- ChimeraX-users - RBVI Mailing Lists

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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