OpenFold prediction: "MMseqs2 API is giving errors", empty MSA gets cached by ChimeraX

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-26.5.2-arm64-arm-64bit-Mach-O
ChimeraX Version: 1.13.dev202607102107 (2026-07-10 21:07:32 UTC)
Description
Colabfold search gave an error in running an OpenFold prediction and no MSA was returned.  But despite this the empty MSA was cached by ChimeraX and used in the next prediction with the same sequence.  The MSA should not be cached if Colabfold raised an error.

Log:
UCSF ChimeraX version: 1.13.dev202607102107 (2026-07-10)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> openfold install /Users/goddard/openfold_py314

Successfully created OpenFold Python environment
/Users/goddard/openfold_py314.  
Now installing OpenFold and required packages from PyPi. This may take tens of
of minutes since OpenFold uses many other packages totaling about 1 Gbyte of
disk space including torch, scipy, rdkit, llvmlite, sympy, pandas, numpy,
wandb, numba...  
/Users/goddard/openfold_py314/bin/python -m pip install
https://github.com/RBVI/openfold-3/archive/chimerax_openfold_preview2.zip  
Collecting
https://github.com/RBVI/openfold-3/archive/chimerax_openfold_preview2.zip  
  
Using cached chimerax_openfold_preview2.zip  
  
Installing build dependencies: started  
  
Installing build dependencies: finished with status 'done'  
  
Getting requirements to build wheel: started  
  
Getting requirements to build wheel: finished with status 'done'  
  
Preparing metadata (pyproject.toml): started  
  
Preparing metadata (pyproject.toml): finished with status 'done'  
  
Collecting awscli (from openfold3==0.4.0)  
  
Using cached awscli-1.45.46-py3-none-any.whl.metadata (11 kB)  
  
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Downloading awscrt-0.35.0-cp311-abi3-macosx_10_15_universal2.whl.metadata (11
kB)  
  
Collecting torch (from openfold3==0.4.0)  
  
Downloading torch-2.13.0-cp311-cp311-macosx_14_0_arm64.whl.metadata (39 kB)  
  
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Using cached pytorch_lightning-2.6.5-py3-none-any.whl.metadata (21 kB)  
  
Collecting numpy (from openfold3==0.4.0)  
  
Using cached numpy-2.4.6-cp311-cp311-macosx_14_0_arm64.whl.metadata (6.6 kB)  
  
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Using cached pandas-3.0.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (79 kB)  
  
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Using cached pyyaml-6.0.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.4 kB)  
  
Collecting requests (from openfold3==0.4.0)  
  
Downloading requests-2.34.2-py3-none-any.whl.metadata (4.8 kB)  
  
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Using cached scipy-1.17.1-cp311-cp311-macosx_14_0_arm64.whl.metadata (62 kB)  
  
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Using cached tqdm-4.68.4-py3-none-any.whl.metadata (57 kB)  
  
Collecting typing-extensions (from openfold3==0.4.0)  
  
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Using cached wandb-0.28.0-py3-none-macosx_12_0_arm64.whl.metadata (11 kB)  
  
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Using cached ml_collections-1.1.0-py3-none-any.whl.metadata (22 kB)  
  
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Using cached biotite-1.6.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.5 kB)  
  
Collecting rdkit (from openfold3==0.4.0)  
  
Using cached rdkit-2026.3.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (3.8
kB)  
  
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Using cached boto3-1.43.46-py3-none-any.whl.metadata (6.6 kB)  
  
Collecting memory_profiler (from openfold3==0.4.0)  
  
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Downloading lmdb-2.2.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (1.2 kB)  
  
Collecting ijson (from openfold3==0.4.0)  
  
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Collecting deepspeed==0.18.4 (from openfold3==0.4.0)  
  
Using cached deepspeed-0.18.4-py3-none-any.whl  
  
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Using cached pdbeccdutils-1.0.4-py3-none-any.whl.metadata (5.5 kB)  
  
