels tutorial where we calculate the Coulombic potential from the protein but then show a surface on pseudoatoms representing a channel calculated by MOLEonline, and then color that channel surface by the protein potential. <https://protect.checkpoint.com/v2/r02/___https://www.rbvi.ucsf.edu/chimerax…> I hope this helps, 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 Mar 15, 2025, at 10:30 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi friends, > On a related issue: > I'd like to explore the effect of replacing Val by Asp on the electrostatic potential 'seen' by a cofactor which is completely surrounded by the protein (this is relevant for understanding the change in reaction rate following such replacement). I thought of the following steps: > > • Omit the cofactor from the pdb2pqr and APBS. > • Read into chimerax the complete pdb (i.e. including the cofactor). > • Generate the surfaces (protein and cofactor). > • Render the electrostatic potential on both surfaces (i.e. Cofactor and protein surrounding it) and probe the potential on the cofactor. > • Does it make sense? Does APBS generate potential values in the void where the cofactor resides even though it wasn't present in the input pdb2pqr (i.e. in the void where the cofactor resides). > I'd appreciate your input. > Boaz >

1 0

Re: ChimeraX-users Digest, Vol 99, Issue 28
by Boaz Shaanan 16 Mar '25

16 Mar '25

Hi friends, On a related issue: I'd like to explore the effect of replacing Val by Asp on the electrostatic potential 'seen' by a cofactor which is completely surrounded by the protein (this is relevant for understanding the change in reaction rate following such replacement). I thought of the following steps: 1. Omit the cofactor from the pdb2pqr and APBS. 2. Read into chimerax the complete pdb (i.e. including the cofactor). 3. Generate the surfaces (protein and cofactor). 4. Render the electrostatic potential on both surfaces (i.e. Cofactor and protein surrounding it) and probe the potential on the cofactor. 5. Does it make sense? Does APBS generate potential values in the void where the cofactor resides even though it wasn't present in the input pdb2pqr (i.e. in the void where the cofactor resides). I'd appreciate your input. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il ________________________________ From: chimerax-users-request(a)cgl.ucsf.edu <chimerax-users-request(a)cgl.ucsf.edu> Sent: Friday, 14 March 2025 21:00 To: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> Subject: ChimeraX-users Digest, Vol 99, Issue 28 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. sybyl vs amber atom types in ChimeraX (laurene.jacquot) 2. Re: sybyl vs amber atom types in ChimeraX (David A Case) ---------------------------------------------------------------------- Message: 1 Date: Fri, 14 Mar 2025 09:47:39 +0000 From: "laurene.jacquot" <laurene.jacquot(a)etu.chimieparistech.psl.eu> Subject: [chimerax-users] sybyl vs amber atom types in ChimeraX To: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> Message-ID: <MR1P264MB2612AFE1D7D6BEF80D0B069A92D22(a)MR1P264MB2612.FRA P264.PROD.OUTLOOK.COM> Content-Type: multipart/alternative; boundary="_000_MR1P264MB2612AF E1D7D6BEF80D0B069A92D22MR1P264MB2612FRAP_" Dear ChimeraX community, I hope this message finds you well. I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein. Chimera does not manage to parametrize my protein at all, which is why I switched to ChimeraX. ChimeraX does manage to generate a mol2 file, but it writes sybyl atom types. Despite looking on forums, I have not found a feature like in Chimera to write amber atom types instead. I was wondering if such a feature exists in ChimeraX ? Thanks in advance, Best, Laurène Jacquot PSL University, ChimieParisTech -------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: not available Type: text/html Size: 3823 bytes Desc: not available ------------------------------ Message: 2 Date: Fri, 14 Mar 2025 09:08:36 -0600 From: David A Case <dacase1(a)gmail.com> Subject: [chimerax-users] Re: sybyl vs amber atom types in ChimeraX To: "laurene.jacquot" <laurene.jacquot(a)etu.chimieparistech.psl.eu>, chimerax-users(a)cgl.ucsf.edu Message-ID: <20250314150836.x2iskz4ufcygpsqt(a)pop-os.localdomain> Content-Type: text/plain; charset=us-ascii; format=flowed On Fri, Mar 14, 2025, laurene.jacquot via ChimeraX-users wrote: > >I am a master student currently working on a project where I need to >generate a mol2 file with amber atom types for a protein. I don't have a ChimeraX answer here, but rather a question: why do you need a protein mol2 file with Amber atom types? Amber workflows would not create a mol2 file for an entire protein; but of course, you may need such a file for some other purpose. If so, we may be able to find some Amber tools that does this (or avoids needing it), if the ChimeraX folks themselves don't have a solution. ....dave case ------------------------------ Subject: Digest Footer _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu Archives: https://protect.checkpoint.com/v2/r02/___https://mail.cgl.ucsf.edu/mailman/… ------------------------------ End of ChimeraX-users Digest, Vol 99, Issue 28 **********************************************

