- ChimeraX-users - RBVI Mailing Lists

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

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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

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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

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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 >

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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

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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

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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

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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

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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/>

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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