raise ValueError("z_align endpoints must be distinct")

[kristen.browne@…]

This may be an issue with the file itself, but wanted to check as have not seen this error when re-run previously:
...
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/preset_mgr/cmd.py", line 50, in preset_cmd
run_preset(session, cat, matches[0])
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/preset_mgr/cmd.py", line 71, in run_preset
session.presets.preset_function(category, preset)()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/preset_mgr/manager.py", line 60, in cb
bi.run_provider(self.session, name, self)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/home/nih3duser/.local/share/ChimeraX/1.6/site-packages/chimerax/nih_presets/__init__.py", line 22, in run_provider
run_preset(session, name, mgr, **kw)
File "/home/nih3duser/.local/share/ChimeraX/1.6/site-packages/chimerax/nih_presets/presets.py", line 302, in run_preset
mgr.execute(cmd)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/preset_mgr/manager.py", line 88, in execute
run(self.session, line, log=False)
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/coulombic/cmd.py", line 88, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/coulombic/coulombic.py", line 99, in assign_charges
add_charges(session, charged_residues, method=charge_method, status=status,
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/add_charge/charge.py", line 26, in add_charges
add_nonstandard_res_charges(session, res_list, estimate_net_charge(res_list[0].atoms),
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/add_charge/charge.py", line 318, in add_nonstandard_res_charges
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/add_charge/charge.py", line 514, in nonstd_charge
extras.update(_methylate(na, nbnb, element_counts))
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/add_charge/charge.py", line 413, in _methylate
for pos in bond_positions(nn.coord, 4, 1.1, [na.coord]):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/atomic/bond_geom.py", line 78, in bond_positions
return tetra_pos(bondee, bonded, bond_len, toward, away, toward2, away2)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/atomic/bond_geom.py", line 158, in tetra_pos
pos = angle_pos(bondee, cur_bonded[0], bond_len, 109.5, coplanar=coplanar)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/atomic/bond_geom.py", line 242, in angle_pos
xforms = [z_align(atom_pos, bond_pos)]
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/geometry/place.py", line 567, in z_align
raise ValueError("z_align endpoints must be distinct")
ValueError: z_align endpoints must be distinct

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>
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5601 Fishers Lane, Room 4A60
Rockville, MD 20852
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[kristen.browne@…]

Added by email2trac

[Eric Pettersen]

I am not getting any kind of error when running this through the current pipeline script. Was this error from the script, or from using a particular preset on its own?

[kristen.browne@…]

This was the error in the NIH 3D logs, so it would be following the sequence outlined there

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________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, December 19, 2022 7:35:42 PM
Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [ChimeraX] #8195: raise ValueError("z_align endpoints must be distinct")

#8195: raise ValueError("z_align endpoints must be distinct")
-----------------------------------------+----------------------
          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            |
-----------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback


Comment:

 I am not getting any kind of error when running this through the current
 pipeline script.  Was this error from the script, or from using a
 particular preset on its own?

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[Eric Pettersen]

Well, like I said I don't get any error when I run this through the cx_unified.py script, so I would need more details about how to reproduce the problem...