Opened 3 years ago

Closed 3 years ago

#7627 closed defect (fixed)

ChimeraX/ISOLDE version problems

Reported by: mille153@… Owned by: pett
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202209140201 (2022-09-14 02:01:28 UTC)
Description
opening ISOLDE 

Log:
UCSF ChimeraX version: 1.5.dev202209140201 (2022-09-14)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde start

> set selectionWidth 4

Failed to extract font properties from /System/Library/Fonts/Apple Color
Emoji.ttc: In FT2Font: Could not set the fontsize (error code 0x17)  
Failed to extract font properties from /Library/Fonts/NISC18030.ttf: In
FT2Font: Could not set the fontsize (error code 0x17)  
Failed to extract font properties from /System/Library/Fonts/LastResort.otf:
tuple indices must be integers or slices, not str  
generated new fontManager  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/tool.py", line 42, in _launch_main_gui  
tw = self.tool_window = IsoldeMainWin(self)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/main_win.py", line 56, in __init__  
self.restraints_tab = RestraintsTab(self.session, self.isolde, self, tabw)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/ui_base.py", line 226, in __init__  
self.populate()  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/__init__.py", line 20, in populate  
self.addWidget(ReferenceModelPanel(session, isolde, parent, gui))  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 16, in
__init__  
cd = self.content = ReferenceModelDialog(session, isolde, gui, self)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 85, in
__init__  
opt = self.options = ReferenceModelOptions(self.session, gui, options_frame)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 464, in
__init__  
drfi = self.distance_fuzziness_indicator =
DistanceRestraintFuzzinessIndicator(session, dsl, dfl)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 636, in
__init__  
self._create_dummy_model()  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 704, in
_create_dummy_model  
dr = self._dummy_restraint = drm.add_restraint(a1, a2)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 2883, in add_restraint  
r = self._get_restraints(Atoms([atom1]), Atoms([atom2]), True)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 2864, in _get_restraints  
return self._plural_restraint_getter(ret[:num])  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 97, in
_adaptive_distance_restraints  
return AdaptiveDistanceRestraints(p)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 556, in __init__  
super().__init__(c_pointers, AdaptiveDistanceRestraint,  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
Error processing trigger "new frame":  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 556, in __init__  
super().__init__(c_pointers, AdaptiveDistanceRestraint,  
  
See log for complete Python traceback.  
  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1790, in _get_and_process_changes  
return self._process_changes(changes)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1775, in _process_changes  
changed_obj = class_funcs[1](changed_ptrs)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 97, in
_adaptive_distance_restraints  
return AdaptiveDistanceRestraints(p)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 556, in __init__  
super().__init__(c_pointers, AdaptiveDistanceRestraint,  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
Error processing trigger "new frame":  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 556, in __init__  
super().__init__(c_pointers, AdaptiveDistanceRestraint,  
  
See log for complete Python traceback.  
  

