- ChimeraX-users - RBVI Mailing Lists

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 28 May '25

28 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 28 May '25

28 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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remotecontrol observations and suggestions
by Roden Deng Luo 23 May '25

23 May '25

Hi, This is to share my observations and practices mainly with people using `remotecontrol xmlrpc`, likely developers. `xmlrpc` has a very high overhead, `remotecontrol rest` with "multipart/form-data" header POST requests should be a better option. First, the REST method can also be used programmatically in scripts or applications fairly easily. I have been sending GET requests using the REST method. Then, I hit "Request-URI Too Long" as I am sending decent sized json data (17KB). Then I tried XML-RPC and realized the frame rate dropped from 58 to 8. The frame rate can be displayed at the status line via `graphics rate true`. Then GPT guided me to try POST with "application/x-www-form-urlencoded" as Content-Type. I got stuck here for a while and found _parse_post <https://github.com/RBVI/ChimeraX/blob/3233aaaf01623ca24bccff7196410401872ce…> returns "fields" in binary and the program could not parse args["command"] <https://github.com/RBVI/ChimeraX/blob/3233aaaf01623ca24bccff7196410401872ce…> as what's inside is b"command". Then I refactored my client to POST with "multipart/form-data" and it worked. More details in my conversations with bots: URL too long: https://chatgpt.com/share/682c856c-174c-8003-bfc9-96fa7e2db0c3 Frame rate cmd: https://chatgpt.com/share/682c8589-2da0-8003-8c14-a59b75927c6b XML-RPC overhead: https://chatgpt.com/share/682c85a7-5f40-8003-8615-095e0a28fccd POST: https://chatgpt.com/share/682c85ca-9938-8003-bb0b-1fb7dd7938ef Best, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Commercial vs personal use
by Smith, Timothy 22 May '25

22 May '25

Hello, I previously used ChimeraX for my academic work during my PhD and would like to continue using it for personal use. I do work for a biotech company and while I don't use ChimeraX for work related to my job, I do only have a work issued computer where IT needs to install software. My question is would I still need a commercial license even if I only use it for personal use on my work computer? Thanks, Tim

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1.10 Release Candidates Available Now
by Zach Pearson 22 May '25

22 May '25

Hello ChimeraX users, The first release candidate of ChimeraX 1.10 is available for download today. — Zach

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