- ChimeraX-users - RBVI Mailing Lists

reduce gridpoints on the cryoEM map (640 x 640 x 640 ) to ( 320 x 320 x 320)
by arangarajan＠initialtx.com 27 Apr '25

27 Apr '25

hi, i need to reduce the grid points to make the map work with MOE. I am not sure if this is possible in chimerax and i would appreciate some suggestions for creating a mrc file with reduced grid points. please let me know your thoughts. best amith

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Morphing of structures with different chain numbers
by Enrico Martinez 26 Apr '25

26 Apr '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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VR on ubuntu workstation
by arangarajan＠initialtx.com 24 Apr '25

24 Apr '25

Hi, i got steam VR installed but later found out that Oculus does not support linux. Is there a work around for using chimerax VR on latest ubuntu machine with oculus rift s headset? i can get other headset also if it will fit this purpose. thanks in advance, best amith

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How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified?
by 1025049892＠qq.com 24 Apr '25

24 Apr '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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Labeling chains in MD simulation trajectories of a multimer
by Alexandra Zahradnikova 24 Apr '25

24 Apr '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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Effect of clearing ChimeraX cache from Mac?
by Radford, Katelyn M. (Kate) 23 Apr '25

23 Apr '25

Hi there! I'm in the throes of a memory-expensive project and my computer is running out of space. A little bit of googling led me to conclude that it would probably make sense for me to clear my system's cache, as my system files take up about a third of my disk space. ChimeraX cache files account for a substantial portion of that memory usage. As I make figures, I save .cxs files of each figure so that it's easy to go back and edit things that need to be changed. My ChimeraX also has a bunch of plug-ins installed (e.g. ISOLDE). I'm wondering: how much damage will I do to my installation and to my .cxs files if I delete the ChimeraX cache? System and software details: ChimeraX version: 1.9 MacOS: Ventura 13.0 Chip: Apple M2 Max Thank you all so much for the excellent work you do, Best wishes, Kate Kate Radford (she/they) PhD candidate, Biochemistry and Molecular Biophysics California Institute of Technology 1200 E California Blvd Pasadena, CA 91125

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Re: cartoon not displaying in ChimeraX despite complete backbone
by amith ranga 22 Apr '25

22 Apr '25

Dear ChimeraX users, I'm unable to display the cartoon representation for pdb file in ChimeraX, even though the residues and atoms appear complete. The structure contains standard RNA residues (A, G, U) , Each residue includes all expected backbone atoms (P, O5', C5', C4', C3', O3', C1', O4', etc.) as well as complete base atoms and hydrogens. The file was written out from MOE software and I am not sure if this is an issue. Some tips on how to edit the pdb file would be helpful Thanks, amith

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[ISOLDE] Handling Lys-Asp iso-peptide bonds and D-amino acids
by Yang Lee 22 Apr '25

22 Apr '25

Addressing this to Tristan, in all likelihood. Is there a way of parameterising KD isopeptide bonds and D-amino acids? Perhaps a secret three letter code I can rename the residues to make them play nice? Unfortunately, I'm trying to model a peptide that has both of these exotic elements. Cheers, Yang

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Color of unrolled density maps
by Sen, Anindito 21 Apr '25

21 Apr '25

Dear ChimeraX Team, Is there a way we can keep/restore the color of the unrolled helical density maps ? Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

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Re: Regarding peptide bond formation using chimeraX
by Tom Goddard 21 Apr '25

21 Apr '25

Hi Harpreet, I'm not sure how you deleted the bond. If you deleted a peptide bond with delete bonds /A:102@C /A:103@N or the equivalent menu Actions / Atoms and Bonds / delete then you could just recreate it with bond /A:102@C /A:103@N I'm not sure why you would do that since there is no need to delete a bond to move the two pieces of the structure. Instead maybe you split the protein into two separate models. In that case you can't simply add a bond between different models, instead you have to combine the models (e.g. command "combine #1,2"). You might get better answers on the ChimeraX mailing list, so I have CC'ed that list. Tom > On Apr 21, 2025, at 4:06 PM, Singh, Harpreet <harpreet.singh2(a)ucsf.edu> wrote: > > Dear Professor Goddard, > > I hope you are doing well. > > I am a Postdoctoral scholar from the Robert M. Stroud lab. I recently deleted a peptide bond from our protein structure to adjust the model for cryo-electron microscopy (cryo-EM) mapping. I am now attempting to reconstruct the peptide bond using the Build Structure tool. However, I am encountering an error message indicating that there are no chain-terminal carbons in the atoms. > > I would appreciate your assistance in resolving this issue. > > Thank you for your time and consideration. > > Best regards, > Harpreet Singh > Postdoctoral Fellow, Stroud lab > Department of Biochemistry and Biophysics > UCSF

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