Collecting kalign-python (from openfold3==0.4.0)  
  
Downloading kalign_python-3.6.0-cp311-cp311-macosx_14_0_arm64.whl.metadata (15
kB)  
  
Collecting einops (from deepspeed==0.18.4->openfold3==0.4.0)  
  
Using cached einops-0.8.2-py3-none-any.whl.metadata (13 kB)  
  
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Collecting msgpack (from deepspeed==0.18.4->openfold3==0.4.0)  
  
Using cached msgpack-1.2.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (8.3 kB)  
  
Collecting ninja (from deepspeed==0.18.4->openfold3==0.4.0)  
  
Using cached ninja-1.13.0-py3-none-macosx_10_9_universal2.whl.metadata (5.1
kB)  
  
Collecting packaging>=20.0 (from deepspeed==0.18.4->openfold3==0.4.0)  
  
Using cached packaging-26.2-py3-none-any.whl.metadata (3.5 kB)  
  
Collecting psutil (from deepspeed==0.18.4->openfold3==0.4.0)  
  
Using cached psutil-7.2.2-cp36-abi3-macosx_11_0_arm64.whl.metadata (22 kB)  
  
Collecting py-cpuinfo (from deepspeed==0.18.4->openfold3==0.4.0)  
  
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Collecting torchmetrics>0.7.0 (from pytorch-lightning>=2.1->openfold3==0.4.0)  
  
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Collecting attrs>=17.3.0 (from
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Requirement already satisfied: setuptools>=77.0.3 in
/Users/goddard/openfold_py314/lib/python3.11/site-packages (from
torch->openfold3==0.4.0) (82.0.1)  
  
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Using cached hjson-3.1.0-py3-none-any.whl (54 kB)  
  
Downloading ijson-3.5.1-cp311-cp311-macosx_11_0_arm64.whl (60 kB)  
  
Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)  
  
Using cached markupsafe-3.0.3-cp311-cp311-macosx_11_0_arm64.whl (12 kB)  
  
Downloading kalign_python-3.6.0-cp311-cp311-macosx_14_0_arm64.whl (221 kB)  
  
Downloading lmdb-2.2.1-cp311-cp311-macosx_11_0_arm64.whl (114 kB)  
  
Using cached memory_profiler-0.61.0-py3-none-any.whl (31 kB)  
  
Using cached ml_collections-1.1.0-py3-none-any.whl (76 kB)  
  
Using cached absl_py-2.5.0-py3-none-any.whl (137 kB)  
  
Using cached ninja-1.13.0-py3-none-macosx_10_9_universal2.whl (310 kB)  
  
Using cached pandas-3.0.3-cp311-cp311-macosx_11_0_arm64.whl (9.9 MB)  
  
Using cached pdbeccdutils-1.0.4-py3-none-any.whl (1.1 MB)  
  
Using cached gemmi-0.7.5-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB)  
  
Using cached pillow-12.3.0-cp311-cp311-macosx_11_0_arm64.whl (4.8 MB)  
  
Using cached rdkit-2026.3.3-cp311-cp311-macosx_11_0_arm64.whl (29.9 MB)  
  
Using cached psutil-7.2.2-cp36-abi3-macosx_11_0_arm64.whl (129 kB)  
  
Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)  
  
Using cached wandb-0.28.0-py3-none-macosx_12_0_arm64.whl (24.3 MB)  
  
Using cached protobuf-7.35.1-cp310-abi3-macosx_10_9_universal2.whl (433 kB)  
  
Using cached click-8.4.2-py3-none-any.whl (119 kB)  
  
Using cached gitpython-3.1.50-py3-none-any.whl (212 kB)  
  
Using cached gitdb-4.0.12-py3-none-any.whl (62 kB)  
  
Using cached smmap-5.0.3-py3-none-any.whl (24 kB)  
  
Using cached sentry_sdk-2.64.0-py3-none-any.whl (498 kB)  
  
