alt locs not copied

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\Suzuki Lab\Downloads\6qwy.pdb" format pdb

6qwy.pdb title:  
Hewl lysozyme, crystallized from nacl solution [more info...]  
  
Chain information for 6qwy.pdb #1  
---  
Chain | Description  
A | lysozyme C  
  
Non-standard residues in 6qwy.pdb #1  
---  
CL — chloride ion  
NA — sodium ion  
  

> ui tool show "Crystal Contacts"

> crystalcontacts #1 distance 30

49 pairs of asymmetric units of 6qwy.pdb contact at distance 30.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
      1148     0      6      0  0  0      0         1
      1147     0      2      0  0 -1      0         1
      1142     0      3     -1  0  0      0         1
      1110     0      7      0  0  0      0         1
      1102     0      7      0  0 -1      0         1
      1083     0      0      0  0 -1      0         1
      1016     0      2      0  0  0      0         1
       998     0      5     -1  0  0      0         1
       989     0      0      0  0  1      0         1
       982     0      5      0  0 -1      0         1
       880     0      1      0  1  0      0         1
       851     0      3     -1  0 -1      0         1
       798     0      5      0  0  0      0         1
       777     0      1      0  1 -1      0         1
       767     0      6      0  0  1      0         1
       736     0      1      0  0 -1      0         1
       650     0      1      0  0  0      0         1
       364     0      6      0  0 -1      0         1
       359     0      4     -1  0 -1      0         1
       349     0      5     -1  0 -1      0         1
       217     0      4     -1 -1 -1      0         1
       212     0      2      0  0 -2      0         1
       153     0      7      0  0 -2      0         1
       150     0      5     -1  0  1      0         1
       144     0      3     -1  0  1      0         1
       124     0      5      0  0  1      0         1
       112     0      4      0  0  0      0         1
        91     0      4      0  0 -1      0         1
        66     0      7      1  0  0      0         1
        65     0      6      0  1  0      0         1
        64     0      7      0  1  0      0         1
        55     0      4      0 -1  0      0         1
        53     0      6     -1  0  0      0         1
        51     0      7      0  0  1      0         1
        42     0      4      0 -1 -1      0         1
        33     0      3     -1 -1  0      0         1
        30     0      2     -1  0 -1      0         1
        26     0      2      0  0  1      0         1
        16     0      7      1  0 -1      0         1
        15     0      4     -1  0  0      0         1
        14     0      7      0  1 -1      0         1
        10     0      2      0 -1 -1      0         1
         8     0      6      0  1 -1      0         1
         8     0      4     -1  0 -2      0         1
         7     0      4     -1 -1 -2      0         1
         7     0      3      0  0  0      0         1
         7     0      3     -1  0 -2      0         1
         5     0      4     -1 -1  0      0         1
         4     0      6     -1  0 -1      0         1
    

  

