April 2025 - ChimeraX-users - RBVI Mailing Lists

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

20 Jun '25

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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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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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RMSD for all frames in a trajectory
by Alexandra Zahradnikova 07 May '25

07 May '25

Dear All, I am working with a trajectory of a tetramer. I would like to align the A chains in all frame of the trajectory and then calculate the rmsd of all chains in all frames relative to the respective chain of the first frame (i.e., align only chains A but calculate for all chains), and write the results to a text file. Is that possible? I can do a similar calculation with a script in old Chimera but don’t know how to do it in ChimeraX. I attach the zipped script for old Chimera. Best regards Sasha

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How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified?
by 1025049892＠qq.com 04 May '25

04 May '25

Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match? Thank you for your attention. I'm looking forward to your reply.

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Morphing of structures with different chain numbers
by Enrico Martinez 01 May '25

01 May '25

Dear ChimeraX Users, I am trying to perform a morphing between two cryo-EM structures of the same complex, where one structure has twice the number of chains as the other (PDBs 3J9K and 8Y6Q). However, the larger structure causes an error during morphing. I have attempted to write a script that aligns the two structures and deletes the unmatched chains from the larger structure. Unfortunately, the script is not working as expected. from chimerax.core.commands import run def delete_unmatched_chains(session): # Get models #1 and #2 m1 = next((m for m in session.models if m.id == (1,)), None) m2 = next((m for m in session.models if m.id == (2,)), None) if m1 is None or m2 is None: session.logger.info("Model #1 or #2 not found.") return chains1 = {chain.chain_id for chain in m1.chains} chains2 = {chain.chain_id for chain in m2.chains} unmatched = chains1 - chains2 if unmatched: chain_ids = ",".join(unmatched) # Deleting unmatched chains run(session, f"delete /{chain_ids}") session.logger.info(f"Deleted chains: {', '.join(unmatched)}") else: session.logger.info("No unmatched chains found.") Could you please help me or alternatively propose another solution? Any suggestions would be greatly appreciated. Thank you in advance ! Enrico

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Saving Images with Specific Dimensions and DPI in ChimeraX
by svle＠tiscali.it 30 Apr '25

30 Apr '25

Hi, In Chimera, when saving an image, it's possible to specify the output size in centimeters and the resolution in DPI. This feature is very useful for preparing figures for theses and publications. Is it possible to do the same in ChimeraX? I've read the documentation for the save command, but it's not entirely clear to me how to achieve this. Do you have any suggestions? Best regards, Saverio

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Reproducing the Chimera Preset Publication 5 ( flat ribbon ) in ChimeraX
by svle＠tiscali.it 29 Apr '25

29 Apr '25

Hi, it is possible to reproduce the Chimera Preset Publication 5 ( flat ribbon ) in ChimeraX? What are the commands to use in order to have this type of preset in ChimeraX? This is a very nice preset. Thanks. Saverio

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How to apply symmetry I to generate an icosahedron model
by 唐延婷 29 Apr '25

29 Apr '25

Hi doctor, when I open a map (ID 1) and a model (ID 2), the map is the whole icosahedron while the model is the protomer of the icosahedron. I want to apply symmetry I to generate an icosahedron model. I have rotated and translated the model into a reasonable position inside the map and then done a “fit in map” to get the initial placement for sym. Then I enter a command ''measure center #1''，center of mass xyz coordinates for map_sharp.mrc = (238.08, 238.08, 238.08)，enter another command ''sym #2 I,222 center 238.08, 238.08, 238.08'' I can see an icosahedron model fit in map. But when I save the icosahedron model.pdb, I found the icosahedron model actually is the model of the protomer. How can I apply symmetry I to generate a true icosahedron model, used for subsequent model refine in coot and real_space_refine in Phenix. Thank you very much. Best wishes! yanting 延婷 yanting.tang(a)mail.nankai.edu.cn

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Issues with find cavities tool
by Marino, Claudia 28 Apr '25

28 Apr '25

Greetings, I am not sure why I recently cannot longer use the tool “find cavities”. My ChimeraX version is 1.9 and my MacOS is Sequoia 15.4. Please, find below the screenshot of the Error message. [cid:image001.png@01DBA7F0.57B85750] Thank you very much in advance for your help. Sincerely, Claudia.

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