- ChimeraX-users - RBVI Mailing Lists

ChimeraX REST remotecontrol: CORS for localhost clients?
by Boris Steipe 18 Dec '25

18 Dec '25

Dear ChimeraX team - I am writing a local, interactive tutorial (Quarto HTML) that I want drive ChimeraX via the REST remotecontrol interface. I can send commands in JavaScript, but not read responses. Quarto serves my page locally - page origin: http://localhost:5779 - ChimeraX endpoint: http://127.0.0.1:61803/run?command=... ... but if I issue in the JS console: fetch("http://127.0.0.1:61803/run?command=help") .then(r => r.text()).then(console.log).catch(console.error); I get: Console error: - CORS blocked: “No ‘Access-Control-Allow-Origin’ header is present…” - Network panel shows 200 OK, but the Fetch promise rejects with TypeError: Failed to fetch. So: Is there a supported way (or could there be) for remotecontrol rest to emit CORS headers for localhost-only clients? Something like: - Access-Control-Allow-Origin: http://localhost:5779 (or a configurable allow-list, possibly including http://127.0.0.1:*) - Access-Control-Allow-Methods: GET, POST, OPTIONS - Access-Control-Allow-Headers: Content-Type - Handling preflight OPTIONS requests (e.g. relevant for POST ) - Even an "allow only loopback origins" mode would be sufficient. Ideally, enabling CORS would be controllable at runtime from within ChimeraX (e.g., as an option to remotecontrol rest start or a subsequent ChimeraX command), so that a teaching workflow can be fully self-contained. For example, something like: • remotecontrol rest start port 61803 cors allow-origin http://localhost:* • or: remotecontrol rest cors allow-origin http://localhost:* If there’s already an option/flag for this I would be grateful for pointers. (Or perhaps I have missed a recommended pattern.) Thank you! Boris (Nb. I do understand the security implications of CORS; this use case is strictly local (loopback only), with the goal to enable processing measurements/queries in browser-based teaching material. ) -- Boris Steipe MD, PhD Professor em. Department of Biochemistry Temerty Faculty of Medicine University of Toronto

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kvFinder tool
by George Tzotzos 18 Dec '25

18 Dec '25

I’ve opened 1PN9.pdb deleted all but chain A. I used kvfinder #1 probeIn 1.4 probeOut 4.0 The largest cavity has an ID 1.1.5. How does one identify the residues that line the cavity? Thank you

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Coloring amino acid residues by type
by Elaine Meng 18 Dec '25

18 Dec '25

Hello, I may not understand your comment, but you can certainly color amino acids specified by residue type. For example, ChimeraX commands: color :asp,glu red color :lys,arg blue color :his dodger blue I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 18, 2025, at 12:13 PM, B. Sharmila Sri <e6123008(a)sriher.edu.in> wrote: > > easy to use, but coloring the aminoacid residues by code is not working properly kindly make it possible > _______________________________________________ > Chimerax-registration mailing list -- chimerax-registration(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-registration-leave(a)cgl.ucsf.edu

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Regarding Internal Server Error while Downloading Chimera X
by Piyush Mohanty 16 Dec '25

16 Dec '25

Dear Administrator, I encountered an Internal Server Error while accessing the server today while downloading the candidate version of ChimeraX. The error message suggested contacting you at root@localhost. The exact error stated was : " Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error. More information about this error may be available in the server error log." Could you please look into this issue and correct the misconfiguration at the earliest convenience? Thank you for your assistance. Best regards, Piyush Mohanty

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Download UCSF ChimeraX Internal Server Error
by Mark Guthridge 16 Dec '25

