ISOLDE/Clipper: Spgr_descr: No such HM symbol

[arronsullivan@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
attepted to use ISOLDE for the first time and got the error in the log attached.

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

> open C:\Users\robot\Desktop\Modeling\Herceptin_FC_Lys_v1.cxs format session

Log from Mon Apr 19 13:13:53 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6IQG

Summary of feedback from opening 6IQG fetched from pdb  
---  
notes | Fetching compressed mmCIF 6iqg from
http://files.rcsb.org/download/6iqg.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
Fetching CCD HCS from http://ligand-expo.rcsb.org/reports/H/HCS/HCS.cif  
  
6iqg title:  
X-ray crystal structure of Fc and peptide complex [more info...]  
  
Chain information for 6iqg #1  
---  
Chain | Description  
A B | Immunoglobulin gamma-1 heavy chain  
C D | 18-mer peptide G(HCS)DCAYHRGELVWCT(HCS)H(NH2)  
  
Non-standard residues in 6iqg #1  
---  
BMA — beta-D-mannopyranose  
CL — chloride ion  
FUC — alpha-L-fucopyranose  
HCS — 2-amino-4-mercapto-butyric acid  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> select /C/D

228 atoms, 236 bonds, 28 residues, 1 model selected  

> remove

Unknown command: remove  

> remove selected

Unknown command: remove selected  

> remove /c

Unknown command: remove /c  

> hide /c

> select clear

> hide /c

> select /C:613

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select /C/D

228 atoms, 236 bonds, 28 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Show Sequence Viewer"

> sequence chain /A /B

Alignment identifier is 1  

> select ::name="LYS"

324 atoms, 288 bonds, 36 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 324 atom styles  

> surface sel

> transparency (#!1 & sel) 50

> surface style mesh

> select clear

> select /B:246@CE

1 atom, 1 residue, 1 model selected  

> select /B:246@NZ

1 atom, 1 residue, 1 model selected  

> select /B:248@NZ

1 atom, 1 residue, 1 model selected  

> ui tool show Distances

> distance /B:246@NZ /B:248@NZ

Distance between /B LYS 246 NZ and LYS 248 NZ: 11.620Å  
Drag select of 2 residues  

> select /B:246@CE

1 atom, 1 residue, 1 model selected  

> distance /B:246@CE /B:290@CE

Distance between /B LYS 246 CE and LYS 290 CE: 13.306Å  

> select clear

> select ::name="LYS"

