Opened 17 months ago

Closed 17 months ago

#15433 closed defect (duplicate)

AlphaFold JSON opened as MOLE JSON

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-107-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

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

> open "/home/sandip/Documents/Soham/stpk
> structure/fold_msmeg_0030/fold_msmeg_0030_full_data_0.json"

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/__main__.py", line 863, in init  
commands.run(sess, 'open %s' % StringArg.unparse(arg))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mole/__init__.py", line 27, in open  
return mole.read_mole_json(session, data, file_name, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mole/mole.py", line 40, in read_mole_json  
models = channel_models(session, j['Channels'], transparency/100.0)  
KeyError: 'Channels'  
  
KeyError: 'Channels'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mole/mole.py", line 40, in read_mole_json  
models = channel_models(session, j['Channels'], transparency/100.0)  
  
See log for complete Python traceback.  
  

> open "/home/sandip/Documents/Soham/stpk
> structure/matches/fold_msmeg_2410_model_0.cif" format mmcif

Chain information for fold_msmeg_2410_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> open "/home/sandip/Documents/Soham/stpk
> structure/fold_msmeg_0030/fold_msmeg_0030_model_0.cif"

Chain information for fold_msmeg_0030_model_0.cif #2  
---  
Chain | Description  
A | .  
  

> ui tool show Matchmaker

> matchmaker #2 to #1 cutoffDistance 0.84 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 0.84  
  
Matchmaker fold_msmeg_2410_model_0.cif, chain A (#1) with
fold_msmeg_0030_model_0.cif, chain A (#2), sequence alignment score = 85.6  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: fold_msmeg_2410_model_0.cif
#1/A, fold_msmeg_0030_model_0.cif #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 3 pruned atom pairs is 0.297 angstroms; (across all 183 pairs:
32.628)  
  

> ui tool show Matchmaker

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 455, in set_value  
self._float_widget.set_text("")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 455, in set_value  
self._float_widget.set_text("")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 455, in set_value  
self._float_widget.set_text("")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 455, in set_value  
self._float_widget.set_text("")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 455, in set_value  
self._float_widget.set_text("")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 455, in set_value  
self._float_widget.set_text("")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 455, in set_value  
self._float_widget.set_text("")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 455, in set_value  
self._float_widget.set_text("")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 455, in set_value  
self._float_widget.set_text("")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type NZDoubleSpinBox has been deleted  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 1015, in set_text  
self.blockSignals(True)  
  
See log for complete Python traceback.  
  

> matchmaker #2 to #1 cutoffDistance 5.0 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 5  
  
Matchmaker fold_msmeg_2410_model_0.cif, chain A (#1) with
fold_msmeg_0030_model_0.cif, chain A (#2), sequence alignment score = 85.6  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: fold_msmeg_2410_model_0.cif
#1/A, fold_msmeg_0030_model_0.cif #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 19 pruned atom pairs is 3.633 angstroms; (across all 183 pairs:
32.319)  
  




OpenGL version: 3.3.0 NVIDIA 470.239.06
OpenGL renderer: Quadro P400/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_IN.ISO8859-1
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: HP
Model: HP Z2 Tower G4 Workstation
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          7.6Gi       2.5Gi       2.2Gi        30Mi       3.0Gi       4.8Gi
	Swap:          30Gi          0B        30Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP107GL [Quadro P400] [10de:1cb3] (rev a1)	
	Subsystem: Hewlett-Packard Company GP107GL [Quadro P400] [103c:11be]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    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: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    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
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    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: 5.1.0
    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: 5.1.0
    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
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    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: 6.3.2
    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
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    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: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 17 months ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → AlphaFold JSON opened as MOLE JSON

comment:2 by Tom Goddard, 17 months ago

Resolution: → duplicate
Status: assigned → closed

Fixed long ago.

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