> isolde demo cryo_em_intro modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb #1  
---  
Chain | Description | UniProt  
A | capsid protein VP1 | CAPSD_NVN68  
B | capsid protein VP1 | CAPSD_NVN68  
C | capsid protein VP1 | CAPSD_NVN68  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 51 residues in model #1 to IUPAC-IUB
standards.  
6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb  
---  
Chain | Description | UniProt  
1.2/A | capsid protein VP1 | CAPSD_NVN68  
1.2/B | capsid protein VP1 | CAPSD_NVN68  
1.2/C | capsid protein VP1 | CAPSD_NVN68  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 240, in _load_demo  
load_fn(session, **kwargs)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 1483, in load_cryo_em_demo  
session.isolde.selected_model = m  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 433, in selected_model  
self.change_selected_model(model)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 771, in change_selected_model  
self._change_selected_model(self, model=model, force=True)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 823, in _change_selected_model  
sx.get_rota_annotator(m)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/session_extensions.py", line 216, in
get_rota_annotator  
return RotamerAnnotator(model)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/validation/rota_annotation.py", line 74, in __init__  
self.track_whole_model = True  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/validation/rota_annotation.py", line 109, in
track_whole_model  
self._selected_rotamers = self._mgr.get_rotamers(res)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1602, in get_rotamers  
return _rotamers(f(self._c_pointer, residues._c_pointers, n))  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 78, in _rotamers  
return Rotamers(p)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 306, in __init__  
super().__init__(c_pointers, Rotamer, Rotamers)  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
Error processing trigger "new frame":  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 306, in __init__  
super().__init__(c_pointers, Rotamer, Rotamers)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 4043, in _model_changes_cb  
self.update_graphics(update_visibility)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 4087, in update_graphics  
self._last_visibles = self.visible_restraints  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 3980, in visible_restraints  
return self._ARRAY_GETTER(f(self._c_pointer))  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 3627, in _ARRAY_GETTER  
return _proper_dihedral_restraints(p)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 132, in
_proper_dihedral_restraints  
return ProperDihedralRestraints(p)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 835, in __init__  
super().__init__(c_pointers, ProperDihedralRestraint,
ProperDihedralRestraints)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 732, in __init__  
super().__init__(c_pointers, singular_py_class, array_py_class)  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
Error processing trigger "changes":  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 732, in __init__  
super().__init__(c_pointers, singular_py_class, array_py_class)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 4043, in _model_changes_cb  
self.update_graphics(update_visibility)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 4087, in update_graphics  
self._last_visibles = self.visible_restraints  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 3980, in visible_restraints  
return self._ARRAY_GETTER(f(self._c_pointer))  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 3627, in _ARRAY_GETTER  
return _proper_dihedral_restraints(p)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 132, in
_proper_dihedral_restraints  
return ProperDihedralRestraints(p)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 835, in __init__  
super().__init__(c_pointers, ProperDihedralRestraint,
ProperDihedralRestraints)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 732, in __init__  
super().__init__(c_pointers, singular_py_class, array_py_class)  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
Error processing trigger "changes":  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 732, in __init__  
super().__init__(c_pointers, singular_py_class, array_py_class)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 4043, in _model_changes_cb  
self.update_graphics(update_visibility)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 4087, in update_graphics  
self._last_visibles = self.visible_restraints  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 3980, in visible_restraints  
return self._ARRAY_GETTER(f(self._c_pointer))  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 3627, in _ARRAY_GETTER  
return _proper_dihedral_restraints(p)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 132, in
_proper_dihedral_restraints  
return ProperDihedralRestraints(p)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 835, in __init__  
super().__init__(c_pointers, ProperDihedralRestraint,
ProperDihedralRestraints)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 732, in __init__  
super().__init__(c_pointers, singular_py_class, array_py_class)  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
Error processing trigger "changes":  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 732, in __init__  
super().__init__(c_pointers, singular_py_class, array_py_class)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 575X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 220.270.93.0.0
      SMC Version (system): 2.46f12

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G95)
      Kernel Version: Darwin 18.7.0
      Time since boot: 118 days 2:49

Graphics/Displays:

    Radeon Pro 575X:

      Chipset Model: Radeon Pro 575X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c4
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A14GP-003
      EFI Driver Version: 01.01.042
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.1
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    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: 1.41.2
    ChimeraX-AtomicLibrary: 7.0.3
    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
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0
    ChimeraX-CheckWaters: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0.2
    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.dev202209140201
    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-ISOLDE: 1.4
    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: 1.8.1
    ChimeraX-Map: 1.1.1
    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: 2.0.7
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.1
    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
    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: 2.6.7
    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
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.1
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    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
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.0.0
    filelock: 3.7.1
    fonttools: 4.37.1
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.1
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.1
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.1
    python-dateutil: 2.8.2
    pytz: 2022.2.1
    pyzmq: 23.2.1
    qtconsole: 5.3.1
    QtPy: 2.2.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.5.0
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.8.1