324 atoms, 288 bonds, 2 pseudobonds, 36 residues, 2 models selected  

> surface style dot

> surface style solid

> transparency (#!1 & sel) 80

> select clear

> select /B:290@CE

1 atom, 1 residue, 1 model selected  

> select /B:246@CG

1 atom, 1 residue, 1 model selected  

> select clear

> hide #2.1 models

> show #2.1 models

> hide #!2 models

> select /B:274@CE

1 atom, 1 residue, 1 model selected  

> distance /B:274@CE /B:322@CE

Distance between /B LYS 274 CE and LYS 322 CE: 7.003Å  

> show #!2 models

> select /B:274@CE

1 atom, 1 residue, 1 model selected  

> distance /B:274@CE /B:326@NZ

Distance between /B LYS 274 CE and LYS 326 NZ: 11.172Å  

> select /B:322@CE

1 atom, 1 residue, 1 model selected  

> select /B:274@CD

1 atom, 1 residue, 1 model selected  

> select /B:288@CE

1 atom, 1 residue, 1 model selected  

> distance /B:288@CE /B:290@CE

Distance between /B LYS 288 CE and LYS 290 CE: 9.280Å  

> select /B:322@CE

1 atom, 1 residue, 1 model selected  

> distance /B:320@NZ /B:322@CE

Distance between /B LYS 320 NZ and LYS 322 CE: 9.849Å  

> select /B:320@NZ

1 atom, 1 residue, 1 model selected  

> select /B:320@NZ

1 atom, 1 residue, 1 model selected  

> distance /B:317@CE /B:320@NZ

Distance between /B LYS 317 CE and LYS 320 NZ: 12.281Å  

> select clear

> select /B:317@CE

1 atom, 1 residue, 1 model selected  

> distance /B:317@CE /B:340@NZ

Distance between /B LYS 317 CE and LYS 340 NZ: 14.146Å  

> select /B:340@NZ

1 atom, 1 residue, 1 model selected  

> distance /B:338@NZ /B:340@NZ

Distance between /B LYS 338 NZ and LYS 340 NZ: 9.588Å  
Drag select of 6iqg_A SES surface, 15 of 202702 triangles, 6iqg_B SES surface,
414 of 203562 triangles, 5 atoms, 2 residues, 3 bonds  

> select /B:439@CE

1 atom, 1 residue, 1 model selected  

> distance /A:360@CE /B:439@CE

Distance between /A LYS 360 CE and /B LYS 439 CE: 9.669Å  

> select /B:370@NZ

1 atom, 1 residue, 1 model selected  

> distance /A:409@NZ /B:370@NZ

Distance between /A LYS 409 NZ and /B LYS 370 NZ: 5.420Å  

> select /A:414@CE

1 atom, 1 residue, 1 model selected  

> select clear

> select /B:414@CE

1 atom, 1 residue, 1 model selected  

> distance /B:360@CG /B:414@CE

Distance between /B LYS 360 CG and LYS 414 CE: 8.721Å  

> select /B:392@NZ

1 atom, 1 residue, 1 model selected  

> distance /B:392@NZ /B:409@NZ

Distance between /B LYS 392 NZ and LYS 409 NZ: 9.394Å  

> select /B:409@NZ

1 atom, 1 residue, 1 model selected  

> distance /A:370@CE /B:409@NZ

Distance between /A LYS 370 CE and /B LYS 409 NZ: 4.309Å  

> view sel

> select clear

> rotate

Unknown command: rotate  

> wobble

> stop

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\robot\Desktop\movie3.mp4

Movie saved to \C:Users\\...\Desktop\movie3.mp4  
  

> save C:/Users/robot/Desktop/Modeling/Herceptin_FC_Lys_v1.cxs

> set bgColor white

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> distance style color black