2 1

Ubuntu 24 ARM Daily Builds
by Zach Pearson 15 Mar '25

15 Mar '25

ARM daily builds for Ubuntu 24.04 are now available. — Zach

1 0

Feature suggestion: cubic interpolation for image display
by Ricardo Righetto 14 Mar '25

14 Mar '25

Dear ChimeraX team, (I have a vague memory of discussing this before, apologies if duplicate!) When displaying volumes as images (e.g. cryo-ET volume slices), I see that by default it uses linear interpolation: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#style Would it be possible to offer higher-order interpolation options such as cubic? I love how customizable it is to make figures in ChimeraX, but this is the one feature that we really miss compared e.g. to 3dmod from IMOD. Thank you! -- Ricardo Diogo Righetto

2 7

Dockprep Inquiry
by Emir MALOVIC 13 Mar '25

13 Mar '25

Hello, I am trying to perform some simple docking between a small molecule and a protein. I get the following warning: (UNL) `bash.exe: warning: could not find /tmp, please create!` I was browsing around and noticed I may need to set up ChimeraX Development Environment. Is this true? Thank you, Emir

2 1

ISOLDE refine.eff and phenix.refine
by Shawn Rumrill 13 Mar '25

13 Mar '25

Dear ChimeraX Community, Not strictly ChimeraX related, but probably interesting to some and I've seen some feedback for ISOLDE here... I am using ISOLDE to rebuild a mid-resolution protein/NA model (still adjusting to using ISOLDE, but really powerful tool). I want to refine using phenix.refine, but I am running into a problem with the refine.eff file. The error from the terminal output is below. I've gathered that this is due to a change in parameter terminology from Phenix 1.20 to 1.21. My question is, is there some way to write the refine.eff file with the required information? I would hate to have to manually edit the .eff output file each time I want to run a new refinement in Phenix. Thanks, Shawn Error: Processing files: ------------------------------------------------------------------------------- Found phil, refine.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ refine.eff Unrecognized PHIL parameters: ----------------------------- refinement.input.pdb.file_name (file "refine.eff", line 6) refinement.input.xray_data.file_name (file "refine.eff", line 9) refinement.input.xray_data.labels (file "refine.eff", line 10) refinement.input.xray_data.high_resolution (file "refine.eff", line 11) refinement.input.xray_data.low_resolution (file "refine.eff", line 12) refinement.input.xray_data.r_free_flags.file_name (file "refine.eff", line 14) refinement.input.xray_data.r_free_flags.label (file "refine.eff", line 15) refinement.input.xray_data.r_free_flags.test_flag_value (file "refine.eff", line 16) Sorry: Some PHIL parameters are not recognized by phenix.refine. Please run this program with the --show-defaults option to see what parameters are available. PHIL parameters in files should be fully specified (e.g. "output.overwrite" instead of just "overwrite")

2 1

Re: Inquiry to docking protein onto lipid bilayer
by You, Youngki 12 Mar '25

12 Mar '25

Hello Tommy, You can use this server (PPM in OPM site), https://opm.phar.umich.edu/ppm_server3_cgopm , to determine the orientation and depth of your protein in the membranes. After that, you can use the model from PPM in CHARMM-GUI. Best, Youngki ________________________________PNNL__ Youngki You, PhD Post Doctorate RA, Biochemical Mechanisms Structure, Function & Design Biological Sciences Division Pacific Northwest National Laboratory Tel: +1 (509) 371-6660

1 0

Inquiry to docking protein onto lipid bilayer
by Tommy Tong 12 Mar '25

12 Mar '25

Dear ChimeraX experts, Good afternoon. My name is Tommy from San Diego Biomed. I am a beginner to ChimeraX version 1.9. May I ask if it is possible to use ChimeraX to dock a membrane protein into a lipid bilayer? I obtained Phosphotidylcholine bilayer (POPC) structure from CHARMM-GUI webpage https://charmm-gui.org/?doc=archive&lib=lipid_pure, and was wondering if it is possible to “place” a protein into this POPC structure in ChimeraX. Your help and advice on this is greatly appreciated. Thank you. Sincerely, Tommy