Using cached platformdirs-4.10.0-py3-none-any.whl (22 kB)  
  
Building wheels for collected packages: openfold3  
  
Building wheel for openfold3 (pyproject.toml): started  
  
Building wheel for openfold3 (pyproject.toml): finished with status 'done'  
  
Created wheel for openfold3: filename=openfold3-0.4.0-py3-none-any.whl
size=6693175
sha256=4b1ce7167f769e1ccc1ca67fe8ed2cee60e976d0fa5af7af2f07eea7308e83a2  
  
Stored in directory:
/private/var/folders/jb/f14hkn9s19l691b68w_lvm0w0000gn/T/pip-ephem-wheel-
cache-
uhzfajo_/wheels/25/04/58/ce909e85e21805a2ce378164c4710e7ed450781c03f8300c78  
  
Successfully built openfold3  
  
Installing collected packages: py-cpuinfo, mpmath, hjson, func_timeout,
urllib3, typing-extensions, tqdm, sympy, smmap, six, PyYAML, pyasn1, psutil,
protobuf, propcache, platformdirs, pillow, packaging, numpy, ninja, networkx,
multidict, msgpack, MarkupSafe, lmdb, jmespath, ijson, idna, gemmi, fsspec,
frozenlist, filelock, einops, docutils, colorama, click, charset_normalizer,
certifi, awscrt, attrs, annotated-types, aiohappyeyeballs, absl-py, yarl,
typing-inspection, sentry-sdk, scipy, rsa, requests, rdkit, python-dateutil,
pydantic-core, ml-collections, memory_profiler, lightning-utilities, kalign-
python, jinja2, gitdb, aiosignal, torch, pydantic, pdbeccdutils, pandas,
gitpython, botocore, biotraj, aiohttp, wandb, torchmetrics, s3transfer,
deepspeed, biotite, pytorch-lightning, boto3, awscli, openfold3  
  
  
  
Successfully installed MarkupSafe-3.0.3 PyYAML-6.0.3 absl-py-2.5.0
aiohappyeyeballs-2.7.1 aiohttp-3.14.1 aiosignal-1.4.0 annotated-types-0.7.0
attrs-26.1.0 awscli-1.45.46 awscrt-0.35.0 biotite-1.6.0 biotraj-1.2.2
boto3-1.43.46 botocore-1.43.46 certifi-2026.6.17 charset_normalizer-3.4.9
click-8.4.2 colorama-0.4.6 deepspeed-0.18.4 docutils-0.19 einops-0.8.2
filelock-3.29.7 frozenlist-1.8.0 fsspec-2026.6.0 func_timeout-4.3.5
gemmi-0.7.5 gitdb-4.0.12 gitpython-3.1.50 hjson-3.1.0 idna-3.18 ijson-3.5.1
jinja2-3.1.6 jmespath-1.1.0 kalign-python-3.6.0 lightning-utilities-0.15.3
lmdb-2.2.1 memory_profiler-0.61.0 ml-collections-1.1.0 mpmath-1.3.0
msgpack-1.2.1 multidict-6.7.1 networkx-3.6.1 ninja-1.13.0 numpy-2.4.6
openfold3-0.4.0 packaging-26.2 pandas-3.0.3 pdbeccdutils-1.0.4 pillow-12.3.0
platformdirs-4.10.0 propcache-0.5.2 protobuf-7.35.1 psutil-7.2.2 py-
cpuinfo-9.0.0 pyasn1-0.6.4 pydantic-2.13.4 pydantic-core-2.46.4 python-
dateutil-2.9.0.post0 pytorch-lightning-2.6.5 rdkit-2026.3.3 requests-2.34.2
rsa-4.7.2 s3transfer-0.19.1 scipy-1.17.1 sentry-sdk-2.64.0 six-1.17.0
smmap-5.0.3 sympy-1.14.0 torch-2.13.0 torchmetrics-1.9.0 tqdm-4.68.4 typing-
extensions-4.16.0 typing-inspection-0.4.2 urllib3-2.7.0 wandb-0.28.0
yarl-1.24.2  
  
