- ChimeraX-users - RBVI Mailing Lists

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/

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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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