Overflow encountered in geometry.camera.double_scalars()

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7KNE format mmcif fromDatabase pdb

7kne title:  
Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 5.5 [more
info...]  
  
Chain information for 7kne #1  
---  
Chain | Description  
A B C | Spike glycoprotein  
D | Angiotensin-converting enzyme 2  
  
Non-standard residues in 7kne #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> select /D:19-614

4862 atoms, 5002 bonds, 596 residues, 1 model selected  

> color sel cornflower blue

> select /C:26-1146

7771 atoms, 7956 bonds, 8 pseudobonds, 1006 residues, 2 models selected  

> select /B:26-1148

8003 atoms, 8199 bonds, 7 pseudobonds, 1029 residues, 2 models selected  

> color (#!1 & sel) orange red

> select /C:26-1146

7771 atoms, 7956 bonds, 8 pseudobonds, 1006 residues, 2 models selected  

> color (#!1 & sel) light sea green

> show (#!1 & sel) target ab

> hide (#!1 & sel) target a

No Surface models open  
No Surface models open  

> cartoon (#!1 & sel)

> undo

> style sel sphere

Changed 7771 atom styles  

> undo

> style (#!1 & sel) stick

Changed 7771 atom styles  

> undo

> select /A:26-1146

7771 atoms, 7956 bonds, 8 pseudobonds, 1006 residues, 2 models selected  

> color (#!1 & sel) dim gray

> lighting full

> style sel ball

Changed 7771 atom styles  

> undo

> show (#!1 & sel) target ab

> undo

> cartoon (#!1 & sel)

> undo

No Surface models open  

> surface (#!1 & sel)

> color (#!1 & sel) dark gray

> color (#!1 & sel) dim gray

> select /A:26-1146

7771 atoms, 7956 bonds, 8 pseudobonds, 1006 residues, 2 models selected  

> select /C:26-1146

7771 atoms, 7956 bonds, 8 pseudobonds, 1006 residues, 2 models selected  

> surface (#!1 & sel)

> color (#!1 & sel) cornflower blue

> color (#!1 & sel) light sea green

> save /Users/ls/Desktop/image4.png supersample 3

> save /Users/ls/Desktop/image5.png supersample 3

> save /Users/ls/Desktop/image6.png supersample 3

> save /Users/ls/Desktop/image7.png supersample 3

> save /Users/ls/Desktop/image8.png supersample 3

> save /Users/ls/Desktop/image9.png supersample 3

> select down

7771 atoms, 7956 bonds, 8 pseudobonds, 1006 residues, 3 models selected  

> select down

7771 atoms, 7956 bonds, 8 pseudobonds, 1006 residues, 3 models selected  

> save /Users/ls/Desktop/image10.png supersample 3

> save /Users/ls/Desktop/SARS-CoV2_Spike_Protein_7KNE.cxs

> lighting full

> lighting soft

> lighting full

> style sel sphere

Changed 7771 atom styles  

> open 4L72

Summary of feedback from opening 4L72 fetched from pdb  
---  
notes | Fetching compressed mmCIF 4l72 from
http://files.rcsb.org/download/4l72.cif  
Fetching CCD BMA from http://ligand-expo.rcsb.org/reports/B/BMA/BMA.cif  
  
4l72 title:  
Crystal structure of MERS-CoV complexed with human DPP4 [more info...]  
  
Chain information for 4l72 #2  
---  
Chain | Description  
A | Dipeptidyl peptidase 4  
B | MERS-CoV RBD  
  
Non-standard residues in 4l72 #2  
---  
BMA — beta-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
4l72 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_and_software_defined_assembly  
3| software_defined_assembly  
  

> hide #2 models

> open 4L72 format mmcif fromDatabase pdb

4l72 title:  
Crystal structure of MERS-CoV complexed with human DPP4 [more info...]  
  
Chain information for 4l72 #3  
---  
Chain | Description  
A | Dipeptidyl peptidase 4  
B | MERS-CoV RBD  
  
Non-standard residues in 4l72 #3  
---  
BMA — beta-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
4l72 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_and_software_defined_assembly  
3| software_defined_assembly  
  

> open 7KNE format mmcif fromDatabase pdb

7kne title:  
Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 5.5 [more
info...]  
  
