AddH: More than 2 coplanar positions specified

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\Users\Ferna\OneDrive\Escritorio\Controles\3b7e_VZZ\3b7e_CA_002_ZMR_02_7.3.pdb
> format pdb

Summary of feedback from opening
C:\Users\Ferna\OneDrive\Escritorio\Controles\3b7e_VZZ\3b7e_CA_002_ZMR_02_7.3.pdb  
---  
warnings | Ignored bad PDB record found on line 703  
ATOM 700 N TYR A169A -4.611 15.895 -26.542 1.00 0.00 A2 N  
  
Ignored bad PDB record found on line 704  
ATOM 701 CA TYR A169A -3.492 16.688 -27.022 1.00 0.00 A2 C  
  
Ignored bad PDB record found on line 705  
ATOM 702 C TYR A169A -3.968 17.962 -27.734 1.00 0.00 A2 C  
  
Ignored bad PDB record found on line 706  
ATOM 703 O TYR A169A -3.143 18.825 -28.043 1.00 0.00 A2 O  
  
Ignored bad PDB record found on line 707  
ATOM 704 CB TYR A169A -2.552 15.875 -27.926 1.00 0.00 A2 C  
  
41 messages similar to the above omitted  
CONECT record to nonexistent atom: (695, 700)  
CONECT record for nonexistent atom: 700  
  
Chain information for 3b7e_CA_002_ZMR_02_7.3.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> coulombic

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 215, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1386, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run  
f(s)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\cmd.py", line 102, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 95, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 259, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 585, in find_hbonds  
donor_hyds = hyd_positions(donor_atom)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\hbonds\hydpos.py", line 77, in hyd_positions  
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 84, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 140, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
ValueError: More than 2 coplanar positions specified!  
  
ValueError: More than 2 coplanar positions specified!  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 Core Profile Context 24.30.22.01.250106
OpenGL renderer: AMD Radeon(TM) 890M Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS Zenbook S 16 UM5606WA_UM5606WA
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 33,413,771,264
MaxProcessMemory: 137,438,953,344
CPU: 24 AMD Ryzen AI 9 HX 370 w/ Radeon 890M           
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
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    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
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    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
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    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
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    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
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    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
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    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
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    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
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    ChimeraX-PubChem: 2.2
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    ChimeraX-RenderByAttr: 1.6.2
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    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
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    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
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    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
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    ChimeraX-Zone: 1.0.1
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    wheel: 0.43.0
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    WMI: 1.5.1

[pett]

Bad PDB file