June 2025 - ChimeraX-users - RBVI Mailing Lists

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

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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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