Chain information for 7kne #4  
---  
Chain | Description  
A B C | Spike glycoprotein  
D | Angiotensin-converting enzyme 2  
  
Non-standard residues in 7kne #4  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> open 4L72 format mmcif fromDatabase pdb

4l72 title:  
Crystal structure of MERS-CoV complexed with human DPP4 [more info...]  
  
Chain information for 4l72 #5  
---  
Chain | Description  
A | Dipeptidyl peptidase 4  
B | MERS-CoV RBD  
  
Non-standard residues in 4l72 #5  
---  
BMA — beta-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
4l72 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_and_software_defined_assembly  
3| software_defined_assembly  
  

> hide #3 models

> hide #!4 models

> hide #!1 models

> select #5/A:39-766

5963 atoms, 6140 bonds, 728 residues, 1 model selected  

> open 4L72 format mmcif fromDatabase pdb

4l72 title:  
Crystal structure of MERS-CoV complexed with human DPP4 [more info...]  
  
Chain information for 4l72 #6  
---  
Chain | Description  
A | Dipeptidyl peptidase 4  
B | MERS-CoV RBD  
  
Non-standard residues in 4l72 #6  
---  
BMA — beta-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
4l72 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_and_software_defined_assembly  
3| software_defined_assembly  
  

> select #5

7705 atoms, 7936 bonds, 944 residues, 1 model selected  

> sequence chain #6/A

Alignment identifier is 6/A  

> select #6/A:39-766

5963 atoms, 6140 bonds, 728 residues, 1 model selected  

> open 4L72 format mmcif fromDatabase pdb

4l72 title:  
Crystal structure of MERS-CoV complexed with human DPP4 [more info...]  
  
Chain information for 4l72 #7  
---  
Chain | Description  
A | Dipeptidyl peptidase 4  
B | MERS-CoV RBD  
  
Non-standard residues in 4l72 #7  
---  
BMA — beta-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
4l72 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_and_software_defined_assembly  
3| software_defined_assembly  
  
/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/camera.py:598: RuntimeWarning: overflow encountered
in double_scalars  
d = - (2 * z_far * z_near) / (z_far - z_near)  
/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py:66: RuntimeWarning: overflow encountered
in double_scalars  
return dx*dx + dy*dy + dz*dz  

> open 4L72

4l72 title:  
Crystal structure of MERS-CoV complexed with human DPP4 [more info...]  
  
Chain information for 4l72 #8  
---  
Chain | Description  
A | Dipeptidyl peptidase 4  
B | MERS-CoV RBD  
  
Non-standard residues in 4l72 #8  
---  
BMA — beta-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
4l72 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_and_software_defined_assembly  
3| software_defined_assembly  
  
Traceback (most recent call last):  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 491, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 626, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 697, in pause  
p = self.view.picked_object(x, y)  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 787, in picked_object  
max_transparent_layers = max_transparent_layers)  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 818, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1024, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1041, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 595, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 628, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 986, in first_intercept  
atom = self.visible_atoms[anum]  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
IndexError: index 4445409744 is out of bounds for axis 0 with size 286  
  
IndexError: index 4445409744 is out of bounds for axis 0 with size 286  
  
File
"/private/var/folders/ps/34hn8lcj5vnd34psljhxjr2h0000gn/T/AppTranslocation/369D2EAC-32FC-4C08-BE70-356C129F34DA/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.16
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,1
      Processor Name: Intel Core i5
      Processor Speed: 2,3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 180.0.0.0.0
      SMC Version (system): 2.39f39

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G3020)
      Kernel Version: Darwin 18.7.0
      Time since boot: 10:32

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[Tom Goddard]

First there are two warnings double floating point overflow in Camera trying to compute the projection matrix, maybe znear == zfar or znear or zfar is enormous and a distance calculation. None of the command give a clue how those happened. Then an index out of bounds on a mouse hover trying to pick an atom trying to use index 4.4e9 (> 2e32) when the list of visible atoms is only 286 long. Unclear how that could happen without memory corruption. Index was produced by C++ code. Looking at that code it looks like it could return an uninitialized value if all atom coordinates were NaN. I have fixed that.

Not enough info to debug. Seems like some NaN atom coordinates may have caused the errors.