ISOLDE symmetry handler: Spgr_descr: No such HM symbol

[mks131@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

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

> open /Users/ubcg90c/Downloads/cryosparc_P208_J2848_007_volume_map_sharp.mrc

Opened cryosparc_P208_J2848_007_volume_map_sharp.mrc, grid size 282,282,282,
pixel 1.3, shown at level 0.228, step 2, values float32  

> volume #1 level 0.351

> volume #1 step 1

> volume #1 level 0.4011

> volume #1 level 0.2342

> open
> /Users/ubcg90c/Downloads/6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708_P1.pdb

Chain information for
6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708_P1.pdb #2  
---  
Chain | Description  
A E | No description available  
B | No description available  
C G | No description available  
D H | No description available  
F | No description available  
I | No description available  
J | No description available  
  

> open
> /Users/ubcg90c/Downloads/6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708_P1.pdb

Chain information for
6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708_P1.pdb #3  
---  
Chain | Description  
A E | No description available  
B | No description available  
C G | No description available  
D H | No description available  
F | No description available  
I | No description available  
J | No description available  
  

> open
> /Users/ubcg90c/Downloads/cryosparc_P208_J2708_007_volume_map_sharp-2.mrc

Opened cryosparc_P208_J2708_007_volume_map_sharp-2.mrc, grid size 286,286,286,
pixel 1.3, shown at level 0.182, step 2, values float32  

> open
> /Users/ubcg90c/Desktop/Tf_new_data/RealSpaceRefine_237/6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708_P1_real_space_refined.cif

Summary of feedback from opening
/Users/ubcg90c/Desktop/Tf_new_data/RealSpaceRefine_237/6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708_P1_real_space_refined.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 917  
Missing entity information. Treating each chain as a separate entity.  
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "DA" near line 7080  
Missing first residue in struct_conn "C00001"  
Missing first residue in struct_conn "C00002"  
Missing first residue in struct_conn "C00003"  
Missing first residue in struct_conn "C00004"  
Missing first residue in struct_conn "C00005"  
6 messages similar to the above omitted  
Missing second residue in struct_conn "C00012"  
Missing first residue in struct_conn "C00013"  
Missing first residue in struct_conn "C00014"  
Missing first residue in struct_conn "C00015"  
Missing first residue in struct_conn "C00016"  
Missing first residue in struct_conn "C00017"  
12 messages similar to the above omitted  
Missing second residue in struct_conn "C00030"  
Missing first residue in struct_conn "C00031"  
Missing first residue in struct_conn "C00032"  
Missing first residue in struct_conn "C00033"  
Missing first residue in struct_conn "C00034"  
Missing first residue in struct_conn "C00035"  
16 messages similar to the above omitted  
Missing second residue in struct_conn "C00052"  
Missing first residue in struct_conn "C00053"  
Missing first residue in struct_conn "C00054"  
Missing first residue in struct_conn "C00055"  
Missing first residue in struct_conn "C00056"  
Missing first residue in struct_conn "C00057"  
32 messages similar to the above omitted  
Missing second residue in struct_conn "C00090"  
Missing first residue in struct_conn "C00091"  
Missing first residue in struct_conn "C00092"  
Missing first residue in struct_conn "C00093"  
Missing first residue in struct_conn "C00094"  
Missing first residue in struct_conn "C00095"  
4 messages similar to the above omitted  
Missing second residue in struct_conn "C00100"  
Missing first residue in struct_conn "C00101"  
Missing first residue in struct_conn "C00102"  
Missing first residue in struct_conn "C00103"  
Missing first residue in struct_conn "C00104"  
Missing first residue in struct_conn "C00105"  
2 messages similar to the above omitted  
Missing second residue in struct_conn "C00108"  
Missing first residue in struct_conn "C00109"  
Missing first residue in struct_conn "C00110"  
Missing first residue in struct_conn "C00111"  
Missing first residue in struct_conn "C00112"  
Missing first residue in struct_conn "C00113"  
26 messages similar to the above omitted  
Missing second residue in struct_conn "C00140"  
Missing second residue in struct_conn "C00141"  
Missing first residue in struct_conn "C00142"  
Missing first residue in struct_conn "C00143"  
Missing first residue in struct_conn "C00144"  
Missing first residue in struct_conn "C00145"  
Missing first residue in struct_conn "C00146"  
Missing second residue in struct_conn "C00147"  
Missing first residue in struct_conn "C00148"  
Missing first residue in struct_conn "C00149"  
Missing first residue in struct_conn "C00150"  
Missing first residue in struct_conn "C00151"  
Missing first residue in struct_conn "C00152"  
32 messages similar to the above omitted  
Missing second residue in struct_conn "C00185"  
Missing first residue in struct_conn "C00186"  
Missing first residue in struct_conn "C00187"  
Missing first residue in struct_conn "C00188"  
Missing first residue in struct_conn "C00189"  
Missing first residue in struct_conn "C00190"  
14 messages similar to the above omitted  
Missing second residue in struct_conn "C00205"  
Missing first residue in struct_conn "C00206"  
Missing first residue in struct_conn "C00207"  
Missing first residue in struct_conn "C00208"  
Missing first residue in struct_conn "C00209"  
Missing first residue in struct_conn "C00210"  
18 messages similar to the above omitted  
Missing second residue in struct_conn "C00229"  
Missing first residue in struct_conn "C00230"  
Missing first residue in struct_conn "C00231"  
Missing first residue in struct_conn "C00232"  
Missing first residue in struct_conn "C00233"  
Missing first residue in struct_conn "C00234"  
30 messages similar to the above omitted  
Missing second residue in struct_conn "C00265"  
Missing first residue in struct_conn "C00266"  
Missing first residue in struct_conn "C00267"  
Missing first residue in struct_conn "C00268"  
Missing first residue in struct_conn "C00269"  
Missing first residue in struct_conn "C00270"  
3 messages similar to the above omitted  
Missing second residue in struct_conn "C00274"  
Missing first residue in struct_conn "C00275"  
Missing first residue in struct_conn "C00276"  
Missing first residue in struct_conn "C00277"  
Missing first residue in struct_conn "C00278"  
Missing first residue in struct_conn "C00279"  
2 messages similar to the above omitted  
Missing second residue in struct_conn "C00282"  
Missing first residue in struct_conn "C00283"  
Missing first residue in struct_conn "C00284"  
Missing first residue in struct_conn "C00285"  
Missing first residue in struct_conn "C00286"  
Missing first residue in struct_conn "C00287"  
28 messages similar to the above omitted  
Missing second residue in struct_conn "C00316"  
Missing second residue in struct_conn "C00317"  
Missing first residue in struct_conn "C00318"  
Missing first residue in struct_conn "C00319"  
Missing first residue in struct_conn "C00320"  
Missing first residue in struct_conn "C00321"  
Missing first residue in struct_conn "C00322"  
Missing second residue in struct_conn "C00323"  
Missing first residue in struct_conn "C00324"  
Missing first residue in struct_conn "C00325"  
Missing first residue in struct_conn "C00326"  
Missing first residue in struct_conn "C00327"  
Missing first residue in struct_conn "C00328"  
354 messages similar to the above omitted  
Bad residue range for struct_conf "4" near line 105  
Bad residue range for struct_conf "8" near line 109  
Bad residue range for struct_conf "17" near line 118  
Bad residue range for struct_conf "21" near line 122  
Bad residue range for struct_conf "31" near line 132  
1 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for
6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708_P1_real_space_refined.cif
#5  
---  
Chain | Description  
A E | No description available  
B | No description available  
C G | No description available  
D H | No description available  
F | No description available  
  

