Hanging 6B1T

[kristen.browne@…]

We're running into several entries that are repeatedly hanging in ChimeraX.  The files open ok, but it may have to do with the sequence of events happening.  I'll file separate tickets for each.

This was a quicksubmit of 6B1T:


In this log you can see at 14:21:52 Preset implemented in Python; no expansion to individual ChimeraX commands available.

Then the task is killed after a long hang:

/tmp/prefect-otxftk23: line 1: 52 Killed /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_py_un945 --voxel_size_file /tmp/nih3d_job_py_un945/voxel_size.json --pixel_spacing_file /tmp/nih3d_job_py_un945/pixel_spacing.json --molecule_size_file /tmp/nih3d_job_py_un945/molecule_size.json --pdb 6B1T'


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

logs (6).txt​

[kristen.browne@…]

Added by email2trac

[Eric Pettersen]

6 million atoms

[Eric Pettersen]

Fixes for other similar structures has cut down the execution time here to minutes instead of hours.