May 2025 - ChimeraX-users - RBVI Mailing Lists

Comparing Maps
by Abhilash Padavannil 02 Jun '25

02 Jun '25

Hello, I have five different cryoEM maps coming from similar samples. The maps are at different resolutions. I want to compare the density at the region of interest across these maps. How do I normalize the maps say to the first map to make accurate analysis. I know I could scale them using vop scale, but I am wondering which of the parameters I should use. Thanks in advance for your suggestions. Abhilash.

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How to create singlke protein from assembly of 5 individual chains
by Jacek Jagodzinski 29 May '25

29 May '25

Hi, I am medicinal chemist. I used ChimeraX to model missing parts/loops of the protein for which I had cryo-EM structure. It is transmembrane protein consisting of 5 individual chains. I managed to reconstruct missing parts using as a template known sequences of publicly available X-ray structures of proteins and known sequences. I have now a nice assembly of five individual “repaired” proteins perfectly aligned with parts of my cryo-EM structure. However the PDB file of those FIVE individual proteins is not recognized as ONE protein with five separate chains by my other programs. I suppose there is a way to get the result I need, but I cannot find the solution by myself. Can you help? Jacek Jagodzinski, PhD

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Use minimization in chimerax using command line
by TUSHAR GUPTA 29 May '25

29 May '25

Good morning I would like to appreciate your work and efforts in developing and maintaining ChimeraX, it has always been so useful tool in my research. I was initially using Chimera that had excellent feature of using amber force field for energy minimization of structure and making movie using topology and coordinate file. I am working on inducing mutation in nucleic acid and protein structures. I wish to incorporate the minimization step in my research using Chimerax. I will be highly grateful if you could guide me how can I use minimization steps in Chimerax using command line codes. Thank you Tushar Gupta PhD biotechnology Bennett University Greater Noida India "He that can have patience can have what he will." - Benjamin Franklin _____________________________________________ Vineet Jain (Chancellor) Inspiration

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Issue in using vop maximum to make composite map
by Dr. Heng Zhou 29 May '25

29 May '25

Dear ChimeraX developers, I have an issue when using vop maximum command to combine two local maps. Map A and Map B have an overlapping area with each other. The hinge point of structural flexibility is at the center of the overlapping area. Therefore, the left part of Map A and the right part of Map B have a better local density quality, which I want to keep in the composite map. But vop maximum did it on the opposite, resulting in a worse local resolution at the edges of the overlapping area (e.g., Region 1 and 2). Technically, this is not an issue of vop maximium itself. In Region 1, Map A has a better local density quality, while Map B has higher values in some voxels. So the composite map has more voxels derived from Map B in Region 1. Vice versa for Region 2. The only solution in my mind is to split both Map A and B at the hinge point, then do vop maximum for only the left part of Map A and the right part of Map B. But this is time-consuming since I have many local maps to combine. I wonder if you have a better solution? I would appreciate it if you could give advices. Thanks! Best regards, Heng Heng Zhou, PhD | Postdoctoral research fellow Stefan Raunser lab | Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11, 44227 Dortmund, Germany Phone: +49 231-133-2326

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Disulfide bridges
by Pascal Rochaix 28 May '25

28 May '25

Hello, I am a long time user of PyMOL and I am testing ChimeraX for the first time. Is there a simple command to show the disulfide bridges ? It is easy in PyMOL but I don't find it in ChimeraX... Thanks in advance, Pascal Rochaix Protein Scientist www.metafora-biosystems.com<http://www.metafora-biosystems.com> [Logo mail]Pépinière Paris Biotech Santé 29 rue du Faubourg Saint Jacques | 75014 Paris | France

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Working with c-beta truncated models in ISOLDE
by Vorländer,Matthias Kopano 28 May '25

28 May '25

Hi everyone, Is there a way to work with c-beta truncated models in ISOLDE? For truncated residues, Isolde brings up the unparameterized residues dialog, and matches as a possible template the ligand “TRUNC_CB”, which seems reasonable. Since the model also contains complete sidechains, I would not want to rebuild all residues to template, and doing it residue-by-residue is impractical, too. Can the “rebuild to template for all residues of this name” be limited to a selection? Thanks a lot, Matthias

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swapna command extremely slow for large structures
by Vorländer,Matthias Kopano 27 May '25

27 May '25

Dear ChimeraX team, I have noticed that on some structure I am working with, the swapna command is extremely slow, making it almost unusable for structure manipulation. For a single nucleotide substitution, ChimeraX froze for >5 minutes before finishing the operation (that particular structure had ~300 000 atoms). When I however first delete all proteins from the structure, the operation is very fast. What is the rate limiting step in the swapna command? Does it invoke renumbering of all atoms in the PDB file? Without having quantified it, I experienced similar behavior for the build replace command. Would be fantastic if there would be a way to speed this up to increase its usability! Many thanks in advance, Matthias

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Taking control of the string displayed in a pbond associated tooltip
by svle＠tiscali.it 27 May '25

27 May '25

Hi, I have specified some pseudobonds using pbond. It is possible to add a string, conveying other related informations , to that displayed in the tooltip when hovering the mouse on the pseudobond? Also, it is possible to take the complete control of what is displayed in the tooltip? Thanks. Saverio

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How do I get Modeller structure if there was a connection timeout error on ChimeraX?
by Andy Liwang 23 May '25

23 May '25

Dear ChimeraX, I used “Model Loops” on a large protein and even though ChimeraX indicated “Modeller Webservice: 1 of 1 models generated”, it also gave the following error message: modeller refine<help:user/commands/modeller.html#refine> 1:1:all-missing 1/A:1:all-missing numModels 1 fast false adjacentFlexible 1 protocol standard Webservices job id: RO5U9U0YU7YY6TM5 2025-05-23 15:51:56,220 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<urllib3.connection.HTTPConnection object at 0x32f0aa350>, 'Connection to webservices.rbvi.ucsf.edu timed out. (connect timeout=None)')': /cxservices/api/v1/chimerax/jobs/RO5U9U0YU7YY6TM5/files Am I able to retrieve the model from webservices.rbvi.ucsf.edu<http://webservices.rbvi.ucsf.edu/>? Sincerely yours, Andy LiWang Professor of Chemistry & Biochemistry University of California Merced, CA 95343

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Problem using pbond
by svle＠tiscali.it 23 May '25

23 May '25

Hi, I would like to use pbond with a pair of atoms. For one of these it is available the model number , the chain ID and the atom serial number. How it is possible to give the atom specification ,having the previous three information, for using it in pbond? Thanks. Saverio

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