Fatal error: maxassem 1 has no models in it

[kristen.browne@…]

Below is an output from a run we did recently on NIH 3D.  This is a QS for 5TEP.  It looked into the pdbe_bio database and found no assemblies, and that seems to have errored it out.
According to Phil, the behaviour should be that if it doesn't find anything there, it should just use the open:5TEP command and try there.  This should be successful by our testing in ChimeraX.

Thanks!

K

NIH 3D Job (chimerax_flow -- 4f771bd8-f0a6-45a9-9c52-ab06d42fa0f8) Workflows version: 0.5.1 Run ID: a74fee15-2391-49e2-85a5-3fc3c3b5b394 Submission ID: 6870 File ID: None Input file URL: None Status URL: https://api-app-testing.threed.niaiddev.net/submissions/6870/runs/status Output file URL: https://api-app-testing.threed.niaiddev.net/submissions/6870/output-files Output files list URL: https://api-app-testing.threed.niaiddev.net/submissions/6870/runs/a74fee15-2391-49e2-85a5-3fc3c3b5b394/output-files File metadata URL: https://api-app-testing.threed.niaiddev.net/files/{file_id}/metadata<https://api-app-testing.threed.niaiddev.net/files/%7bfile_id%7d/metadata> Job directory: /tmp/nih3d_job_v44rk70d Input file: None treatment: None level: None accession code: 5TEP external database: ExternalDatabase.PDB is quick-submit: True
Task 'init_job': Finished task run for task with final state: 'Success'
Task 'get_file_local': Starting task run...
Task 'get_file_local': Finished task run for task with final state: 'Success'
Task 'check_file_extension': Starting task run...
Task 'check_file_extension': Finished task run for task with final state: 'Success'
Task 'get_chimerax_command': Starting task run...
Using: ExternalDatabase.PDB 5TEP
ChimeraX command: /usr/bin/chimerax --offscreen --exit --script '/usr/local/lib/python3.9/site-packages/nih_3d_workflows/flows/chimerax_flow/chimera_x_scripts/cx_unified.py --outdir /tmp/nih3d_job_v44rk70d --voxel_size_file /tmp/nih3d_job_v44rk70d/voxel_size.json --pixel_spacing_file /tmp/nih3d_job_v44rk70d/pixel_spacing.json --molecule_size_file /tmp/nih3d_job_v44rk70d/molecule_size.json --messages_file /tmp/nih3d_job_v44rk70d/messages.json --pdb 5TEP'
Task 'get_chimerax_command': Finished task run for task with final state: 'Success'
Task 'ShellTask': Starting task run...
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-nih3duser'
INFO:
available bundle cache has not been initialized yet
Qt WebEngine seems to be initialized from a plugin. Please set Qt::AA_ShareOpenGLContexts using QCoreApplication::setAttribute and QSGRendererInterface::OpenGLRhi using QQuickWindow::setGraphicsApi before constructing QGuiApplication.
INFO:
Executing: runscript /usr/local/lib/python3.9/site-packages/nih_3d_workflows/flows/chimerax_flow/chimera_x_scripts/cx_unified.py --outdir /tmp/nih3d_job_v44rk70d --voxel_size_file /tmp/nih3d_job_v44rk70d/voxel_size.json --pixel_spacing_file /tmp/nih3d_job_v44rk70d/pixel_spacing.json --molecule_size_file /tmp/nih3d_job_v44rk70d/molecule_size.json --messages_file /tmp/nih3d_job_v44rk70d/messages.json --pdb 5TEP
INFO:
Executing: open pdbe_bio:5TEP maxAssemblies 1 autoStyle false
STATUS:
No biogical assemblies available for 5TEP
INFO:
No biogical assemblies available for 5TEP
STATUS:
No biogical assemblies available for 5TEP
NIH3D FATAL ERROR: pdbe_bio:5TEP maxassem 1 has no models in it
Command failed with exit code 1


Kristen Browne, MSc, MscBMC
Contractor - MSC, Inc. | A Guidehouse Company
3D Modeling and Biovisualization Specialist
Bioinformatics and Computational Biosciences Branch (BCBB)<https://www.niaid.nih.gov/research/bioinformatics-computational-biosciences-branch>
OCICB/OSMO/OD/NIAID/NIH

5601 Fishers Lane, Room 4A60
Rockville, MD 20852
Office 202-253-5228

[Eric Pettersen]

Hi Kristen,

The 5TEP entry is obsolete and has been replaced by 6X47. The command works fine for 6X47. Maybe we can discuss this situation on Thursday too?

--Eric

[kristen.browne@…]

Sure.  I'll talk to Phil as he did not want to replace obsolete entries with the "new" data.  We may need to switch these from QS to CIF files instead if the problem is we can't fetch the data in these circumstances.

Thanks!

K

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Tuesday, December 6, 2022 4:05 PM
Cc: goddard@cgl.ucsf.edu; Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu
Subject: [EXTERNAL] Re: [ChimeraX] #8138: Fatal error: maxassem 1 has no models in it

#8138: Fatal error: maxassem 1 has no models in it
---------------------------------------+----------------------
          Reporter:  kristen.browne@...  |      Owner:  pett
              Type:  defect            |     Status:  feedback
          Priority:  normal            |  Milestone:
         Component:  Input/Output      |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback


Comment:

 Hi Kristen,
         The 5TEP entry is obsolete and has been replaced by 6X47.  The  command works fine for 6X47.  Maybe we can discuss this situation on  Thursday too?

 --Eric

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[Eric Pettersen]

It was decided to use the updated versions of these entries.