> distance style color #005500

> distance style color #aaaa00

> distance style color black

> distance style color #00007f

> distance style color #550000

> distance style color #55007f

> distance style color #005500

> distance style color #d7eaf8

> distance style color #cccccc

> distance style color #f0f0f0

> distance style color #fafafa

> distance style color white

> distance style color black

> distance style color white

> distance style color #ffefc3

> distance style color white

> distance style color #ff1a1a

> distance style color black

> distance style color white

> distance style color #c52a2a

> distance style color white

> distance style color #c72e2e

> distance style color white

> distance style color #7a5656

> distance style color #eddcdc

> distance style color #f2e1e1

> distance style color #2d1b1b

> distance style color #6769d2

> distance style color #6b72de

> distance style color #6565c3

> distance style color #554a6d

> distance style color #eddede

> distance style color white

> distance style color black

> distance style color #62594e

> distance style color white

> distance style color black

> distance style color #ff3939

> distance style color #ff3535

> distance style color black

> distance style color #f13131

> distance style color #ff3535

> distance style color #ff3636

> distance style color #b02d2d

> distance style color #9e2c2c

> distance style color black

> distance style color white

> distance style color black

> distance style color #6c2b2b

> distance style color #b22d2d

> distance style color #ff3232

> distance style color #ff3d3d

> distance style color #ff3535

> distance style color black

> distance style color white

> distance style color #e4d7d7

> distance style color #d7d4e9

> distance style color #d2cfe2

> distance style color #d7d4e9

> distance style color #dbd7ef

> distance style color #c0bcd8

> distance style color #bfbbd7

> distance style color #5e515a

> distance style color #f0f0f0

> distance style color black

> distance style color #828790

> distance style color #f0f0f0

> distance style color #aa0000

> distance style color #f0f0f0

> distance style color #005500

> lighting full

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\robot\Desktop\movie4.mp4

Movie saved to \C:Users\\...\Desktop\movie4.mp4  
  

> select /B:320@CD

1 atom, 1 residue, 1 model selected  

> select /B:317@CG

1 atom, 1 residue, 1 model selected  

> select /B:274@CD

1 atom, 1 residue, 1 model selected  

> select /B:290@CG

1 atom, 1 residue, 1 model selected  

> select /B:288@CG

1 atom, 1 residue, 1 model selected  

> select /B:334@CD

1 atom, 1 residue, 1 model selected  

> distance /B:334@CD /B:340@NZ

Distance between /B LYS 334 CD and LYS 340 NZ: 14.834Å  

> select /B:360@O

1 atom, 1 residue, 1 model selected  

> select /B:360@O

1 atom, 1 residue, 1 model selected  

> select /B:360@CG

1 atom, 1 residue, 1 model selected  

> ~distance /B:360@CG /B:414@CE

> select /B:414@NZ

1 atom, 1 residue, 1 model selected  

> distance /B:360@CE /B:414@NZ

Distance between /B LYS 360 CE and LYS 414 NZ: 9.752Å  

> distance style color #aa0000

> distance style color #005500

> select /B:414@NZ

1 atom, 1 residue, 1 model selected  

> select /A:439@CE

1 atom, 1 residue, 1 model selected  

> select /B:360@CE

1 atom, 1 residue, 1 model selected  

> distance /A:439@CE /B:360@CE

Distance between /A LYS 439 CE and /B LYS 360 CE: 10.094Å  

> distance style color #aa0000

> distance style color #005500

> select /B:414@CE

1 atom, 1 residue, 1 model selected  

> select clear

> select /B:414@CB

1 atom, 1 residue, 1 model selected  

> select /A:409@NZ

1 atom, 1 residue, 1 model selected  

> select /B:409@CG

1 atom, 1 residue, 1 model selected  

> select /A:370@NZ

1 atom, 1 residue, 1 model selected  

> select /B:392@CG

1 atom, 1 residue, 1 model selected  

> select /B:409@CG

1 atom, 1 residue, 1 model selected  

> select /B:409@CD

1 atom, 1 residue, 1 model selected  

> select /B:409@CA

1 atom, 1 residue, 1 model selected  

> select /A:370@CE

1 atom, 1 residue, 1 model selected  

> select /B:409@NZ

1 atom, 1 residue, 1 model selected  

> select /B:360@CD

1 atom, 1 residue, 1 model selected  

> select /A:360@CG

1 atom, 1 residue, 1 model selected  

> save C:/Users/robot/Desktop/Modeling/Herceptin_FC_Lys_v1.cxs

opened ChimeraX session  

> open 1HZH

Summary of feedback from opening 1HZH fetched from pdb  
---  
notes | Fetching compressed mmCIF 1hzh from
http://files.rcsb.org/download/1hzh.cif  
Fetching CCD GAL from http://ligand-expo.rcsb.org/reports/G/GAL/GAL.cif  
  
1hzh title:  
Crystal structure of the intact human igg B12 with broad and potent activity
against primary hiv-1 isolates: A template for hiv vaccine design [more
info...]  
  
Chain information for 1hzh #3  
---  
Chain | Description  
H K | immunoglobulin heavy chain  
L M | IMMUNOGLOBULIN LIGHT CHAIN,Uncharacterized protein  
  
Non-standard residues in 1hzh #3  
---  
BMA — beta-D-mannopyranose  
FUC — alpha-L-fucopyranose  
GAL — beta-D-galactopyranose  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> hide #2.1 models

> hide #!2 models

> hide #!1 models

> view orient

> select ::name="LYS"

1117 atoms, 997 bonds, 16 pseudobonds, 124 residues, 3 models selected  

> show sel & #!3 atoms

> color sel & #!3 bychain

> select clear

> select clear

> color #!3 bychain

> show #!3 atoms

> hide #!3 models

> show #!1 models

> show #!3 models

> ui tool show "Show Sequence Viewer"