2 1

Obtain individual RMSD values
by javisanchezdelrio＠gmail.com 12 Mar '25

12 Mar '25

Hello, I have an issue when applying matchmaker command in ChimeraX. When I execute the command: matchmaker #1 to #2 showAlignment true I obtain the alignment with the bars in the upper layer showing the individual RMSD of each residue. But the results yields the overall RMSD of the alignment (i.e. RMSD between 108 pruned atoms). Is there any way to obtain those individual RMSDs of the alignment as a file or have them printed in the log for post-processing? Thank you in advance

3 2

Dividing a huge model (& map) into smaller chunks
by Alejandro Buschiazzo 12 Mar '25

12 Mar '25

Dear chimeraX developers/users Using version 1.9, I am trying to divide a very big mmcif model (230K + nonH atoms; >130 chains) and corresponding mrc map, into a number of smaller mmcif files (and corresponding cropped maps, covering just those parts). What I’ve tried so far unsuccessfully: I can create dummy atoms with build start atom, at desired x,y,z points, so that I can then use select zone to select a radius and keep parts near each dummy atom. Yet, that is suboptimal: I would largely prefer to keep (build) boxes, and not spheres, ensuring complete recovery and no blind spots. So that each box slightly overlaps with the neighboring one, and systematically covers the whole original map volume. 1. How can I generate a script that will do this "systematic windowing” screening, making boxes of a defined side-length at each step, and keeping the model within? 2. How should I then crop the original map, so that it covers each box (with a small padding on the borders)? 3. How should I stitch back the models, so that I don’t loose any atomic coordinates information? (of course that stitching will be done after I do some refinement work on each boxed model vs map) So sorry for the many questions! I’ve been trying hard to find this kind of strategy, and just can’t seem to succeed…. Thank you very much in advance Alejandro -- Alejandro Buschiazzo, PhD Associate Professor Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 ext. 120 Fax: +598 25224185 https://pasteur.uy/en/laboratories/molecular-and-structural-microbiology/

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General ?s - Foldseek (Sequence Plot) and Similar Structures Table
by Emir MALOVIC 11 Mar '25

11 Mar '25

Hello, Quick question: When I load the sequence plot, I receive 2 sequence images separated by a very large black space. When I save the image as a PNG, the black space between the sequence images is retained. Basically, the image is mostly black space. Is there a way to change that or is this a bug? Am I able to somehow copy the Similar Structures table or export it into Excel? A copy/paste function would be ideal and quick. I am using the Chimera 1.10 dev. Please let me know at your earliest convenience! Thank you, Emir

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Suggestion for improvement
by James Raymond 11 Mar '25

11 Mar '25

I love ChimeraX and use it often for my work, e.g. this one <https://www.pnas.org/doi/10.1073/pnas.2421910122>. When using AlphaFold to predict protein structure, the sequence is pasted into the sequence box. It does not allow entering the fasta name ">name" before the sequence.. Allowing a name to be included can avoid much confusion. Presently, the screen shows the output as "best_model" which becomes very confusing when several best models are shown on the screen. James Raymond Univ. Nevada Las Vegas

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What is the .exe file for ChimeraX Toolbox?
by m.i.bashir＠bham.ac.uk 11 Mar '25

11 Mar '25

Hi all, First time posting here. I'm looking to find the name and location of the file/folder that manages the ChimeraX in-app browser. The way I launch the browser is to go to 'tools' in the top bar, then press 'more tools', and then it brings up the ChimeraX Toolshed Where is the .exe file that controls this in app browser? I am attempting to find the .exe file and black list it, so we can use ChimeraX for an exam Thanks,

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SASA in MDS
by Gabriel López Velázquez 10 Mar '25

10 Mar '25

Dear Elaine, I am sorry; I did not state the subject of my previous email. I would ask for help. How can I calculate SASA as a function of time from the MD simulations in Chimerax? What archives need to perform it? Thanks in advance! Gabriel.

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(no subject)
by Gabriel López Velázquez 10 Mar '25

10 Mar '25

Dear Elaine, I would ask for help. How can I calculate SASA as a function of time from the MD simulations in Chimerax? What archives need to perform it? Thanks in advance! Gabriel.