> hide #5 models

> show #!4 models

> hide #!4 models

> show #5 models

> show #!4 models

> hide #5 models

> hide #!4 models

> show #5 models

> hide #3 models

> hide #2 models

> show #!4 models

> hide #!4 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> open /Users/ubcg90c/Downloads/P208_J2708_07_new.mrc

Opened P208_J2708_07_new.mrc, grid size 286,286,286, pixel 1.3, shown at level
0.182, step 2, values float32  

> volume #6 level 0.3206

Drag select of 489 atoms, 223 bonds, 6 P208_J2708_07_new.mrc  

> select #3/J:72@O3'

1 atom, 1 residue, 1 model selected  
Drag select of 9 atoms, 3 bonds, 6 P208_J2708_07_new.mrc  
Drag select of 731 atoms, 384 bonds, 6 P208_J2708_07_new.mrc  

> nucleotides sel ladder

> rainbow sel

> nucleotides sel atoms

> style nucleic & sel stick

Changed 353 atom styles  

> hide sel surfaces

> ui tool show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 531, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1253, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/__init__.py", line 139, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/tool.py", line 186, in __init__  
self.isolde = isolde.Isolde(self)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 559, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 1027, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2486, in _change_selected_model  
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 573, in __init__  
spotlight_mode=spotlight_mode)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 601, in add_model  
self.cell, self.spacegroup, self.grid, self.resolution, self._has_symmetry =
f(*args)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 202, in
symmetry_from_model_metadata  
return symmetry_from_model_metadata_pdb(model)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 447, 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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1501, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/cmd.py", line 187, in ui_tool_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Spgr_descr: No such HM symbol  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Spgr_descr: No such HM symbol  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  
'ISOLDE_ToolUI' object has no attribute 'isolde'  

> ui tool show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 531, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1253, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/__init__.py", line 139, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/tool.py", line 186, in __init__  
self.isolde = isolde.Isolde(self)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 559, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 1027, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2486, in _change_selected_model  
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 573, in __init__  
spotlight_mode=spotlight_mode)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 601, in add_model  
self.cell, self.spacegroup, self.grid, self.resolution, self._has_symmetry =
f(*args)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 202, in
symmetry_from_model_metadata  
return symmetry_from_model_metadata_pdb(model)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 447, 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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1501, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/cmd.py", line 187, in ui_tool_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Spgr_descr: No such HM symbol  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Spgr_descr: No such HM symbol  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.23
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1713)
      Kernel Version: Darwin 19.6.0
      Time since boot: 11 days 18:52

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-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: 1.1.1
    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-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    versioneer: 0.20
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[Eric Pettersen]

Reported by Manoj

[Tristan Croll]

This, too, should be fixed if you update to 1.3. Please let me know if it's not and I'll reopen.