Index Error: list index out of range

[kristen.browne@…]

Using most recent NIH 3D preset
The attached is failing in NIH 3D with the following logs:

...
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/hbonds/hbond.py", line 603, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/hbonds/acceptor_geom.py", line 115, in acc_theta_tau
up_pos = bisectors[0]
IndexError: list index out of range
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__main__.py", line 747, in init
run(sess, 'runscript %s' % script)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/runscript.py", line 38, in runscript
open_python_script(session, open(script_file, 'rb'), script_file, argv=argv)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/scripting.py", line 90, in open_python_script
raise UserError('Error opening python file %s' % stream.name)
chimerax.core.errors.UserError: Error opening python file /usr/local/lib/python3.9/site-packages/nih_3d_workflows/flows/chimerax_flow/chimera_x_scripts/cx_unified.py
Command failed with exit code 70


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

HAG1.pdb​

[kristen.browne@…]

Added by email2trac

[pett]

Okay, this structure is a complete mess. For instance, look at residue 377. What do you want to do in a case like this? Actually throw an error, or try to soldier on and output whatever files happen to "work", such as it is?

[pett]

Actually this is a case where, because the coordinates are so bad, rebonding actually makes things worse. Of course, there are far more cases where rebonding improves things. Sigh.

[kristen.browne@…]

If this is a really bad structure, let me talk to Phil about replacing the file.  If it's something that's not trivial to fix and is an exception rather than a rule, we shouldn't try to accommodate.  Sometimes errors are there for a reason 😊

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Friday, December 16, 2022 12:34 AM
Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu; Cruz, Phil (NIH/NIAID) [C] <phil.cruz@nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #8198: Index Error: list index out of range

#8198: Index Error: list index out of range
-----------------------------------------+----------------------
          Reporter:  kristen.browne@…    |      Owner:  pett
              Type:  defect              |     Status:  feedback
          Priority:  normal              |  Milestone:
         Component:  Structure Analysis  |    Version:
        Resolution:                      |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+----------------------

Comment (by pett):

 Actually this is a case where, because the coordinates are so bad,  rebonding actually makes things worse.  Of course, there are far more  cases where rebonding improves things.  Sigh.

--
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[kristen.browne@…]

Phil says to "try to soldier on and output whatever files happen to "work", such as it is.  He wants to try and accommodate models that are at various stages of refinement.

K

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Friday, December 16, 2022 8:41 AM
To: pett@cgl.ucsf.edu; Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>
Cc: Cruz, Phil (NIH/NIAID) [C] <phil.cruz@nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #8198: Index Error: list index out of range

#8198: Index Error: list index out of range
-----------------------------------------+----------------------
          Reporter:  kristen.browne@…    |      Owner:  pett
              Type:  defect              |     Status:  feedback
          Priority:  normal              |  Milestone:
         Component:  Structure Analysis  |    Version:
        Resolution:                      |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+----------------------

Comment (by kristen.browne@…):

 {{{
 If this is a really bad structure, let me talk to Phil about replacing the  file.  If it's something that's not trivial to fix and is an exception  rather than a rule, we shouldn't try to accommodate.  Sometimes errors are  there for a reason 😊

 -----Original Message-----
 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 Sent: Friday, December 16, 2022 12:34 AM
 Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>;  pett@cgl.ucsf.edu; Cruz, Phil (NIH/NIAID) [C] <phil.cruz@nih.gov>
 Subject: [EXTERNAL] Re: [ChimeraX] #8198: Index Error: list index out of  range

 #8198: Index Error: list index out of range
 -----------------------------------------+----------------------
           Reporter:  kristen.browne@…    |      Owner:  pett
               Type:  defect              |     Status:  feedback
           Priority:  normal              |  Milestone:
          Component:  Structure Analysis  |    Version:
         Resolution:                      |   Keywords:
         Blocked By:                      |   Blocking:
 Notify when closed:                      |   Platform:  all
            Project:  ChimeraX            |
 -----------------------------------------+----------------------

 Comment (by pett):

  Actually this is a case where, because the coordinates are so bad,  rebonding actually makes things worse.  Of course, there are far more  cases where rebonding improves things.  Sigh.

 --
 Ticket URL:
 <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F8198%23comment%3A3&data=05%7C01%7Ckristen.browne%40nih.gov%7C2c03bd435d714c9f32f608dadf6b2698%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638067948566961190%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=6HoS5TlYd1OwpFVDiwaNXc7D2DkElQPy74gpmP%2BiVaY%3D&reserved=0>
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 <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C01%7Ckristen.browne%40nih.gov%7C2c03bd435d714c9f32f608dadf6b2698%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638067948566961190%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yIwvCiIEN7NCO3ngjs8kZG7dc4V8IhiDSFC9vS23Ouk%3D&reserved=0>
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 }}}

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[pett]

Changed cx_unified.py so that if rebonding produces a mess (atoms with > 4 bonds), it reverts to the original bonds. Michal, it seems like GitHub integrated this latest change with the currently pending pull request.