16 Dec '25

Dear Sir/Madam I am getting an Internal Sever Error when trying to download ChimeraX from https://www.rbvi.ucsf.edu/chimerax/download.html The error message indicates, "contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error." The times of the errors occurred between 4:20pm and 4:30pm AEDT (ie. in the 10min period before I sent this email so you can check logs for my timezone). My IP is 14.2.62.78 The errors occur: * After deleting my cache * In multiple browsers (chrome, firefox, edge) * For multiple releases of ChimeraX spanning 2017-2025 * My local home network and also my phone hotspot * For both ChimeraX and Chimera * Incognito browser Could you please help? Cheers Mark Could you please help A/Professor Mark Guthridge Room L2.09.02 Centre for Cellular and Molecular Biology (CCMB) School of Life & Env. Sciences Deakin University Burwood Highway Burwood VIC 3125 +61 3 924 45796 Important Notice: The contents of this email are intended solely for the named addressee and are confidential; any unauthorised use, reproduction or storage of the contents is expressly prohibited. If you have received this email in error, please delete it and any attachments immediately and advise the sender by return email or telephone. Deakin University does not warrant that this email and any attachments are error or virus free.

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Download Links for ChimeraX 1.11 broken
by Simon Michnowicz 16 Dec '25

16 Dec '25

Dear Group the download links for the latest Chimera on page https://www.rbvi.ucsf.edu/chimerax/download.html#candidate are broken, i..e the following link is broken.. <goog_247633214> https://www.rbvi.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?file=curr… as well as other Unix distros regards *---Simon Michnowicz * Senior Application Specialist, High-Performance Computing *Research Support Services - eSolutions* *Monash eResearch Centre* Monash University 15 Innovation Walk, Building 75, Clayton Campus Wellington Road, VIC 3800 Australia T: +61 3 9902 0794 M: +61 3 0418 302 046 E: simon.michnowicz(a)monash.edu monash.edu

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"Nearby" atoms are within X angstroms of cavity points
by Berenice E Cowfer Chavez 15 Dec '25

15 Dec '25

Hello, What is the default value of "Nearby" atoms are within X angstroms of cavity points in the Find Cavities tool? I remember it used to be 5.0 A but now when I use the tool it shows 6.0 A. Sincerely, Berenice E. Cowfer Chavez, M.S. Lab Manager, Profs. Johnson and Shoulders Labs Massachusetts Institute of Technology

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Adding models as a group/subgroup using Python
by huybk81＠gmail.com 15 Dec '25

15 Dec '25

I tried to read the Programming API but was unable to find out. Right now: I created surface A1,A2,B1,B2,D1,D2, etc.. I added these surfaces in a list surfs = [] surfs.append(A1) surfs.append(A2) ... surfs.append(D2) session.models.add_group(surfs, name="All surface") This make A1,A2 as models #1.1,#1.2 etc Interestingly, I cannot even find the document for add_group. I learned this from ChimeraX recipes. Anyway, I want to organize the data a bit better to have it like this #1; Surface ---> #1.1 Surf A -------> #1.1.1 A1 -------> #1.1.2 A2 ---> #1.2 Surf B -------> #1.2.1 B1 -------> #1.2.2 B1 How can we do that? Best,

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Security Inquiries
by Anh-Huy Le 15 Dec '25

15 Dec '25

Hi ChimeraX folks, I know that this is mostly research software offered through educational channels, but as part of an internal security review of software we are using, I am writing you to inquire if ChimeraX already has any systems in place to report security related issues which could include any of the following: * System breaches on your end that could affect our organization (e.g.: payment information or other types of information being stolen/breached) * Uptime status of services your provide (e.g.: like this Amazon dashboard) * Systems that when queried report the latest updates to combat known security vulnerabilities. If you do not provide these services currently, do you plan on providing these services in the future? If you do not plan on providing these services in the future, would you consider offering professional services to develop these features? Thank you so much for answering ahead of time. Sincerely, Anh-Huy Phan Le, PhD (He/him) Sr. R&D Solution Architect [signature_2852565164]-- Vir Biotechnology, Inc. ale(a)vir.bio<mailto:ale@vir.bio> | Mobile: 714-269-9663 --

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bug report - pip list failure
by replacement2＠gmail.com 15 Dec '25

15 Dec '25

Hi, My apologies if this is not the best place to report a bug. There appears to be an issue with `pip list`, which may be caused by a typo in `pip.py`. Please see the traceback. It'd be great if someone can verify. Thanks. Traceback (most recent call last): File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute cmd.run(cmd_text) File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/pip.py", line 71, in pip pip_cmd.appendf("list") ^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'appendf' cui5

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