- ChimeraX-users - RBVI Mailing Lists

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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Adding chain description and Uniprot accession number to a pdb file
by Rayees Mattoo 20 Jun '25

20 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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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 17 Jun '25

17 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 16 Jun '25

16 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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Get model chain color
by Walshe, James 13 Jun '25

13 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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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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