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Inquiry About Favorable Contacts and Display Methods in ChimeraX
by 田畑　健士郎 07 Mar '25

07 Mar '25

Subject: Inquiry About Favorable Contacts and Display Methods in ChimeraX Dear ChimeraX Developers, My name is Kenshiro Tabata. I hope this email finds you well. I am currently using ChimeraX to analyze the effects of point mutations on protein structure, particularly in cases where a larger side chain (e.g., methionine) is replaced by a smaller one (e.g., valine). In such cases, I expect that interactions with the opposing amino acids may be reduced due to the decreased side-chain volume. To investigate this, I would like to ask for your guidance regarding the interpretation and visualization of favorable contacts. ________________________________ 1) Understanding Favorable Contacts I understand that the contacts command identifies all types of interactions, whereas the clashes command detects only unfavorable interactions. Based on this, I interpreted the positive VDW overlap as indicating unfavorable (repulsive) interactions, while an overlap between 0 and -0.4 represents favorable (attractive) interactions. Could you confirm if this understanding is correct? ________________________________ 2) Best Approach for Displaying Only Favorable Contacts To analyze how the mutation affects interactions, I would like to display only favorable contacts. Below is the approach I have considered: Proposed Approach 1. Retrieve all interactions (favorable, neutral, and unfavorable) using the contacts command contacts overlapCutoff -0.4 saveFile all_contacts.txt 2. Retrieve only neutral and unfavorable interactions contacts overlapCutoff 0 saveFile non_favorable_contacts.txt 3. Compute the difference between these two sets using Python, extract only favorable contacts, and format them into a ChimeraX pseudobond file # File paths all_contacts_path = "all_contacts.txt" non_favorable_contacts_path = "non_favorable_contacts.txt" favorable_contacts_path = "favorable_contacts.pb" # Read files with open(all_contacts_path, "r") as f: all_contacts = set(f.readlines()) with open(non_favorable_contacts_path, "r") as f: non_favorable_contacts = set(f.readlines()) # Extract favorable contacts favorable_contacts = all_contacts - non_favorable_contacts # Convert to ChimeraX pseudobond file format with open(favorable_contacts_path, "w") as f: f.write("; Pseudobond file for favorable contacts\n") f.write("; radius = 0.1\n; color = green\n; dashes = 6\n") for line in favorable_contacts: parts = line.strip().split() if len(parts) >= 4: atom1 = f"/{parts[0]}:{parts[1]}@{parts[2]}" atom2 = f"/{parts[3]}:{parts[4]}@{parts[5]}" f.write(f"{atom1} {atom2}\n") 4. Load the extracted favorable contacts into ChimeraX for visualization open favorable_contacts.pb Would this be an appropriate approach? Alternatively, is there a simpler or more precise way to achieve this in ChimeraX? I appreciate your time and assistance, and I look forward to your advice. Best regards, Kenshiro Tabata

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AI in ChimeraX
by Elaine Meng 07 Mar '25

07 Mar '25

On Mar 7, 2025, at 6:01 AM, Veach, Kevin G. <kevin.veach(a)uky.edu> wrote: > > Hi Elaine: > Does Chimera-X use Artificial Intelligence or Large Language Learning Models? > Thank you, > > Kevin > Kevin Veach, Computer Support Specialist II > University of Kentucky, Animal & Food Sciences Dept. Hi Kevin, Please use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here for general questions about ChimeraX -- I'm not the top expert on all parts of ChimeraX, so you may get better answers from other developers or our user community. Regarding your question, my understanding is that ChimeraX itself does not use these kinds of calculations, but it has tools that interface to web services or other calculations (run outside of ChimeraX) that do use them. The ones that I can think of are AlphaFold/ColabFold and ESMFold: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html#predict> I hope this helps, 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

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Creating movie in ChimeraX from YASARA simulation
by ibogdanov 07 Mar '25

07 Mar '25

Hi ! I have the following question - How can I create a movie, when I cannot use the YASARA.sce file from which I converted/extracted xtc.file(the trajectories) when I have all the snapshots(pdb and sim.files) created as separate files during the performed simulation in YASARA...I've uploaded for example the first pdb file of the series and the xtc.file but isn't the saved xtc.file(trajectories) of the whole simulation(for all the structures)? How would you suggest me to solve this problem, if ChimeraX doesn't support sce.files ? Thank you in advance! Kind Regards, Ivan Bogdanov

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Problem installing on OSX
by Thom Hughes 06 Mar '25

06 Mar '25

I apologize for the dumb question, but here it is. I want to install the isolde extension. When I go to more tools, isolde, and click the install button a .whl file downloads correctly. But then nothing happens. I’m running OSX 15.3.1. thanks in advance for any pointers!