Installing kalign sequence alignment program to
/Users/goddard/openfold_py314/bin  
/Users/goddard/openfold_py314/bin/python
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/openfold/install_kalign.py  
Installed kalign  
Downloading OpenFold model parameters (2 GB) to ~/.openfold3  
/Users/goddard/openfold_py314/bin/python
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/openfold/download_weights.py  
W0710 17:23:21.538000 8742 site-
packages/torch/distributed/elastic/multiprocessing/redirects.py:35] NOTE:
Redirects are currently not supported in MacOs.  
  
Setting up OpenFold cache directory...  
  
OpenFold3 parameters may already be installed at: /Users/goddard/.openfold3  
  
Using existing parameters at: /Users/goddard/.openfold3  
  
Starting Biotite CCD setup...  
  
Downloading s3://openfold3-data/components.bcif (0.06 GB) to
/Users/goddard/openfold_py314/lib/python3.11/site-
packages/biotite/structure/info/components.bcif...  
  
components.bcif: 0%| | 0.00/63.4M [00:00<?, ?B/s] components.bcif: 0%| | 262k/63.4M [00:00<01:10, 901kB/s] components.bcif: 12%|█▏ | 7.60M/63.4M [00:00<00:02, 24.2MB/s] components.bcif: 31%|███ | 19.4M/63.4M [00:00<00:00, 53.7MB/s] components.bcif: 50%|████▉ | 31.5M/63.4M [00:00<00:00, 74.3MB/s] components.bcif: 65%|██████▍ | 40.9M/63.4M [00:00<00:00, 79.2MB/s] components.bcif: 79%|███████▉ | 50.3M/63.4M [00:00<00:00, 76.1MB/s] components.bcif: 93%|█████████▎| 58.9M/63.4M [00:01<00:00, 54.1MB/s] components.bcif: 100%|██████████| 63.4M/63.4M [00:01<00:00, 36.2MB/s]  
  
Download complete.  
  
OpenFold model parameters are installed in ~/.openfold3  
Successfully installed OpenFold program and neural net weights.  

> ui tool show OpenFold

/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/grako/codegen/objectmodel.py:20: SyntaxWarning: "\d" is an invalid
escape sequence. Such sequences will not work in the future. Did you mean
"\\\d"? A raw string is also an option.  
NODE_NAME_PATTERN = '(?!\d)\w+(' + BASE_CLASS_TOKEN + '(?!\d)\w+)*'  
[Repeated 1 time(s)]

> openfold predict protein Q52085 name Q52085

Running OpenFold prediction of protein with 320 residues on gpu  
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/OpenFoldMSA/Q52085  
Confidence pTM 0.75, , pLDDT 81  
OpenFold prediction completed in 119 seconds (start openfold 41 sec,
initialize neural net 26 sec, sequence search 0 sec, structure inference 40
sec)  
Please cite OpenFold-1 Democratizing Biomolecular Interaction Modeling.
BioRxiv https://doi.org/10.1101/2024.11.19.624167 if you use these
predictions.  

> open
> /Users/goddard/Desktop/openfold/Q52085_2/Q52085/seed_42/Q52085_seed_42_sample_1_model.cif
> logInfo false

> openfold predict protein Q52085 protein Q52085 name Q52085

Running OpenFold prediction of protein with 640 residues on gpu  
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/OpenFoldMSA/Q52085  
Confidence pTM 0.45, ipTM 0.11, pLDDT 76  
OpenFold prediction completed in 197 seconds (start openfold 3 sec, initialize
neural net 25 sec, sequence search 0 sec, structure inference 154 sec)  

> open
> /Users/goddard/Desktop/openfold/Q52085_3/Q52085/seed_42/Q52085_seed_42_sample_1_model.cif
> logInfo false

> open 9q70

Summary of feedback from opening 9q70 fetched from pdb  
---  
note | Fetching compressed mmCIF 9q70 from https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/q7/pdb_00009q70/structures/pdb_00009q70.cif.gz  
  
9q70 title:  
Solution-State Structures of Arachidonic acid-Liganded LFABP Liver Fatty Acid-
Binding Protein [more info...]  
  