Change History (3)

in reply to:  1 ; comment:1 by mille153@…, 3 years ago 

I installed the wrong version of Chimera X and ISODLE on the Mac I'm using at work.  I reinstalled the most up to date versions and things seem to be working now ie the software on the computer is now matching the ISODLE tutorial screen shots and it follows the directions
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, September 19, 2022 2:18 PM
To: Miller, Andrew S <mille153@purdue.edu>
Subject: [ChimeraX] #7627: ChimeraX bug report submission

---- External Email: Use caution with attachments, links, or sharing data ----


#7627: ChimeraX bug report submission
------------------------+-----------------------------
 Reporter:  mille153@…  |                Type:  defect
   Status:  new         |            Priority:  normal
Component:  Unassigned  |          Blocked By:
 Blocking:              |  Notify when closed:
------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        macOS-10.14.6-x86_64-i386-64bit
 ChimeraX Version: 1.5.dev202209140201 (2022-09-14 02:01:28 UTC)
 Description
 opening ISOLDE

 Log:
 UCSF ChimeraX version: 1.5.dev202209140201 (2022-09-14)
 © 2016-2022 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > isolde start

 > set selectionWidth 4

 Failed to extract font properties from /System/Library/Fonts/Apple Color
 Emoji.ttc: In FT2Font: Could not set the fontsize (error code 0x17)
 Failed to extract font properties from /Library/Fonts/NISC18030.ttf: In
 FT2Font: Could not set the fontsize (error code 0x17)
 Failed to extract font properties from
 /System/Library/Fonts/LastResort.otf:
 tuple indices must be integers or slices, not str
 generated new fontManager
 Traceback (most recent call last):
 File
 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/chimerax/core/triggerset.py", line 134, in invoke
 return self._func(self._name, data)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/tool.py", line 42, in _launch_main_gui
 tw = self.tool_window = IsoldeMainWin(self)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/ui/main_win.py", line 56, in __init__
 self.restraints_tab = RestraintsTab(self.session, self.isolde, self, tabw)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/ui/ui_base.py", line 226, in __init__
 self.populate()
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/ui/restraints_tab/__init__.py", line 20, in
 populate
 self.addWidget(ReferenceModelPanel(session, isolde, parent, gui))
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 16,
 in
 __init__
 cd = self.content = ReferenceModelDialog(session, isolde, gui, self)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 85,
 in
 __init__
 opt = self.options = ReferenceModelOptions(self.session, gui,
 options_frame)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 464,
 in
 __init__
 drfi = self.distance_fuzziness_indicator =
 DistanceRestraintFuzzinessIndicator(session, dsl, dfl)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 636,
 in
 __init__
 self._create_dummy_model()
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 704,
 in
 _create_dummy_model
 dr = self._dummy_restraint = drm.add_restraint(a1, a2)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 2883, in add_restraint
 r = self._get_restraints(Atoms([atom1]), Atoms([atom2]), True)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 2864, in _get_restraints
 return self._plural_restraint_getter(ret[:num])
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 97, in
 _adaptive_distance_restraints
 return AdaptiveDistanceRestraints(p)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 556, in __init__
 super().__init__(c_pointers, AdaptiveDistanceRestraint,
 TypeError: __init__() takes 3 positional arguments but 4 were given

 Error processing trigger "new frame":
 TypeError: __init__() takes 3 positional arguments but 4 were given

 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 556, in __init__
 super().__init__(c_pointers, AdaptiveDistanceRestraint,

 See log for complete Python traceback.

