- ChimeraX-users - RBVI Mailing Lists

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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ChimeraX Boltz prediction running eternally
by Sam Allen 10 Dec '25

10 Dec '25

Hello Tom and co., I am currently trying to use ChimeraX Boltz tool to predict the structure of some small ligands onto a GPCR and my prediction running timer just never stops. I initially attempted to install and run the tool on Windows but the install failed to import the mols folder properly multiple times (uninstall and reinstalled), after manually untaring the folder in Powershell it still didn't run (Timeout while submitting to MSA server). I then decided to switch over to my mac (M1 16GB) and while the install of Boltz in ChimeraX no longer had any error and the prediction didn't error either, the timer just continued to go up (to 26000 eventually). I figured the protein was too large (471 residues, makes sense), so I tried to rerun one of your test examples (8rf4, https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/runtimes.html) and still no prediction output after 20 minutes. I've tried switching from default compute device to GPU or CPU and still no difference. Additionally, in activity monitor it shows ChimeraX is taking up nearly no GPU or CPU usage, so I'm confused as to what is happening. Do you have any advice or know anything that might be going wrong that I can fix? Regards, Sam

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ChimeraX Boltz prediction running eternally or failing submission to MSA server
by Sam Allen 10 Dec '25

10 Dec '25

Hello, I am currently trying to use ChimeraX Boltz tool to predict the structure of some small ligands onto a GPCR and my prediction running timer just never stops. I initially attempted to install and run the tool on Windows but the install failed to import the mols folder properly multiple times (uninstall and reinstalled), after manually untaring the folder in Powershell it still didn’t run (Timeout while submitting to MSA server). I then decided to switch over to my mac (M1 16GB) and while the install of Boltz in ChimeraX no longer had any error and the prediction didn’t error either, the timer just continued to go up (to 26000 eventually). I figured the protein was too large (471 residues, makes sense), so I tried to rerun one of your test examples (8rf4, https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/runtimes.html) and still no prediction output after 20 minutes. I’ve tried switching from default compute device to GPU or CPU and still no difference. Additionally, in activity monitor it shows ChimeraX is taking up nearly no GPU or CPU usage, so I’m confused as to what is happening. Do you have any advice or know anything that might be going wrong that I can fix? Update: After this email I downloaded the daily ChimeraX version and attempted to run Boltz through that. Instead now the same error as the windows appeared (No authentication provided for MSA server; Failed to process; Skipping. Error: Too many failed attempts for the MSA generation request..) Below is the error in its entirety: Running boltz prediction failed with exit code 0: command: /Users/samuelallen/boltz22/bin/boltz predict /Users/samuelallen/Desktop/boltz_testingtesting123/testingtesting123.yaml --use_msa_server --accelerator gpu --no_kernels stdout: Boltz version 2.2.0 MSA server enabled: https://api.colabfold.com MSA server authentication: no credentials provided Checking input data. Processing 1 inputs with 1 threads. Generating MSA for /Users/samuelallen/Desktop/boltz_testingtesting123/testingtesting123.yaml with 1 protein entities. Calling MSA server for target testingtesting123 with 1 sequences MSA server URL: https://api.colabfold.com MSA pairing strategy: greedy No authentication provided for MSA server Failed to process /Users/samuelallen/Desktop/boltz_testingtesting123/testingtesting123.yaml. Skipping. Error: Too many failed attempts for the MSA generation request.. stderr: 0%| | 0/1 [00:00<?, ?it/s] 0%| | 0/150 [elapsed: 00:00 remaining: ?][A SUBMIT: 0%| | 0/150 [elapsed: 00:00 remaining: ?][AError while fetching result from MSA server. Retrying... (1/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (2/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (3/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (4/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (5/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (6/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) SUBMIT: 0%| | 0/150 [elapsed: 01:04 remaining: ?] Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 534, in _make_request response = conn.getresponse() ^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connection.py", line 571, in getresponse httplib_response = super().getresponse() ^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1395, in getresponse response.begin() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 325, in begin version, status, reason = self._read_status() ^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 286, in _read_status line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py", line 706, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1314, in recv_into return self.read(nbytes, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1166, in read return self._sslobj.read(len, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TimeoutError: The read operation timed out The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/adapters.py", line 667, in send resp = conn.urlopen( ^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 841, in urlopen retries = retries.increment( ^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/util/retry.py", line 474, in increment raise reraise(type(error), error, _stacktrace) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/util/util.py", line 39, in reraise raise value File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 787, in urlopen response = self._make_request( ^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 536, in _make_request self._raise_timeout(err=e, url=url, timeout_value=read_timeout) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 367, in _raise_timeout raise ReadTimeoutError( urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/data/msa/mmseqs2.py", line 77, in submit res = requests.post( ^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/api.py", line 115, in post return request("post", url, data=data, json=json, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/api.py", line 59, in request return session.request(method=method, url=url, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/sessions.py", line 589, in request resp = self.send(prep, **send_kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/sessions.py", line 703, in send r = adapter.send(request, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/adapters.py", line 713, in send raise ReadTimeout(e, request=request) requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/main.py", line 581, in process_input compute_msa( File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/main.py", line 477, in compute_msa unpaired_msa = run_mmseqs2( ^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/data/msa/mmseqs2.py", line 201, in run_mmseqs2 out = submit(seqs_unique, mode, N) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/data/msa/mmseqs2.py", line 92, in submit raise Exception( Exception: Too many failed attempts for the MSA generation request. 100%|██████████| 1/1 [01:04<00:00, 64.69s/it] 100%|██████████| 1/1 [01:04<00:00, 64.69s/it] GPU available: True (mps), used: True TPU available: False, using: 0 TPU cores HPU available: False, using: 0 HPUs /Users/samuelallen/boltz22/lib/python3.11/site-packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76: Starting from v1.9.0, `tensorboardX` has been removed as a dependency of the `pytorch_lightning` package, due to potential conflicts with other packages in the ML ecosystem. For this reason, `logger=True` will use `CSVLogger` as the default logger, unless the `tensorboard` or `tensorboardX` packages are found. Please `pip install lightning[extra]` or one of them to enable TensorBoard support by default Regards, Sam

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