Chain information for 9q70  
---  
Chain | Description | UniProt  
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A 3.13/A 3.14/A 3.15/A | Fatty acid-binding protein, liver | FABPL_RAT 1-127  
  

> view

> openfold predict protein #3.1/A name 9q70

Running OpenFold prediction of protein with 127 residues on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Running openfold prediction failed with exit code 1:  
command:  
/Users/goddard/openfold_py314/bin/run_openfold predict --query_json=9q70.json
--runner_yaml=msa_path.yaml --num_diffusion_samples=1 --device=gpu  
stdout:  
  
stderr:  
W0710 17:33:12.713000 9116 site-
packages/torch/distributed/elastic/multiprocessing/redirects.py:35] NOTE:
Redirects are currently not supported in MacOs.  
2026-07-10 17:33:14,843 - INFO - No inference_ckpt_path or inference_ckpt_name
provided, selecting default checkpoint.  
2026-07-10 17:33:14,843 - INFO - Set diffusion samples to 1  
2026-07-10 17:33:14,849 - INFO - Operating system is Darwin, not Linux.
Skipping ulimit adjustments.  
2026-07-10 17:33:14,852 - INFO - Loading weights from
/Users/goddard/.openfold3/of3-p2-155k.pt  
2026-07-10 17:33:15,262 - INFO - Finished loading weights  
2026-07-10 17:33:15,262 - INFO - Loading model state dictionary  
2026-07-10 17:33:40,373 - WARNING - No version_tensor is found for this
checkpoint.Assuming the user knows checkpoints are parameters are compatible,
continuing...  
2026-07-10 17:33:40,519 - INFO - Finished loading model state dictionary  
2026-07-10 17:33:40,541 - INFO - Beginning prediction inference  
2026-07-10 17:33:40,544 - INFO - GPU available: True (mps), used: True  
2026-07-10 17:33:40,544 - INFO - TPU available: False, using: 0 TPU cores  
2026-07-10 17:33:40,544 - INFO - 💡 Tip: For seamless cloud logging and
experiment tracking, try installing
[litlogger](https://pypi.org/project/litlogger/) to enable LitLogger, which
logs metrics and artifacts automatically to the Lightning Experiments
platform.  
2026-07-10 17:33:40,545 - INFO - 💡 Tip: For seamless cloud uploads and
versioning, try installing [litmodels](https://pypi.org/project/litmodels/) to
enable LitModelCheckpoint, which syncs automatically with the Lightning model
registry.  
2026-07-10 17:33:40,545 - INFO - Using output directory: colabfold_msas for
ColabFold MSAs.  
2026-07-10 17:33:40,546 - INFO - Submitting 1 sequences to the Colabfold MSA
server for main MSAs...  
0%| | 0/150 [elapsed: 00:00 remaining: ?] SUBMIT: 0%| | 0/150 [elapsed: 00:00 remaining: ?]2026-07-10 17:33:41,371 - ERROR - Server didn't reply with json: invalid ID  
  
