Hbonds: wrong number of acc_phi_psi() positional arguments

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\ra93kol\Dropbox\NZALLA-Giovanni\GH8\Docking xyl\docking
> xylose.pdb" format pdb

Summary of feedback from opening C:\Users\ra93kol\Dropbox\NZALLA-
Giovanni\GH8\Docking xyl\docking xylose.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 TRP A 21
PHE A 32 1 12  
Start residue of secondary structure not found: HELIX 2 2 SER A 50 VAL A 62 1
13  
Start residue of secondary structure not found: HELIX 3 3 ARG A 66 LEU A 80 1
15  
Start residue of secondary structure not found: HELIX 4 4 SER A 111 TRP A 128
1 18  
Start residue of secondary structure not found: HELIX 5 5 PRO A 131 HIS A 147
1 17  
24 messages similar to the above omitted  
  
Chain information for docking xylose.pdb  
---  
Chain | Description  
1.1/A | No description available  
  

> save "C:/Users/ra93kol/Dropbox/NZALLA-Giovanni/GH8/Docking xyl/model 2.pdb"
> displayedOnly true

> select add #1

2903 atoms, 3006 bonds, 3 pseudobonds, 369 residues, 4 models selected  

> show #!1.1 target m

> select subtract #1

Nothing selected  

> open "C:/Users/ra93kol/Dropbox/NZALLA-Giovanni/GH8/Docking xyl/docking
> xylose.pdb" "C:/Users/ra93kol/Dropbox/NZALLA-Giovanni/GH8/Docking
> xyl/rank2_confidence-1.18.sdf"

Summary of feedback from opening C:/Users/ra93kol/Dropbox/NZALLA-
Giovanni/GH8/Docking xyl/docking xylose.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 TRP A 21
PHE A 32 1 12  
Start residue of secondary structure not found: HELIX 2 2 SER A 50 VAL A 62 1
13  
Start residue of secondary structure not found: HELIX 3 3 ARG A 66 LEU A 80 1
15  
Start residue of secondary structure not found: HELIX 4 4 SER A 111 TRP A 128
1 18  
Start residue of secondary structure not found: HELIX 5 5 PRO A 131 HIS A 147
1 17  
24 messages similar to the above omitted  
  
Chain information for docking xylose.pdb  
---  
Chain | Description  
2.1/A | No description available  
  

> hide #!1 target m

> hide #!1.1 models

> hide #1.2 models

> hide #2.2 models

> hide #!2.1 models

> hide #!2 models

> show #!1.1 models

> show #3 target m

> style #3#!1.1 ball

Changed 2903 atom styles  

> style #3#!1.1 sphere

Changed 2903 atom styles  
Alignment identifier is 1  
[Repeated 1 time(s)]

> select
> #1.1/A:94-96,102-104,149-152,156-159,172-175,221-224,229-231,353-355,361-363
> #2.1/A:94-96,102-104,149-152,156-159,172-175,221-224,229-231,353-355,361-363

528 atoms, 538 bonds, 62 residues, 2 models selected  

> select #1.1/A:363 #2.1/A:363

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select #1.1/A:362-363 #2.1/A:362-363

42 atoms, 44 bonds, 4 residues, 2 models selected  
1 [ID: 1] region 2 chains [362-363] RMSD: 0.000  
  

> select
> #1.1/A:21-32,50-62,66-80,111-128,131-147,165-167,177-179,182-191,196-198,201-203,205-211,242-251,256-273,295-308,311-324,336-349
> #2.1/A:21-32,50-62,66-80,111-128,131-147,165-167,177-179,182-191,196-198,201-203,205-211,242-251,256-273,295-308,311-324,336-349

2836 atoms, 2910 bonds, 348 residues, 2 models selected  

> hide #!1 models

> show #!1 models

> hide #!1.1 models

> show #!1.1 models

> close #1.1

> close

> open "C:/Users/ra93kol/Dropbox/NZALLA-Giovanni/GH8/Docking xyl/docking
> xylose.pdb" "C:/Users/ra93kol/Dropbox/NZALLA-Giovanni/GH8/Docking
> xyl/rank2_confidence-1.18.sdf"

Summary of feedback from opening C:/Users/ra93kol/Dropbox/NZALLA-
Giovanni/GH8/Docking xyl/docking xylose.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 TRP A 21
PHE A 32 1 12  
Start residue of secondary structure not found: HELIX 2 2 SER A 50 VAL A 62 1
13  
Start residue of secondary structure not found: HELIX 3 3 ARG A 66 LEU A 80 1
15  
Start residue of secondary structure not found: HELIX 4 4 SER A 111 TRP A 128
1 18  
Start residue of secondary structure not found: HELIX 5 5 PRO A 131 HIS A 147
1 17  
24 messages similar to the above omitted  
  
Chain information for docking xylose.pdb  
---  
Chain | Description  
1.1/A | No description available  
  

> hide #1.2 models

Alignment identifier is 1.1/A  

> select add #2

10 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 10 atom styles  

> select subtract #2

Nothing selected  

> select add #1.1

2893 atoms, 2996 bonds, 3 pseudobonds, 368 residues, 2 models selected  

> select #1.1/A:41

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1.1/A:41

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select
> #1.1/A:21-32,50-62,66-80,111-128,131-147,165-167,177-179,182-191,196-198,201-203,205-211,242-251,256-273,295-308,311-324,336-349

1418 atoms, 1455 bonds, 174 residues, 1 model selected  

> select #1.1/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1.1/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1.1/A:41

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1.1/A:41

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select
> #1.1/A:21-32,50-62,66-80,111-128,131-147,165-167,177-179,182-191,196-198,201-203,205-211,242-251,256-273,295-308,311-324,336-349

1418 atoms, 1455 bonds, 174 residues, 1 model selected  

> select #1.1/A:53

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1.1/A:52-53

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #1.1/A:40

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1.1/A:40-47

55 atoms, 55 bonds, 8 residues, 1 model selected  

> select add #2

65 atoms, 65 bonds, 9 residues, 2 models selected  

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

[Repeated 1 time(s)]

> show sel atoms

> select subtract #2

55 atoms, 55 bonds, 8 residues, 1 model selected  

> hide sel atoms

> select #1.1/A:37

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1.1/A:37-45

65 atoms, 65 bonds, 9 residues, 1 model selected  

> select #1.1/A:76

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1.1/A:76-131

443 atoms, 459 bonds, 56 residues, 1 model selected  

> select #1.1/A:41

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1.1/A:41

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1.1/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1.1/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> coulombic sel

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run  
f(s)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 84, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\hbond.py",
line 248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.14830 Core Profile Forward-Compatible Context 21.09.02.01 27.20.20902.1004
OpenGL renderer: AMD Radeon R7 430
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: de_IT.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP EliteDesk 800 G6 Tower PC
OS: Microsoft Windows 10 Education (Build 19045)
Memory: 34,125,086,720
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
OSLanguage: de-DE

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
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    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
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    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
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    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
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    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
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    ChimeraX-Registration: 1.1.1
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    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
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    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
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    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
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    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
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    zipp: 3.11.0

[Eric Pettersen]

Likely bad structure