 Forcefield cache not found or out of date. Regenerating from ffXML files.
 This
 is normal if running ISOLDE for the first time, or after upgrading OpenMM.
 Done loading forcefield
 Traceback (most recent call last):
 File
 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/chimerax/core/triggerset.py", line 134, in invoke
 return self._func(self._name, data)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 1790, in
 _get_and_process_changes
 return self._process_changes(changes)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 1775, in _process_changes
 changed_obj = class_funcs[1](changed_ptrs)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 97, in
 _adaptive_distance_restraints
 return AdaptiveDistanceRestraints(p)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 556, in __init__
 super().__init__(c_pointers, AdaptiveDistanceRestraint,
 TypeError: __init__() takes 3 positional arguments but 4 were given

 Error processing trigger "new frame":
 TypeError: __init__() takes 3 positional arguments but 4 were given

 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 556, in __init__
 super().__init__(c_pointers, AdaptiveDistanceRestraint,

 See log for complete Python traceback.


 > isolde demo cryo_em_intro modelOnly true startIsolde false

 6out.pdb title:
 Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain
 VLP
 asymmetric unit In T=3 symmetry [more info...]

 Chain information for 6out.pdb #1
 ---
 Chain | Description | UniProt
 A | capsid protein VP1 | CAPSD_NVN68
 B | capsid protein VP1 | CAPSD_NVN68
 C | capsid protein VP1 | CAPSD_NVN68

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: Corrected atom nomenclature of 51 residues in model #1 to IUPAC-
 IUB
 standards.
 6out.pdb title:
 Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain
 VLP
 asymmetric unit In T=3 symmetry [more info...]

 Chain information for 6out.pdb
 ---
 Chain | Description | UniProt
 1.2/A | capsid protein VP1 | CAPSD_NVN68
 1.2/B | capsid protein VP1 | CAPSD_NVN68
 1.2/C | capsid protein VP1 | CAPSD_NVN68

 Cached rota8000-val data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-leu data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-ile data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-pro data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-phe data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-tyr data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-trp data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-ser data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-thr data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-cys data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-met data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-lys data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-his data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-arg data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-asp data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-asn data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-gln data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-glu data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Traceback (most recent call last):
 File
 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/chimerax/core/triggerset.py", line 134, in invoke
 return self._func(self._name, data)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/cmd/cmd.py", line 240, in _load_demo
 load_fn(session, **kwargs)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/isolde.py", line 1483, in load_cryo_em_demo
 session.isolde.selected_model = m
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/isolde.py", line 433, in selected_model
 self.change_selected_model(model)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/isolde.py", line 771, in change_selected_model
 self._change_selected_model(self, model=model, force=True)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/isolde.py", line 823, in _change_selected_model
 sx.get_rota_annotator(m)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/session_extensions.py", line 216, in
 get_rota_annotator
 return RotamerAnnotator(model)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/validation/rota_annotation.py", line 74, in
 __init__
 self.track_whole_model = True
 File
 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/chimerax/graphics/drawing.py", line 255, in __setattr__
 super(Drawing, self).__setattr__(key, value)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/validation/rota_annotation.py", line 109, in
 track_whole_model
 self._selected_rotamers = self._mgr.get_rotamers(res)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 1602, in get_rotamers
 return _rotamers(f(self._c_pointer, residues._c_pointers, n))
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 78, in _rotamers
 return Rotamers(p)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 306, in __init__
 super().__init__(c_pointers, Rotamer, Rotamers)
 TypeError: __init__() takes 3 positional arguments but 4 were given

 Error processing trigger "new frame":
 TypeError: __init__() takes 3 positional arguments but 4 were given

 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 306, in __init__
 super().__init__(c_pointers, Rotamer, Rotamers)

 See log for complete Python traceback.