SUBMIT: 0%| | 0/150 [elapsed: 00:00 remaining: ?]  
Traceback (most recent call last):  
File "/Users/goddard/openfold_py314/bin/run_openfold", line 6, in <module>  
sys.exit(cli())  
^^^^^  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/click/core.py", line 1569, in __call__  
return self.main(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/click/core.py", line 1490, in main  
rv = self.invoke(ctx)  
^^^^^^^^^^^^^^^^  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/click/core.py", line 1970, in invoke  
return _process_result(sub_ctx.command.invoke(sub_ctx))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/click/core.py", line 1353, in invoke  
return ctx.invoke(self.callback, **ctx.params)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/click/core.py", line 907, in invoke  
return callback(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/openfold3/run_openfold.py", line 257, in predict  
expt_runner.run(query_set)  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/openfold3/entry_points/experiment_runner.py", line 704, in run  
self.trainer.predict(  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 941, in predict  
return call._call_and_handle_interrupt(  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/pytorch_lightning/trainer/call.py", line 49, in
_call_and_handle_interrupt  
return trainer_fn(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 990, in _predict_impl  
results = self._run(model, ckpt_path=ckpt_path, weights_only=weights_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 1037, in _run  
self._data_connector.prepare_data()  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/pytorch_lightning/trainer/connectors/data_connector.py", line 95, in
prepare_data  
call._call_lightning_datamodule_hook(trainer, "prepare_data")  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/pytorch_lightning/trainer/call.py", line 199, in
_call_lightning_datamodule_hook  
return fn(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/openfold3/core/data/framework/data_module.py", line 604, in
prepare_data  
self.inference_config.query_set = preprocess_colabfold_msas(  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/openfold3/core/data/tools/colabfold_msa_server.py", line 1053, in
preprocess_colabfold_msas  
colabfold_query_runner.query_format_main()  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/openfold3/core/data/tools/colabfold_msa_server.py", line 698, in
query_format_main  
a3m_lines_main = query_colabfold_msa_server(  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/openfold_py314/lib/python3.11/site-
packages/openfold3/core/data/tools/colabfold_msa_server.py", line 279, in
query_colabfold_msa_server  
raise Exception(  
Exception: MMseqs2 API is giving errors.Please confirm your input is a valid
protein sequence.If error persists, please try again an hour later.  
  

> openfold predict protein #3.1/A name 9q70

Running OpenFold prediction of protein with 127 residues on gpu  
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/OpenFoldMSA/9q70  
Confidence pTM 0.73, , pLDDT 82  
OpenFold prediction completed in 46 seconds (start openfold 3 sec, initialize
neural net 26 sec, sequence search 0 sec, structure inference 11 sec)  

> open
> /Users/goddard/Desktop/openfold/9q70_1/9q70/seed_42/9q70_seed_42_sample_1_model.cif
> logInfo false

Matchmaker 9q70, chain A (#3.1) with 9q70_seed_42_sample_1_model.cif, chain A
(#4), sequence alignment score = 635.5  
RMSD between 101 pruned atom pairs is 1.244 angstroms; (across all 127 pairs:
1.777)  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.14.6
Locale: C.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 Performance and 8 Efficiency)
      Memory: 64 GB
      System Firmware Version: 18000.121.3
      OS Loader Version: 18000.121.3

Software:

    System Software Overview:

      System Version: macOS 26.5.2 (25F84)
      Kernel Version: Darwin 25.5.0
      Time since boot: 11 days, 48 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.7.1
    aiohttp: 3.13.4
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.14.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.8.0
    build: 1.5.0
    certifi: 2026.6.17
    cftime: 1.6.5
    charset-normalizer: 3.4.9
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.3.1
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.70.2
    ChimeraX-AtomicLibrary: 14.4.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.13.dev202607102107
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.6
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DAQplugin: 1.0.0
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.4
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.5
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchAlign: 1.2.1
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.4.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.17
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.24
    ChimeraX-ModelPanel: 1.6.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.16.2
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.10.2
    ChimeraX-ProNA3D: 0.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.19.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.20
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.53.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.5
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.4.2
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.15.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.8
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    flatbuffers: 25.12.19
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 1.0.1
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h2: 4.3.0
    h5py: 3.16.0
    hpack: 4.2.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    hyperframe: 6.1.0
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2026.6.26
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.3.0
    ipython: 9.14.1
    ipython_pygments_lexers: 1.1.1
    jedi: 0.20.0
    Jinja2: 3.1.6
    joblib: 1.5.3
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.9.1
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    llvmlite: 0.47.0
    lxml: 6.0.2
    lz4: 4.4.5
    Markdown: 3.8.2
    markdown-it-py: 4.2.0
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.2
    mcp: 1.18.0
    mdurl: 0.1.2
    mlx: 0.31.2
    mlx-metal: 0.31.2
    mrcfile: 1.5.4
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.23.0
    ndindex: 1.10.1
    nest-asyncio2: 1.7.2
    netCDF4: 1.7.4
    networkx: 3.3
    numba: 0.65.1
    numexpr: 2.14.1
    numpy: 2.4.6
    onnxruntime: 1.26.0
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 26.1.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.0
    plotly: 6.8.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    protobuf: 7.34.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.2
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.20.0
    Pygments: 2.18.0
    pyKVFinder: 0.9.3
    pynmrstar: 3.5.1
    pynndescent: 0.6.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.1.1
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.32
    pyzmq: 27.1.0
    qtconsole: 5.7.2
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    rich: 15.0.0
    roman-numerals: 4.1.0
    rpds-py: 2026.6.3
    scikit-learn: 1.9.0
    scipy: 1.17.1
    setuptools: 82.0.1
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.4.5
    stack-data: 0.6.3
    starlette: 1.3.1
    superqt: 0.7.6
    tables: 3.11.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tomlkit: 0.15.0
    tornado: 6.5.7
    tqdm: 4.68.3
    traitlets: 5.15.1
    typing-inspection: 0.4.2
    typing_extensions: 4.16.0
    umap-learn: 0.5.12
    urllib3: 2.7.0
    uv: 0.11.26
    uvicorn: 0.51.0
    wcwidth: 0.8.2
    webcolors: 24.11.1
    wheel: 0.47.0
    wheel-filename: 1.4.2
    yarl: 1.24.2

[Tom Goddard]

I quit ChimeraX and reran this 5 minutes later after removing the ChimeraX MSA cache entry and got the exact same error, and the empty MSA was again cached.

[Tom Goddard]

Tried with different PDB 9rmq 5 minutes later and got the same error. So the problem does not appear to be sequence dependent. The Colabfold MSA server is probably really broken.

[Tom Goddard]

Tried Boltz 9q70 with ChimeraX 1.12 and standalone astral python 3.11 and Colabfold MSA worked with 3922 sequences found.

Then I tried 9q70 again with OpenFold and got the same Colabfold MSA error.

Then I tried 9q70 again with OpenFold with astral python 3.11 and ChimeraX 1.12 and again the Colabfold MSA server failed.

Then I tried 9q70 again with OpenFold using venv and ChimeraX 1.12 and it worked.

Then I tried 9q70 again with OpenFold and astral python 3.11 and my development build and it failed.

So it appears that the problem is that OpenFold use of Colabfold with the astral python 3.11 is failing.

[Tom Goddard]

OpenFold with astral python is using requests version 2.34.2, and does not have certifi
Boltz with astral python is using requests version 2.32.3 and certifi-2026.6.17.
OpenFold with venv and ChimeraX 1.12 does not have requests in the venv so it falls back to the ChimeraX version 2.32.5 and certifi-2025.7.14.

Reinstalling OpenFold with version 2.32.3 of requests and not certifi and the Colabfold MSA search worked. Frighteningly the RBVI OpenFold 3 does not pin versions of many dependencies. Nor does the aqlaboratory OpenFold 3 pin versions.

I tried requests 2.32.5 that ChimeraX 1.12 uses and that also worked with OpenFold and astral python.

I've changed the RBVI OpenFold git repository to pin requests to 2.32.5.

I tested that ChimeraX 1.12 venv install still works with new requests pin.

[Tom Goddard]

Fixed.

Tested the pinned requests 2.32.5 with ChimeraX openfold install using Astral Python 3.11 on Mac, Linux and Windows and Colabfold worked.