- ChimeraX-users - RBVI Mailing Lists

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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Boltz run- Kd values
by Malik, Radhika 08 Dec '25

08 Dec '25

Hello, I am a Research Scientist at Mount Sinai School of Medicine, NY. I have run Boltz in ChimeraX on a protein-ligand complex, however, I am not able to locate the file for the predicted Kd values. Can you please direct me to the file/location? I am attaching a screenshot of what I see after the run. Thanks a lot, Radhika ________________________________ Confidentiality Notice: This electronic mail transmission and any documents, files, or previous email messages attached to it may contain confidential information and are intended solely for the use of the individual or entity to which they are addressed. If you are not the intended recipient, or a person responsible for delivering such information to the intended recipient, you are hereby notified that any further review, disclosure, copying, dissemination, distribution, or use of any of the information contained in or attached to this email transmission is strictly prohibited. If you have received this message in error, please notify the sender immediately by email, discard any paper copies, and delete all electronic files of the message. Thank you for your cooperation.

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NEED HELP TO INSTALL BOLTZ2 in CHIMERAX.
by Dr. V.N. Balaji 07 Dec '25

07 Dec '25

Subject: Bug Report: "Intel Mac" Error Blocking Boltz Install on Windows 11 (NVIDIA 3080 Ti) Dear ChimeraX Team, I am writing to report a platform detection bug in the Boltz installer within ChimeraX (Daily Build 1.12.dev202512040236). When attempting to install Boltz via the boltz install command on a Windows 11 system with a compatible NVIDIA GPU, the installation fails immediately with the following error: "Boltz requires newer Torch versions that are not available on Intel Macs." This appears to be a false positive in the installer's logic, erroneously flagging my Windows/x86_64 system as an unsupported Intel Mac. System Configuration: OS: Windows 11 Pro (x86_64) CPU: Intel Core i9-7940X GPU: NVIDIA GeForce RTX 3080 Ti (12GB VRAM, CUDA 12.x active) ChimeraX Version: 1.12.dev202512040236 (2025-12-04) Context & Troubleshooting: Verified Hardware: I have already successfully installed and verified boltz (v2.2.1) in a standalone PowerShell environment on this same machine; it runs protein-ligand docking with GPU acceleration without issue. Workarounds Attempted: I have tried running ChimeraX in admin mode, using different daily builds, and attempting to manually intervene with pip, but the internal installer aborts before package retrieval begins due to this platform check. Request: Could you advise on a command-line flag or manual workaround to bypass this platform check and force a Windows/CUDA installation? Alternatively, if this requires a patch to the installer script to correctly identify Windows environments, please let me know. Thank you for your assistance. Best regards, V.N. Balaji, Ph.D. Computational Chemist Bangalore, India vnbalaji(a)gmail.com | LinkedIn: vnbalaji

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Can ISOLDE-refined models be directly deposited to the PDB?
by man6ny＠virginia.edu 05 Dec '25

05 Dec '25

Dear all, Maybe an ignorant or previously-asked question... I believe most people refine cryo-EM models using e.g. Phenix real-space-refine before depositing them to the PDB. Is there a strict reason (practical or philosophical) why cryo-EM models refined in ISOLDE cannot be directly deposited without subsequent refinement in Phenix or Refmac? I have a high-resolution map (2.2 A) but the latter programs seem to actually make my model worse (e.g. Phenix tends to give me rotamers that are not supported by the experimental data). I would prefer to use the model refined in ISOLDE but perhaps I am missing something? Many thanks for your insight! Louis

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Opening multiple chimeraX windows at the same time?
by Choy, Jon 05 Dec '25

05 Dec '25

Hi Oliver and Tom or whom it may concern, I was interested in whether it is possible to open multiple .cxs files at the same time? I am comparing structural features across many different proteins and their corresponding maps—and it is very annoying to be only able to open one map and its protein at a time. Although it is possible to load multiple resolved structures and their maps into a single .cxs file, these structures all load onto different spots on the chimeraX interactive space—making side by side comparison a bit cumbersome. Assistance in this would be massively appreciated! Thank you so much and looking forward to hearing from you. Best, Jon

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Calcium ions labeled as solvent, not as ions
by Ute Roehrig 05 Dec '25

05 Dec '25

Hello, I am not sure if this is a problem in the structure or in ChimeraX or intentional, but I remarked that in PDB structure 7tba the calcium ions are labeled as "solvent" and not as "ions", although the element and atom type seem to be OK. I did not see the same in other PDB structures with calcium. Thank you for your help, Ute

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Subject: Request for Detailed Clarification on ChimeraX RMSD, Alignment Metrics, and Pruning Calculations
by EMMANUEL JAIME SIBAYAN 05 Dec '25

05 Dec '25

Hello, Good day. I am using ChimeraX for an academic research project involving protein structure comparison. Before proceeding with my analysis, I would like to request detailed clarification on how ChimeraX obtains specific structural comparison values. In particular, I would like to understand: how ChimeraX gets these values and what formulas or computational methods are used for each measurement. Specifically, I would like to ask about the following: 1. The recommended procedure for computing RMSD between two protein structures in ChimeraX, including the appropriate steps, commands, and settings to ensure a correct and reproducible measurement. 2. How ChimeraX determines aligned residue pairs during Matchmaker or similar alignment tools, including how residues are selected or excluded based on sequence alignment and structural fit. 3. The exact meaning and calculation method for “pruned atom pairs” in the alignment results. In particular, I would like clarification on the pruning process (for example, removal of atom pairs whose distances exceed a threshold) and how this affects the final reported values. 4. Whether RMSD in ChimeraX is calculated using all aligned atom pairs, pruned atom pairs only, or whether both values are available. I would also like to understand how to correctly interpret RMSD before pruning versus RMSD after pruning. 5. How ChimeraX performs structural alignment when the two sequences are identical but the predicted models have local deviations such as altered loops, turns, flexible regions, or insertions. 6. Recommended best practices when comparing three types of structures: • an experimental PDB crystal structure • an AlphaFold predicted structure • a Swiss-Model homology model 7. Any documentation, reference materials, or example workflows that explain the statistical reporting of structural comparison in ChimeraX, especially the following values: • RMSD, calculated as √(1/N Σ di²) • distance measurements between paired atoms, defined as √[(x1 − x2)² + (y1 − y2)² + (z1 − z2)²] • aligned residue counts • pruning thresholds and post-pruning atom pair counts This information will help ensure that the statistical evaluation in my study (including RMSD, aligned residues, and pruned atom pairs) is methodologically correct and consistent with ChimeraX standards. Thank you very much for your time and assistance. Your guidance will greatly improve the accuracy and reliability of my research analysis. Best regards, [Your Name] -- *The information or attachment(s) in this email is(are) strictly confidential and is(are) for the intended recipient only. Any unauthorized use, dissemination, or copy of this message or the information it contains is prohibited. The recipient has the responsibility to ensure the protection of any personal data included in this e-mail and its attachment(s). If you are not the intended recipient or you receive this email by mistake, please notify the sender immediately and delete the original message and attachment(s).*

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bug report - pip list failure
by replacement2＠gmail.com 04 Dec '25

04 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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Recording High Quality MD Trajectory Movie in ChimeraX
by Gourav Das 03 Dec '25

03 Dec '25

Dear ChimeraX users, I am recording the MD trajectory of a simulation as a movie in ChimeraX. However, the output quality of the movie is very low. How can I improve the quality of the movie? I would appreciate your guidance regarding this issue. Thank you for your support. With regards, Gourav Das Research Scholar Indian Institute of Technology Kharagpur West Bengal, India-721302 Mob: +91-6295251060 --

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