chimeraX daily built, 2025 Oct 20, boltz-2 empty sequence line in yaml file
Dear ChimeraX developers, really a great job implementing boltz into chimeraX !! I have just installed the latest daily build 2025 Oct 20 on a Redhat 8 (Rocky 8 derivative) machine. Boltz-2 installs with no visible problem via chimeraX (like before). When I try to run predictions, I get an error which seems to be due to an almost empty yaml file created by chimeraX. Only the first line ("version 1.0") is in the yaml file. Boltz (of course) fails. There should be no problem with permissions. I just installed also the latest release of chimeraX and boltz-1 via chimeraX. Runs as expected. PS: I had no try yet on my mac (will check later). Best wishes, Guenter
Hi Guenter, I have seen that error when you don't specify any sequences to predict. I'll fix the code so it doesn't let you do that and explains the problem. What was your Boltz command shown in the ChimeraX Log? In the Boltz user interface panel you have to press the Add button to add a sequence to the prediction. Tom
On Oct 20, 2025, at 8:24 AM, Guenter Fritz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX developers,
really a great job implementing boltz into chimeraX !!
I have just installed the latest daily build 2025 Oct 20 on a Redhat 8 (Rocky 8 derivative) machine.
Boltz-2 installs with no visible problem via chimeraX (like before). When I try to run predictions, I get an error which seems to be due to an almost empty yaml file created by chimeraX. Only the first line ("version 1.0") is in the yaml file. Boltz (of course) fails.
There should be no problem with permissions. I just installed also the latest release of chimeraX and boltz-1 via chimeraX. Runs as expected.
PS: I had no try yet on my mac (will check later).
Best wishes,
Guenter
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Tom, thanks a lot for the prompt answer! I have checked meanwhile also my macs. Same like on my Rocky8 machine, does not work if I cp paste a sequence there. But surprisingly it works if I use the sequence of a loaded structure, e.g. from #1 => see below C.) daily build versions and macs: An old Intel macbook pro version 1.11.dev202510022155 (2025-10-02) Works (yes slow). I cp /paste a short sequence. Command: /Users/fritzg/boltz22/bin/boltz predict /Users/fritzg/Desktop/boltz_uq-test/uq-test.yaml --use_msa_server --accelerator cpu --no_kernels An M1 macbook pro: A.) version 1.11.dev202509090102 (2025-09-09) Works. I cp /paste a short sequence. Command: /Users/fritzg/boltz22/bin/boltz predict /Users/fritzg/Desktop/boltz_uq-test_20250909/uq-test_20250909.yaml --use_msa_server --accelerator gpu --no_kernels B.) version 1.11.dev202510170018 (2025-10-17) Fails. I cp /paste a short sequence. Command: /Users/fritzg/boltz22/bin/boltz predict /Users/fritzg/Desktop/boltz_uq_test_dev20251017_seq/uq_test_dev20251017_seq.yaml --use_msa_server --accelerator gpu --no_kernels Running boltz prediction failed with exit code 0: command: /Users/fritzg/boltz22/bin/boltz predict /Users/fritzg/Desktop/boltz_uq_test_dev20251017_seq/uq_test_dev20251017_seq.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. Failed to process /Users/fritzg/Desktop/boltz_uq_test_dev20251017_seq/uq_test_dev20251017_seq.yaml. Skipping. Error: 'NoneType' object is not iterable. The yaml input file is just: version: 1 sequences: But it works if I use the sequence of a loaded structure: C.) version 1.11.dev202510170018 (2025-10-17) Works. I use the sequence of mol #1 Command: /Users/fritzg/boltz22/bin/boltz predict /Users/fritzg/Desktop/boltz_uq_test__20251017_from_struc/uq_test__20251017_from_struc.yaml --accelerator gpu --no_kernels The yaml input file is: version: 1 sequences: - protein: id: [A] sequence: QQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLR msa: /Users/fritzg/Downloads/ChimeraX/BoltzMSA/uq-test_20250909/uq-test_20250909_0.csv Many thanks and best regards, Guenter
Hi Guenter,
I have seen that error when you don't specify any sequences to predict. I'll fix the code so it doesn't let you do that and explains the problem.
What was your Boltz command shown in the ChimeraX Log? In the Boltz user interface panel you have to press the Add button to add a sequence to the prediction.
Tom
On Oct 20, 2025, at 8:24 AM, Guenter Fritz via ChimeraX-users<chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX developers,
really a great job implementing boltz into chimeraX !!
I have just installed the latest daily build 2025 Oct 20 on a Redhat 8 (Rocky 8 derivative) machine.
