Opened 3 years ago

Closed 3 years ago

#7604 closed defect (duplicate)

Error in ToolShed error message

Reported by: kmanne@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Tristan Croll, Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.31.1.el7.x86_64-x86_64-with-redhat-7.9-Maipo
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/Refine_10/TSLP_46640_AMG7p8_ALS502_20220902_refine_10.pdb

Chain information for TSLP_46640_AMG7p8_ALS502_20220902_refine_10.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> set bgColor white

> open
> /home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/pointless.mtz
> structure#1

'structure#1' has no suffix  

> open
> /home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/pointless.mtz
> structureModel #1

Summary of feedback from opening
/home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/pointless.mtz  
---  
notes | Discarding unrecognised/unsupported data array
/HKL_base/HKL_base/M_ISYM Y  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/BATCH B  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/FRACTIONCALC
R  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/XDET R  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/YDET R  
2 messages similar to the above omitted  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
Failed on HKL = ( -30, 0, 1)  
N_bins: 60 Imean: -0.2748146101960023 I: -16.93000030517578 sigI:
29.34000015258789 eobs_sq: 30.802584136813227 sig_eobs_sq: -53.38144164107964  
  
Traceback (most recent call last):  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 389, in collated_open  
return func(*func_args, **func_kw)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/__init__.py", line 228, in open  
return open_structure_factors(session, data, **kw)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/xmapset.py", line 189, in __init__  
fill_with_fcalc, exclude_missing_reflections)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 110, in
french_wilson_analytical  
e_xpct = _expected_E_FW_cen(eobs_sq, sig_eobs_sq)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
ValueError: math domain error  
  
ValueError: math domain error  
  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
  
See log for complete Python traceback.  
  

> open
> /home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/pointless.mtz
> structureModel #1

Invalid "structureModel" argument: Must specify 1 model, got 0  

> open
> /home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/Refine_10/TSLP_46640_AMG7p8_ALS502_20220902_refine_10.pdb

Chain information for TSLP_46640_AMG7p8_ALS502_20220902_refine_10.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/pointless.mtz
> structureModel #1

Summary of feedback from opening
/home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/pointless.mtz  
---  
notes | Discarding unrecognised/unsupported data array
/HKL_base/HKL_base/M_ISYM Y  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/BATCH B  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/FRACTIONCALC
R  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/XDET R  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/YDET R  
2 messages similar to the above omitted  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
Failed on HKL = ( -30, 0, 1)  
N_bins: 60 Imean: -0.2748146101960023 I: -16.93000030517578 sigI:
29.34000015258789 eobs_sq: 30.802584136813227 sig_eobs_sq: -53.38144164107964  
  
Traceback (most recent call last):  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 389, in collated_open  
return func(*func_args, **func_kw)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/__init__.py", line 228, in open  
return open_structure_factors(session, data, **kw)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/xmapset.py", line 189, in __init__  
fill_with_fcalc, exclude_missing_reflections)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 110, in
french_wilson_analytical  
e_xpct = _expected_E_FW_cen(eobs_sq, sig_eobs_sq)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
ValueError: math domain error  
  
ValueError: math domain error  
  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
  
See log for complete Python traceback.  
  

> open
> /home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/Refine_10/TSLP_46640_AMG7p8_ALS502_20220902_refine_10.pdb
> format pdb

Chain information for TSLP_46640_AMG7p8_ALS502_20220902_refine_10.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/aimless_all.mtz
> structureModel #1

Summary of feedback from opening
/home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/aimless_all.mtz  
---  
warnings | WARNING: found multiple possible R-free arrays:  
(XDSdataset) N(+),  
(XDSdataset) N(-)  
Automatically choosing "(XDSdataset) N(+)". If this is incorrect, please
either provide a file with a single flag array, or load the file again using
the free_flag_label argument.  
WARNING: multiple experimental reflection datasets found:  
(XDSdataset) IMEAN, SIGIMEAN,  
(XDSdataset) I(+), SIGI(+), I(-), SIGI(-)  
Automatically choosing "(XDSdataset) IMEAN, SIGIMEAN".  
notes | Reflection data provided as intensities. Performing French & Wilson
scaling to convert to amplitudes...  
Failed on HKL = ( -30, 0, 1)  
N_bins: 60 Imean: -1.1910064648093588 I: -10.102652549743652 sigI:
11.225279808044434 eobs_sq: 4.241224900219478 sig_eobs_sq: -4.712518420225886  
  
Traceback (most recent call last):  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 389, in collated_open  
return func(*func_args, **func_kw)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/__init__.py", line 228, in open  
return open_structure_factors(session, data, **kw)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/xmapset.py", line 189, in __init__  
fill_with_fcalc, exclude_missing_reflections)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 110, in
french_wilson_analytical  
e_xpct = _expected_E_FW_cen(eobs_sq, sig_eobs_sq)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
ValueError: math domain error  
  
ValueError: math domain error  
  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
  
See log for complete Python traceback.  
  

> open
> /home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/Refine_10/TSLP_46640_AMG7p8_ALS502_20220902_refine_10.pdb
> format pdb

Chain information for TSLP_46640_AMG7p8_ALS502_20220902_refine_10.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> start isolde

Unknown command: start isolde  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.1.0-cp37-cp37m-linux_x86_64.whl  
Traceback (most recent call last):  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/help_viewer/tool.py", line 389, in download_finished  
session=self.session)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 390.143
OpenGL renderer: Quadro 5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Hewlett-Packard
Model: HP Z600 Workstation
OS: Red Hat Enterprise Linux Workstation 7.9 Maipo
Architecture: 64bit ELF
CPU: 8 Intel(R) Xeon(R) CPU           E5640  @ 2.67GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        8.0G        985M        294M        6.5G        6.8G
	Swap:          7.9G        558M        7.3G

Graphics:
	0f:00.0 VGA compatible controller [0300]: NVIDIA Corporation GF100GL [Quadro 5000] [10de:06d9] (rev a3)	
	Subsystem: Hewlett-Packard Company Device [103c:0770]	
	Kernel driver in use: nvidia
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
    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-Clipper: 0.15.0
    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
    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-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 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-Phenix: 0.3
    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
    distro: 1.5.0
    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
    MolecularDynamicsViewer: 1.1
    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
    Send2Trash: 1.8.0
    SEQCROW: 0.25.2
    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

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tristan Croll added
Component: Unassigned → Tool Shed
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Error in ToolShed error message

comment:2 by Eric Pettersen, 3 years ago

Cc: Eric Pettersen added
Resolution: → duplicate
Status: assigned → closed

Hi Kartik,

This particular problem was fixed awhile ago. You should upgrade your version of ChimeraX/ISOLDE.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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