 Traceback (most recent call last):
 File
 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/chimerax/core/triggerset.py", line 134, in invoke
 return self._func(self._name, data)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 4043, in _model_changes_cb
 self.update_graphics(update_visibility)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 4087, in update_graphics
 self._last_visibles = self.visible_restraints
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 3980, in visible_restraints
 return self._ARRAY_GETTER(f(self._c_pointer))
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 3627, in _ARRAY_GETTER
 return _proper_dihedral_restraints(p)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 132, in
 _proper_dihedral_restraints
 return ProperDihedralRestraints(p)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 835, in __init__
 super().__init__(c_pointers, ProperDihedralRestraint,
 ProperDihedralRestraints)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 732, in __init__
 super().__init__(c_pointers, singular_py_class, array_py_class)
 TypeError: __init__() takes 3 positional arguments but 4 were given

 Error processing trigger "changes":
 TypeError: __init__() takes 3 positional arguments but 4 were given

 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 732, in __init__
 super().__init__(c_pointers, singular_py_class, array_py_class)

 See log for complete Python traceback.

 Traceback (most recent call last):
 File
 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/chimerax/core/triggerset.py", line 134, in invoke
 return self._func(self._name, data)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 4043, in _model_changes_cb
 self.update_graphics(update_visibility)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 4087, in update_graphics
 self._last_visibles = self.visible_restraints
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 3980, in visible_restraints
 return self._ARRAY_GETTER(f(self._c_pointer))
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 3627, in _ARRAY_GETTER
 return _proper_dihedral_restraints(p)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 132, in
 _proper_dihedral_restraints
 return ProperDihedralRestraints(p)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 835, in __init__
 super().__init__(c_pointers, ProperDihedralRestraint,
 ProperDihedralRestraints)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 732, in __init__
 super().__init__(c_pointers, singular_py_class, array_py_class)
 TypeError: __init__() takes 3 positional arguments but 4 were given

 Error processing trigger "changes":
 TypeError: __init__() takes 3 positional arguments but 4 were given

 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 732, in __init__
 super().__init__(c_pointers, singular_py_class, array_py_class)

 See log for complete Python traceback.

 Traceback (most recent call last):
 File
 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/chimerax/core/triggerset.py", line 134, in invoke
 return self._func(self._name, data)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 4043, in _model_changes_cb
 self.update_graphics(update_visibility)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 4087, in update_graphics
 self._last_visibles = self.visible_restraints
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 3980, in visible_restraints
 return self._ARRAY_GETTER(f(self._c_pointer))
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 3627, in _ARRAY_GETTER
 return _proper_dihedral_restraints(p)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molobject.py", line 132, in
 _proper_dihedral_restraints
 return ProperDihedralRestraints(p)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 835, in __init__
 super().__init__(c_pointers, ProperDihedralRestraint,
 ProperDihedralRestraints)
 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 732, in __init__
 super().__init__(c_pointers, singular_py_class, array_py_class)
 TypeError: __init__() takes 3 positional arguments but 4 were given

 Error processing trigger "changes":
 TypeError: __init__() takes 3 positional arguments but 4 were given

 File "/Users/mille153/Library/Application Support/ChimeraX/1.5/site-
 packages/chimerax/isolde/molarray.py", line 732, in __init__
 super().__init__(c_pointers, singular_py_class, array_py_class)

 See log for complete Python traceback.





 OpenGL version: 4.1 ATI-2.11.20
 OpenGL renderer: AMD Radeon Pro 575X OpenGL Engine
 OpenGL vendor: ATI Technologies Inc.

 Python: 3.9.11
 Locale: UTF-8
 Qt version: PyQt6 6.3.1, Qt 6.3.1
 Qt runtime version: 6.3.1
 Qt platform: cocoa
 Hardware:

     Hardware Overview:

       Model Name: iMac
       Model Identifier: iMac19,1
       Processor Name: Intel Core i9
       Processor Speed: 3.6 GHz
       Number of Processors: 1
       Total Number of Cores: 8
       L2 Cache (per Core): 256 KB
       L3 Cache: 16 MB
       Hyper-Threading Technology: Enabled
       Memory: 16 GB
       Boot ROM Version: 220.270.93.0.0
       SMC Version (system): 2.46f12

 Software:

     System Software Overview:

       System Version: macOS 10.14.6 (18G95)
       Kernel Version: Darwin 18.7.0
       Time since boot: 118 days 2:49

 Graphics/Displays:

     Radeon Pro 575X:

       Chipset Model: Radeon Pro 575X
       Type: GPU
       Bus: PCIe
       PCIe Lane Width: x16
       VRAM (Total): 4 GB
       Vendor: AMD (0x1002)
       Device ID: 0x67df
       Revision ID: 0x00c4
       ROM Revision: 113-D0008A-042
       VBIOS Version: 113-D0008A14GP-003
       EFI Driver Version: 01.01.042
       Metal: Supported, feature set macOS GPUFamily2 v1
       Displays:
         iMac:
           Display Type: Built-In Retina LCD
           Resolution: 5120 x 2880 Retina
           Framebuffer Depth: 30-Bit Color (ARGB2101010)
           Main Display: Yes
           Mirror: Off
           Online: Yes
           Rotation: Supported
           Automatically Adjust Brightness: No


 Installed Packages:
     alabaster: 0.7.12
     appdirs: 1.4.4
     appnope: 0.1.3
     asttokens: 2.0.8
     Babel: 2.10.3
     backcall: 0.2.0
     blockdiag: 3.0.0
     build: 0.8.0
     certifi: 2021.10.8
     cftime: 1.6.1
     charset-normalizer: 2.1.1
     ChimeraX-AddCharge: 1.4
     ChimeraX-AddH: 2.2
     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: 1.41.2
     ChimeraX-AtomicLibrary: 7.0.3
     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
     ChimeraX-BundleBuilder: 1.2
     ChimeraX-ButtonPanel: 1.0.1
     ChimeraX-CageBuilder: 1.0.1
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.3.1
     ChimeraX-ChangeChains: 1.0
     ChimeraX-CheckWaters: 1.2
     ChimeraX-ChemGroup: 2.0
     ChimeraX-Clashes: 2.2.4
     ChimeraX-Clipper: 0.18.0
     ChimeraX-ColorActions: 1.0.2
     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.dev202209140201
     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-ISOLDE: 1.4
     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: 1.8.1
     ChimeraX-Map: 1.1.1
     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: 2.0.7
     ChimeraX-MDcrds: 2.6
     ChimeraX-MedicalToolbar: 1.0.2
     ChimeraX-Meeting: 1.0.1
     ChimeraX-MLP: 1.1
     ChimeraX-mmCIF: 2.8
     ChimeraX-MMTF: 2.1
     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
     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: 2.6.7
     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
     ChimeraX-ReadPbonds: 1.0.1
     ChimeraX-Registration: 1.1.1
     ChimeraX-RemoteControl: 1.0
     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
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SelInspector: 1.0
     ChimeraX-SeqView: 2.7.2
     ChimeraX-Shape: 1.0.1
     ChimeraX-Shell: 1.0.1
     ChimeraX-Shortcuts: 1.1.1
     ChimeraX-ShowSequences: 1.0.1
     ChimeraX-SideView: 1.0.1
     ChimeraX-Smiles: 2.1
     ChimeraX-SmoothLines: 1.0
     ChimeraX-SpaceNavigator: 1.0
     ChimeraX-StdCommands: 1.10
     ChimeraX-STL: 1.0
     ChimeraX-Storm: 1.0
     ChimeraX-StructMeasure: 1.1
     ChimeraX-Struts: 1.0.1
     ChimeraX-Surface: 1.0
     ChimeraX-SwapAA: 2.0.1
     ChimeraX-SwapRes: 2.1.3
     ChimeraX-TapeMeasure: 1.0
