Opened 3 years ago

Closed 3 years ago

#8610 closed defect (nonchimerax)

Surface calculation: cannot convert float NaN to integer

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Surface Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.5rc202210312311 (2022-10-31 23:11:39 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.5rc202210312311 (2022-10-31)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/29432/Dropbox (HMS)/Moazed lab
> data/prediction-1-las1l-nol9/results27_10/_unrelaxed_rank_1_model_2.pdb"

Chain information for _unrelaxed_rank_1_model_2.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> select /B:1-336

2632 atoms, 2674 bonds, 336 residues, 1 model selected  

> select /C:1-344

2644 atoms, 2707 bonds, 344 residues, 1 model selected  

> show sel cartoons

> show sel surfaces

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 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\std_commands\show.py", line 47, in show  
show_surfaces(session, objects, only, undo_state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\show.py", line 154, in show_surfaces  
surface(session, extra_atoms)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\surfacecmds.py", line 162, in surface  
threadq.apply_to_list(_calculate_surface, args, nthread)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\threadq.py", line 47, in apply_to_list  
return [func(*a) for a in args]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\threadq.py", line 47, in <listcomp>  
return [func(*a) for a in args]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\surfacecmds.py", line 195, in _calculate_surface  
surf.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 235, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  

> close session

> open "C:/Users/29432/Dropbox (HMS)/Moazed lab data/alphafold2 protein
> interaction prediction/results38_10/_unrelaxed_rank_1_model_3.pdb"

Chain information for _unrelaxed_rank_1_model_3.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F G | No description available  
  

> interfaces ~solvent

5 buried areas: B C 2930, C D 1403, E B 1006, E C 681, E D 313  

> sequence chain #1/F#1/G

Alignment identifier is 1  

> close session

> open "C:/Users/29432/Dropbox (HMS)/Moazed lab data/alphafold2 protein
> interaction prediction/results27_10/_unrelaxed_rank_1_model_2.pdb"

Chain information for _unrelaxed_rank_1_model_2.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> select /B:1-336

2632 atoms, 2674 bonds, 336 residues, 1 model selected  

> sequence chain #1/B

Alignment identifier is 1/B  

> close session

> open "C:/Users/29432/Dropbox (HMS)/Moazed lab data/alphafold2 protein
> interaction prediction/results27_10/_unrelaxed_rank_2_model_1.pdb"

Chain information for _unrelaxed_rank_2_model_1.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> show cartoons

> show surfaces

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 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\std_commands\show.py", line 47, in show  
show_surfaces(session, objects, only, undo_state)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\show.py", line 154, in show_surfaces  
surface(session, extra_atoms)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\surfacecmds.py", line 162, in surface  
threadq.apply_to_list(_calculate_surface, args, nthread)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\threadq.py", line 70, in apply_to_list  
raise r  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\threadq.py", line 31, in run  
r = self.function(*s)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\surfacecmds.py", line 195, in _calculate_surface  
surf.calculate_surface_geometry()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 235, in calculate_surface_geometry  
va, na, ta = surface.ses_surface_geometry(xyz, r, self.probe_radius,
self.grid_spacing)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in ses_surface_geometry  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in <listcomp>  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
ValueError: cannot convert float NaN to integer  
  
ValueError: cannot convert float NaN to integer  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\surface\gridsurf.py", line 29, in  
shape = [int(ceil((xyz_max[a] - xyz_min[a] + 2*pad) / s))  
  
See log for complete Python traceback.  
  

> show atoms

> show cartoons

> style sphere

Changed 16996 atom styles  

> hide surfaces

> rainbow

> coulombic

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 209, in add_hydrogens  
h_positions = bond_positions(atom._addh_coord, geom, bond_length,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\bond_geom.py", line 78, in bond_positions  
return tetra_pos(bondee, bonded, bond_len, toward, away, toward2, away2)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\bond_geom.py", line 211, in tetra_pos  
pl = Plane(unitized)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\plane.py", line 50, in __init__  
ignore, vals, vecs = svd(centered, full_matrices=False)  
File "<__array_function__ internals>", line 180, in svd  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\numpy\linalg\linalg.py",
line 1657, in svd  
u, s, vh = gufunc(a, signature=signature, extobj=extobj)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\numpy\linalg\linalg.py",
line 98, in _raise_linalgerror_svd_nonconvergence  
raise LinAlgError("SVD did not converge")  
numpy.linalg.LinAlgError: SVD did not converge  
  
numpy.linalg.LinAlgError: SVD did not converge  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\numpy\linalg\linalg.py",
line 98, in _raise_linalgerror_svd_nonconvergence  
raise LinAlgError("SVD did not converge")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 512.36
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

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

Manufacturer: LENOVO
Model: 82K8
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 16,498,810,880
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800H with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.10.3
    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
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    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: 1.5rc202210312311
    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
    ChimeraX-Map: 1.1.2
    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
    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: 1.24.3
    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
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    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: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    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: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.2
    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: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    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
    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: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    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: 0.6.0
    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
    WMI: 1.5.1
    zipp: 3.10.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Eric Pettersen added
Component: Unassigned → Surface
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Surface calculation: cannot convert float NaN to integer

There's also a later error when running coulombic where numpy.linalg.svd() did not converge. I suspect bad coordinates.

comment:2 by Tom Goddard, 3 years ago

Resolution: → nonchimerax
Status: assigned → closed

Appears that the PDB file has NaN coordinates. I think our PDB file reader was changed recently to check for this and give an error reading the file.

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