Boltz-2 installs with no visible problem via chimeraX (like before). When I try to run predictions, I get an error which seems to be due to an almost empty yaml file created by chimeraX. Only the first line ("version 1.0") is in the yaml file. Boltz (of course) fails.
There should be no problem with permissions. I just installed also the latest release of chimeraX and boltz-1 via chimeraX. Runs as expected.
PS: I had no try yet on my mac (will check later).
Best wishes,
Guenter
_______________________________________________ ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Guenter, I see the boltz failure is only when you paste a sequence. I see I made a change on October 6, 2025 to check if you specify the "protein" option that it only accepts protein chains (if for instance you specify a whole structure that include both protein and DNA). And that change broke the code if you paste in a protein sequence. I've fixed it, so the October 21, 2025 build will work. Thanks for reporting the problem. Tom
On Oct 20, 2025, at 12:28 PM, Guenter Fritz <guenter.fritz.phenix.ccp4@gmail.com> wrote:
Hi Tom,
thanks a lot for the prompt answer!
I have checked meanwhile also my macs. Same like on my Rocky8 machine, does not work if I cp paste a sequence there. But surprisingly it works if I use the sequence of a loaded structure, e.g. from #1 => see below C.)
daily build versions and macs:
An old Intel macbook pro version 1.11.dev202510022155 (2025-10-02) Works (yes slow). I cp /paste a short sequence. Command: /Users/fritzg/boltz22/bin/boltz predict /Users/fritzg/Desktop/boltz_uq-test/uq-test.yaml --use_msa_server --accelerator cpu --no_kernels
An M1 macbook pro: A.) version 1.11.dev202509090102 (2025-09-09) Works. I cp /paste a short sequence. Command: /Users/fritzg/boltz22/bin/boltz predict /Users/fritzg/Desktop/boltz_uq-test_20250909/uq-test_20250909.yaml --use_msa_server --accelerator gpu --no_kernels
B.) version 1.11.dev202510170018 (2025-10-17) Fails. I cp /paste a short sequence. Command: /Users/fritzg/boltz22/bin/boltz predict /Users/fritzg/Desktop/boltz_uq_test_dev20251017_seq/uq_test_dev20251017_seq.yaml --use_msa_server --accelerator gpu --no_kernels
Running boltz prediction failed with exit code 0: command: /Users/fritzg/boltz22/bin/boltz predict /Users/fritzg/Desktop/boltz_uq_test_dev20251017_seq/uq_test_dev20251017_seq.yaml --use_msa_server --accelerator gpu --no_kernels stdout: Boltz version 2.2.0 MSA server enabled: https://api.colabfold.com <https://api.colabfold.com/> MSA server authentication: no credentials provided Checking input data. Processing 1 inputs with 1 threads. Failed to process /Users/fritzg/Desktop/boltz_uq_test_dev20251017_seq/uq_test_dev20251017_seq.yaml. Skipping. Error: 'NoneType' object is not iterable.
The yaml input file is just: version: 1 sequences:
But it works if I use the sequence of a loaded structure: C.) version 1.11.dev202510170018 (2025-10-17) Works. I use the sequence of mol #1 Command: /Users/fritzg/boltz22/bin/boltz predict /Users/fritzg/Desktop/boltz_uq_test__20251017_from_struc/uq_test__20251017_from_struc.yaml --accelerator gpu --no_kernels
The yaml input file is: version: 1 sequences: - protein: id: [A] sequence: QQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLR msa: /Users/fritzg/Downloads/ChimeraX/BoltzMSA/uq-test_20250909/uq-test_20250909_0.csv
Many thanks and best regards, Guenter
Hi Guenter,
I have seen that error when you don't specify any sequences to predict. I'll fix the code so it doesn't let you do that and explains the problem.
What was your Boltz command shown in the ChimeraX Log? In the Boltz user interface panel you have to press the Add button to add a sequence to the prediction.
Tom
On Oct 20, 2025, at 8:24 AM, Guenter Fritz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> <mailto:chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX developers,
really a great job implementing boltz into chimeraX !!
I have just installed the latest daily build 2025 Oct 20 on a Redhat 8 (Rocky 8 derivative) machine.
Boltz-2 installs with no visible problem via chimeraX (like before). When I try to run predictions, I get an error which seems to be due to an almost empty yaml file created by chimeraX. Only the first line ("version 1.0") is in the yaml file. Boltz (of course) fails.
There should be no problem with permissions. I just installed also the latest release of chimeraX and boltz-1 via chimeraX. Runs as expected.
PS: I had no try yet on my mac (will check later).
Best wishes,
Guenter
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
-
Guenter Fritz -
Tom Goddard