> sequence chain #3/H #3/K

Alignment identifier is 2  

> sequence chain #3/L #3/M

Alignment identifier is 3  

> select clear

> hide atoms

> close session

> open C:/Users/robot/Desktop/Modeling/1igt_eaaak_tails_2_AF488.pdb

Summary of feedback from opening
C:/Users/robot/Desktop/Modeling/1igt_eaaak_tails_2_AF488.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2021-04-23T12:35:55Z  
  
Chain information for 1igt_eaaak_tails_2_AF488.pdb #1  
---  
Chain | Description  
A C | No description available  
B | No description available  
D | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A /C

Alignment identifier is 1  

> sequence chain /B

Alignment identifier is 1/B  

> sequence chain /D

Alignment identifier is 1/D  

> show sel atoms

> show sel atoms

> show sel surfaces

> select clear

> color bychain

> select ::name="KAF"

6540 atoms, 6852 bonds, 102 residues, 1 model selected  

> show sel surfaces

> close session

> open C:\Users\robot\Desktop\Modeling\1igt_eaaak_tails_2_AF488.pdb format pdb

Summary of feedback from opening
C:\Users\robot\Desktop\Modeling\1igt_eaaak_tails_2_AF488.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2021-04-23T12:45:44Z  
  
Chain information for 1igt_eaaak_tails_2_AF488.pdb #1  
---  
Chain | Description  
A C | No description available  
B | No description available  
D | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> sequence chain /D

Alignment identifier is 1/D  

> select ::name="KAF"

6538 atoms, 6850 bonds, 102 residues, 1 model selected  

> show sel atoms

> show sel surfaces

> hide sel surfaces

> color (#!1 & sel) lime

> show sel surfaces

> show sel atoms

> color sel lime

> show sel surfaces

> color (#!1 & sel) lime

> hide sel atoms

> show sel atoms

> ui tool show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 531, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1253, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\Users\robot\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\tool.py", line 186, in __init__  
self.isolde = isolde.Isolde(self)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "C:\Users\robot\AppData\Local\UCSF\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 "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 1027, in _update_model_list  
self._change_selected_model(model=current_model)  
File "C:\Users\robot\AppData\Local\UCSF\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 "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 573, in __init__  
spotlight_mode=spotlight_mode)  
File "C:\Users\robot\AppData\Local\UCSF\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 "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 202, in
symmetry_from_model_metadata  
return symmetry_from_model_metadata_pdb(model)  
File "C:\Users\robot\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1501, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\cmd.py",
line 187, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\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 "C:\Program Files\ChimeraX 1.1\bin\lib\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: 3.3.0 NVIDIA 461.92
OpenGL renderer: GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 68,586,754,048
MaxProcessMemory: 137,438,953,344
CPU: 32 AMD Ryzen Threadripper 1950X 16-Core Processor "
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-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
    gdcm: 2.8.8
    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+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    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
    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
    pywin32: 228
    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: 1.5.0
    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
    WMI: 1.5.1

[Tristan Croll]

This is one of my biggest annoyances about Clipper and the CCP4 libraries. Clipper itself only has an internal dictionary of "standard" space group symbols, and leaves it to client packages to do the work of handling non-standard ones. I did my best, but I guess I missed one... will look into it.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 26 April 2021 17:18
Cc: arronsullivan@gmail.com <arronsullivan@gmail.com>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4555: ISOLDE/Clipper: Spgr_descr: No such HM symbol (was: ChimeraX bug report submission)

#4555: ISOLDE/Clipper: Spgr_descr: No such HM symbol
--------------------------------------+---------------------------
          Reporter:  arronsullivan@…  |      Owner:  Tristan Croll
              Type:  defect           |     Status:  assigned
          Priority:  normal           |  Milestone:
         Component:  Third Party      |    Version:
        Resolution:                   |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+---------------------------
Changes (by Eric Pettersen):

 * status:  new => assigned
 * component:  Unassigned => Third Party
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Tristan Croll


--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4555#comment:1>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tristan Croll]

Hmm... turns out there was a bug in my handling of H-centred space groups when parsing PDB CRYST1 records (forgot to trim off the trailing whitespace causing dictionary lookup to fail). Will have that fixed in the next release.