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