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Unable to open the file after downloading ChimeraX
by Guo-Ping Zhou 05 Mar '25

05 Mar '25

Dear Sir/Madam, After downloading ChimeraX, I automatically get the attached .png in the application as a microsoft word file. However, I can't open the Quick Access Toolbar. Could you please tell me how to make it work? Thanks! Guo-Ping Zhou, Rocky Mount Life Sciences Institute, Rocky Mount, NC 27804

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(no subject)
by FRANGIE Christian 05 Mar '25

05 Mar '25

Dear UCSF ChimeraX Support Team, My name is Christian frangieh, I am currently using Chimera X to visualize my AlphaFold simulations, and I want to check when i introduce a mutation and change one residue (amino acid), whether there is a change in the surface accessibility of the residue. Currenlty i am checking this visually by checking whether the residue is exposed to the surface or hidden. Nevertheless, i would like to know how can i do this with a command or by some form of calculation or structural analysis. Can you please help me with this matter? Warm Regards, Christian

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Can not find Structure Minimization in ChimeraX menu
by N.B. Nugroho 04 Mar '25

04 Mar '25

Dear ChimeraX developers I a little bit confuse to find the Structure Minimization menu in ChimeraX. In Chimera 1.16 it located in menu Tools>Structure Editing>Minimize Structure. Could you please guide me for this little problem. Best regards Nuki B Nugroho

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(no subject)
by junjie han 02 Mar '25

02 Mar '25

Hi, I hope you are doing well. May I ask two questions? First one: Why does the connection part between the side chain and backbone, which is circled in a dashed line in ChimeraX, look so abnormal? How can I make it display normally? [cid:437c0c59-2e31-4251-ac9c-eff3f64af0dd] Second one: Is it possible to show the border only for a specific region of protein without hiding other regions? Thanks, Junjie

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define integer attributes for multiple individual pseudobonds
by hannes.ludewig＠googlemail.com 28 Feb '25

28 Feb '25

Dear developers, I am trying to color pseudobonds by an individual (per-bond) attribute value (integer). I seem to be unable to use .pb files to create individual pseudobonds. And when I am using the pbond command several times providing an individual name for each pseudobond thus creating individual models (#1.1, #1.2, etc) I am unable to assign an attribute and color all pseudobonds according to the corresponding attribute value. What I want to create is similar to the alphafold contacts colored by PAE. Only that the values I am providing aren't PAE and I would like to determine the residue pairs that form each pseudobond. I apologize in case I am overlooking something obvious, but your help and/or clarification would be very much appreciated. Thank you. Best wishes, Hannes

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Disulphide bridges in ISOLDE
by Guillaume Gaullier 28 Feb '25

28 Feb '25

Hello ISOLDE users and Tristan, Is there a distance threshold at which ISOLDE won't let me close a disulphide bridge? I am puzzled, because it seems I can close a disulphide between two Cys about 10 residues apart in sequence and quite far from each other in space. In fact much further apart than a bond length, so the resulting bond looks ridiculously stretched. But it is quickly fixed when running a local simulation, even if it needs to pull the backbone out of density to achieve a reasonable S-S bond length. In the same model, I have two other Cys that follow each other in sequence. When loading the AlphaFold prediction, the two S atoms are close enough (for some reason) that ISOLDE offers to make the disulphide, so I say yes. Later on, wanting to test both options to assess which one is best supported by the map, I can break this disulphide, but once I do there is no way to close it again. In this case, the two S atoms settle about 3.4 Å apart when removing the bond, which is longer than an ideal disulphide, but much shorter than the distance over which ISOLDE still allowed me to form a disulphide in the first case. The documentation doesn't say anything about disulphides (or somehow I missed it). In fact, there seems to be no command to operate on disulphides? Using the menu item does not write anything to the Log, so if there is a command I cannot find what it is and what options it might accept. If someone can help with this, I would appreciate it! Thank you, Guillaume --- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Lägerhyddsvägen 1 752 37 Uppsala Sweden När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Assistance Required: Extracting List of Interacting Residues within 4 Å in UCSF Chimera
by Rashmi Aggarwal 27 Feb '25

27 Feb '25

Dear UCSF Chimera Support Team, I hope this message finds you well. I am currently working on analyzing interactions between two molecular structures using UCSF Chimera. I have successfully identified residues that are within a 4 Å distance between the two molecules. However, I am encountering difficulties in obtaining a clear, textual list of these interacting residues, as reading them directly from the visual representation is challenging. Could you please provide guidance on the specific commands or procedures within Chimera that would allow me to: 1. *Select residues* in one molecule that are within 4 Å of the other molecule. 2. *Generate and export a list* of these selected residues for further analysis. I have attempted various selection and reporting commands but have not yet achieved the desired outcome. Detailed instructions or references to relevant documentation would be greatly appreciated. Thank you very much for your assistance. Best regards, Rashmi

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