     ChimeraX-Test: 1.0
     ChimeraX-Toolbar: 1.1.2
     ChimeraX-ToolshedUtils: 1.2.1
     ChimeraX-Tug: 1.0.1
     ChimeraX-UI: 1.24.1
     ChimeraX-uniprot: 2.2.1
     ChimeraX-UnitCell: 1.0.1
     ChimeraX-ViewDockX: 1.1.3
     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
     ChimeraX-WebServices: 1.1.0
     ChimeraX-Zone: 1.0.1
     colorama: 0.4.5
     cxservices: 1.2
     cycler: 0.11.0
     Cython: 0.29.32
     debugpy: 1.6.3
     decorator: 5.1.1
     docutils: 0.19
     entrypoints: 0.4
     executing: 1.0.0
     filelock: 3.7.1
     fonttools: 4.37.1
     funcparserlib: 1.0.0
     grako: 3.16.5
     h5py: 3.7.0
     html2text: 2020.1.16
     idna: 3.4
     ihm: 0.33
     imagecodecs: 2022.7.31
     imagesize: 1.4.1
     importlib-metadata: 4.12.0
     ipykernel: 6.15.1
     ipython: 8.4.0
     ipython-genutils: 0.2.0
     jedi: 0.18.1
     Jinja2: 3.1.2
     jupyter-client: 7.3.4
     jupyter-core: 4.11.1
     kiwisolver: 1.4.4
     line-profiler: 3.5.1
     lxml: 4.9.1
     lz4: 4.0.2
     MarkupSafe: 2.1.1
     matplotlib: 3.5.2
     matplotlib-inline: 0.1.6
     msgpack: 1.0.4
     nest-asyncio: 1.5.5
     netCDF4: 1.6.0
     networkx: 2.8.5
     numexpr: 2.8.3
     numpy: 1.23.1
     openvr: 1.23.701
     packaging: 21.3
     ParmEd: 3.4.3
     parso: 0.8.3
     pep517: 0.13.0
     pexpect: 4.8.0
     pickleshare: 0.7.5
     Pillow: 9.2.0
     pip: 22.2.2
     pkginfo: 1.8.3
     prompt-toolkit: 3.0.31
     psutil: 5.9.1
     ptyprocess: 0.7.0
     pure-eval: 0.2.2
     pycollada: 0.7.2
     pydicom: 2.3.0
     Pygments: 2.12.0
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 3.0.9
     PyQt6-commercial: 6.3.1
     PyQt6-Qt6: 6.3.1
     PyQt6-sip: 13.4.0
     PyQt6-WebEngine-commercial: 6.3.1
     PyQt6-WebEngine-Qt6: 6.3.1
     python-dateutil: 2.8.2
     pytz: 2022.2.1
     pyzmq: 23.2.1
     qtconsole: 5.3.1
     QtPy: 2.2.0
     RandomWords: 0.4.0
     requests: 2.28.1
     scipy: 1.9.0
     setuptools: 65.1.1
     sfftk-rw: 0.7.2
     six: 1.16.0
     snowballstemmer: 2.2.0
     sortedcontainers: 2.4.0
     Sphinx: 5.1.1
     sphinx-autodoc-typehints: 1.19.1
     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 3.0.0
     sphinxcontrib-devhelp: 1.0.2
     sphinxcontrib-htmlhelp: 2.0.0
     sphinxcontrib-jsmath: 1.0.1
     sphinxcontrib-qthelp: 1.0.3
     sphinxcontrib-serializinghtml: 1.1.5
     stack-data: 0.5.0
     tables: 3.7.0
     tifffile: 2022.7.31
     tinyarray: 1.2.4
     tomli: 2.0.1
     tornado: 6.2
     traitlets: 5.3.0
     urllib3: 1.26.12
     wcwidth: 0.2.5
     webcolors: 1.12
     wheel: 0.37.1
     wheel-filename: 1.4.1
     zipp: 3.8.1

 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7627>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by pett, 3 years ago

Component: Unassigned → Third Party
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → ChimeraX/ISOLDE version problems

comment:3 by pett, 3 years ago

Resolution: → fixed
Status: accepted → closed

Glad it's working now.

--Eric

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