Clipper: Unrecognised space group string (empty string)

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.76.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /localhome/bsmgr/data/myosin_models/lever_to_fit_sim/sarmol/isolde_no_Nterm/new_isolde_models/flag_7/continued_rest/minimised/continued_rest_frame_1501_2p370rmsd_explicit_minimised.pdb
> format pdb

Chain information for
continued_rest_frame_1501_2p370rmsd_explicit_minimised.pdb #1  
---  
Chain | Description  
? | No description available  
  

> open
> /localhome/bsmgr/data/cryo/S1_0503/4285/rextract_250/3dclass/isolde_all_classes_141022/isolde_lever_fitted_map_motor_fitted_2523ints_extended_c6_fitted_n_lobe_7_M.pdb

Chain information for
isolde_lever_fitted_map_motor_fitted_2523ints_extended_c6_fitted_n_lobe_7_M.pdb
#2  
---  
Chain | Description  
B C E F G S | No description available  
J K L | No description available  
M | No description available  
  

> mmaker #31 to #2

No molecules/chains to match specified  

> mmaker #1 to #2

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 | 2  
  
Matchmaker
isolde_lever_fitted_map_motor_fitted_2523ints_extended_c6_fitted_n_lobe_7_M.pdb,
chain M (#2) with continued_rest_frame_1501_2p370rmsd_explicit_minimised.pdb,
chain (blank) (#1), sequence alignment score = 1145.9  
RMSD between 196 pruned atom pairs is 0.554 angstroms; (across all 334 pairs:
48.007)  
  

> open
> /localhome/bsmgr/data/cryo/S1_0503/4285/rextract_250/3dclass/isolde_all_classes_141022/j280_c12_widetarget.mrc

Opened j280_c12_widetarget.mrc as #3, grid size 250,250,250, pixel 2.13, shown
at level 0.000317, step 1, values float32  

> set bgColor white

> volume #3 level 0.1283

> volume #3 color #73d2167f

> volume #3 color #b2b2b2

> volume #3 color #d3d7cf

> volume #3 color #babdb6

> volume transparency 0.5

> ui tool show "Fit in Map"

Fit molecule continued_rest_frame_1501_2p370rmsd_explicit_minimised.pdb (#1)
to map j280_c12_widetarget.mrc (#3) using 17234 atoms  
average map value = 0.3721, steps = 84  
shifted from previous position = 0.46  
rotated from previous position = 1.77 degrees  
atoms outside contour = 3661, contour level = 0.12826  
  
Position of continued_rest_frame_1501_2p370rmsd_explicit_minimised.pdb (#1)
relative to j280_c12_widetarget.mrc (#3) coordinates:  
Matrix rotation and translation  
0.58989848 -0.28787409 0.75441918 146.33586397  
-0.78058996 -0.44239210 0.44155242 378.12460613  
0.20663759 -0.84936314 -0.48567805 402.25414416  
Axis -0.86850200 0.36853643 -0.33148933  
Axis point 0.00000000 312.93521691 64.83282178  
Rotation angle (degrees) 131.99654834  
Shift along axis -121.08325419  
  

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> open
> /localhome/bsmgr/data/cryo/S1_0503/4285/rextract_250/3dclass/class12/isolde_model_dist_rests_lowmap_070822/isolde_lever_fitted_map_motor_fitted_2523ints_extended_c6_map_wt1_moved_empty_6.pdb

Chain information for
isolde_lever_fitted_map_motor_fitted_2523ints_extended_c6_map_wt1_moved_empty_6.pdb
#4  
---  
Chain | Description  
B C E F G S | No description available  
J K L | No description available  
M | No description available  
  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #1 models