> coulombic

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
6qwy.pdb #1/A LEU 129  
6qwy.pdb 0 0 0 sym 6 #2.1/A LEU 129  
6qwy.pdb 0 0 -1 sym 2 #2.2/A LEU 129  
6qwy.pdb -1 0 0 sym 3 #2.3/A LEU 129  
6qwy.pdb 0 0 0 sym 7 #2.4/A LEU 129  
6qwy.pdb 0 0 -1 sym 7 #2.5/A LEU 129  
6qwy.pdb 0 0 -1 sym 0 #2.6/A LEU 129  
6qwy.pdb 0 0 0 sym 2 #2.7/A LEU 129  
6qwy.pdb -1 0 0 sym 5 #2.8/A LEU 129  
6qwy.pdb 0 0 1 sym 0 #2.9/A LEU 129  
6qwy.pdb 0 0 -1 sym 5 #2.10/A LEU 129  
6qwy.pdb 0 1 0 sym 1 #2.11/A LEU 129  
6qwy.pdb -1 0 -1 sym 3 #2.12/A LEU 129  
6qwy.pdb 0 0 0 sym 5 #2.13/A LEU 129  
6qwy.pdb 0 1 -1 sym 1 #2.14/A LEU 129  
6qwy.pdb 0 0 1 sym 6 #2.15/A LEU 129  
6qwy.pdb 0 0 -1 sym 1 #2.16/A LEU 129  
6qwy.pdb 0 0 0 sym 1 #2.17/A LEU 129  
6qwy.pdb 0 0 -1 sym 6 #2.18/A LEU 129  
6qwy.pdb -1 0 -1 sym 4 #2.19/A LEU 129  
6qwy.pdb -1 0 -1 sym 5 #2.20/A LEU 129  
6qwy.pdb -1 -1 -1 sym 4 #2.21/A LEU 129  
6qwy.pdb 0 0 -2 sym 2 #2.22/A LEU 129  
6qwy.pdb 0 0 -2 sym 7 #2.23/A LEU 129  
6qwy.pdb -1 0 1 sym 5 #2.24/A LEU 129  
6qwy.pdb -1 0 1 sym 3 #2.25/A LEU 129  
6qwy.pdb 0 0 1 sym 5 #2.26/A LEU 129  
6qwy.pdb 0 0 0 sym 4 #2.27/A LEU 129  
6qwy.pdb 0 0 -1 sym 4 #2.28/A LEU 129  
6qwy.pdb 1 0 0 sym 7 #2.29/A LEU 129  
6qwy.pdb 0 1 0 sym 6 #2.30/A LEU 129  
6qwy.pdb 0 1 0 sym 7 #2.31/A LEU 129  
6qwy.pdb 0 -1 0 sym 4 #2.32/A LEU 129  
6qwy.pdb -1 0 0 sym 6 #2.33/A LEU 129  
6qwy.pdb 0 0 1 sym 7 #2.34/A LEU 129  
6qwy.pdb 0 -1 -1 sym 4 #2.35/A LEU 129  
6qwy.pdb -1 -1 0 sym 3 #2.36/A LEU 129  
6qwy.pdb -1 0 -1 sym 2 #2.37/A LEU 129  
6qwy.pdb 0 0 1 sym 2 #2.38/A LEU 129  
6qwy.pdb 1 0 -1 sym 7 #2.39/A LEU 129  
6qwy.pdb -1 0 0 sym 4 #2.40/A LEU 129  
6qwy.pdb 0 1 -1 sym 7 #2.41/A LEU 129  
6qwy.pdb 0 -1 -1 sym 2 #2.42/A LEU 129  
6qwy.pdb 0 1 -1 sym 6 #2.43/A LEU 129  
6qwy.pdb -1 0 -2 sym 4 #2.44/A LEU 129  
6qwy.pdb -1 -1 -2 sym 4 #2.45/A LEU 129  
6qwy.pdb 0 0 0 sym 3 #2.46/A LEU 129  
6qwy.pdb -1 0 -2 sym 3 #2.47/A LEU 129  
6qwy.pdb -1 -1 0 sym 4 #2.48/A LEU 129  
6qwy.pdb -1 0 -1 sym 6 #2.49/A LEU 129  

Traceback (most recent call last):  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\toolbar\tool.py", line
202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 379, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1285, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1333, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 389, in try_shortcut  
self.run_shortcut(keys)  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 407, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 326, in run  
f(s)  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 568, in run_expanded_command  
run(session, cmd)  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 511, in run  
run_command(session, command, **kw)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\run.py",
line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2852, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\coulombic\cmd.py", line
90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 74, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\addh\cmd.py", line 63,
in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\addh\cmd.py", line 170,
in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\addh\hbond.py", line
214, in add_hydrogens  
_attach_hydrogens(atom, altloc_hpos_info, bonding_info)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\addh\hbond.py", line
895, in _attach_hydrogens  
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens,
naming_schema)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\addh\cmd.py", line 862,
in add_altloc_hyds  
h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema,  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\addh\cmd.py", line 882,
in new_hydrogen  
metal_pos = metal.get_alt_loc_coord(alt_loc)  
File "atomic_cpp\cymol.pyx", line 587, in
chimerax.atomic.cymol.CyAtom.get_alt_loc_coord  
ValueError: Atom copy of 6qwy.pdb -1 -1 -2 sym 4 #/A NA 202 NA has no alt loc
A  
  
ValueError: Atom copy of 6qwy.pdb -1 -1 -2 sym 4 #/A NA 202 NA has no alt loc
A  
  
File "atomic_cpp\cymol.pyx", line 587, in
chimerax.atomic.cymol.CyAtom.get_alt_loc_coord  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: MouseComputer Co.,Ltd.
Model: H170M-S01
OS: Microsoft Windows 10 Home (Build 19041)
Memory: 8,519,925,760
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
OSLanguage: ja-JP
Locale: ('ja_JP', 'cp932')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
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    comtypes: 1.1.7
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    cycler: 0.10.0
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    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
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    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
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    requests: 2.24.0
    scipy: 1.5.2
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    wheel: 0.36.0
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