- ChimeraX-users - RBVI Mailing Lists

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/

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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)

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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!

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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

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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

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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

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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

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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/>

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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)

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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

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

20 Jun '25

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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/>

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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>

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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

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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

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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/

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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]

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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.

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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

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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

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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

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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

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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 ()

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'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>

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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

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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

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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

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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

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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

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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.

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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

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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.

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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

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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

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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

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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

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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

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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

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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

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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.

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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.

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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

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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

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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

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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

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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

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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

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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

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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

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