> hide #!4 atoms

> show #!4 cartoons

> show #1 models

> close #4

> close #2

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 140 residues in model #1 to IUPAC-IUB
standards.  
Traceback (most recent call last):  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 451, in
symmetry_from_model_metadata_pdb  
spgr_descr = Spgr_descr(symstr, symstr_type)  
RuntimeError: Spgr_descr: No such HM symbol  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line
554, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line
1264, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/__init__.py", line 155, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/tools.py", line 193, in
get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/tool.py", line 186, in __init__  
self.isolde = isolde.Isolde(self)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 317, in __init__  
self._start_gui(gui)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 482, in _start_gui  
self._update_model_list(None, None, force=True)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1050, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2528, in _change_selected_model  
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 579, in __init__  
self.add_model(model, ignore_model_symmetry=ignore_model_symmetry,  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 608, in add_model  
self.cell, self.spacegroup, self.grid, self.resolution, self._has_symmetry =
f(*args)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 202, in
symmetry_from_model_metadata  
return symmetry_from_model_metadata_pdb(model)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 454, in
symmetry_from_model_metadata_pdb  
raise UserError(f'Unrecognised space group string: {symstr}')  
chimerax.core.errors.UserError: Unrecognised space group string:  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1659, in
<lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36,
in run  
results = command.run(text, log=log, return_json=return_json)  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line
2856, in run  
result = ci.function(session, **kw_args)  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/cmd.py", line 219, in
ui_tool_show  
bi.start_tool(session, name)  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line
559, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Unrecognised space group string:  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Unrecognised space group string:  
  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line
559, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1496, in
_add_real_space_map_from_gui  
self.add_real_space_map(existing_volume=v, to_model=self.selected_model)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1386, in add_real_space_map  
map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 183, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2251, in
<lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 654, in
close_request  
tool_instance.delete()  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/tool.py", line 191, in delete  
self.isolde._on_close()  
AttributeError: 'ISOLDE_ToolUI' object has no attribute 'isolde'  
  
AttributeError: 'ISOLDE_ToolUI' object has no attribute 'isolde'  
  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/tool.py", line 191, in delete  
self.isolde._on_close()  
  
See log for complete Python traceback.  
  

> open
> /localhome/bsmgr/data/myosin_models/lever_to_fit_sim/sarmol/isolde_no_Nterm/new_isolde_models/flag_7/continued_rest/minimised/continued_rest_frame_1501_2p370rmsd_explicit_minimised.pdb

Chain information for
continued_rest_frame_1501_2p370rmsd_explicit_minimised.pdb #2  
---  
Chain | Description  
? | No description available  
  
Traceback (most recent call last):  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke  
return self._func(self._name, data)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1019, in _update_model_list  
with slot_disconnected(mmcb.currentIndexChanged, self._change_selected_model):  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1019, in _update_model_list  
with slot_disconnected(mmcb.currentIndexChanged, self._change_selected_model):  
  
See log for complete Python traceback.  
  

> mmaker #2 to #1

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 | 2  
  
Matchmaker continued_rest_frame_1501_2p370rmsd_explicit_minimised.pdb, chain
(blank) (#1) with continued_rest_frame_1501_2p370rmsd_explicit_minimised.pdb,
chain (blank) (#2), sequence alignment score = 5670.7  
RMSD between 1088 pruned atom pairs is 0.000 angstroms; (across all 1088
pairs: 0.000)  
  

> select #2

17234 atoms, 17340 bonds, 1088 residues, 1 model selected  
Traceback (most recent call last):  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke  
return self._func(self._name, data)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 110, in
_selection_changed_cb  
if not self.visible or not self.current_model:  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 325, in visible  
return self.parent.isVisible()  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 321, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "selection changed":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 321, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke  
return self._func(self._name, data)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1106, in _selection_changed  
self._disable_register_shift_frame()  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1757, in
_disable_register_shift_frame  
self.iw._rebuild_register_shift_container.setEnabled(False)  
RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  
Error processing trigger "selection changed":  
RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1757, in
_disable_register_shift_frame  
self.iw._rebuild_register_shift_container.setEnabled(False)  
  
See log for complete Python traceback.  
  

> ~select #2

Nothing selected  
Traceback (most recent call last):  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke  
return self._func(self._name, data)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 110, in
_selection_changed_cb  
if not self.visible or not self.current_model:  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 325, in visible  
return self.parent.isVisible()  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 321, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "selection changed":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 321, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/localhome/Software/install/ucsf-chimerax-1.3-1/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke  
return self._func(self._name, data)  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1106, in _selection_changed  
self._disable_register_shift_frame()  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1757, in
_disable_register_shift_frame  
self.iw._rebuild_register_shift_container.setEnabled(False)  
RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  
Error processing trigger "selection changed":  
RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  
File "/localhome/bsmgr/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1757, in
_disable_register_shift_frame  
self.iw._rebuild_register_shift_container.setEnabled(False)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.84
OpenGL renderer: Quadro P5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 48 Intel(R) Xeon(R) Silver 4116 CPU @ 2.10GHz
Cache Size: 16896 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           187G         12G        123G        1.1G         51G        172G
	Swap:          4.0G          0B        4.0G

Graphics:
	0000:17:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P5000] [10de:1bb0] (rev a1)	
	Subsystem: Dell Device [1028:11b2]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Tristan Croll]

Hmm… probably a malformed CRYST1 card (present, but has information missing
or wrong spacing). Guess I don’t have a handler for that case.

On Mon, 14 Nov 2022 at 18:15, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote: