ISOLDE: No template for residue type

[tomasiak@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.36.2.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
This error comes up on both mac and linux while using the "Isolde" plugin. I am attempting to refine a ligand that is placed using the Ligand function in Isolde. Although Isolde is a plugin by another developer, I am not sure if this is a ChimeraX issue or Isolde. 

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 /data/tsoong/project/Ycf1/cryosparc/CS-
> ycf1-gssg/J80/J80_011_volume_map_sharp.mrc

Opened J80_011_volume_map_sharp.mrc as #1, grid size 440,440,440, pixel 0.684,
shown at level 0.0444, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.08791

> surface dust #1 size 6.84

> volume #1 level 0.07451

> open /data/tsoong/project/Ycf1/cryosparc/CS-
> ycf1-gssg/J80/J80_011_volume_map.mrc

Opened J80_011_volume_map.mrc as #2, grid size 440,440,440, pixel 0.684, shown
at level 0.0359, step 2, values float32  

> open 7M69

7m69 title:  
E1435Q Ycf1 mutant in inward-facing wide conformation [more info...]  
  
Chain information for 7m69 #3  
---  
Chain | Description | UniProt  
A | Metal resistance protein YCF1 | YCFI_YEAST  
  

> volume #2 step 1

> volume #2 level 0.04501

> select #3

21795 atoms, 22013 bonds, 4 pseudobonds, 1390 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.77739,0.42664,-0.46221,261.63,-0.37106,0.28231,0.88466,-5.1597,0.50792,0.85923,-0.061155,-2.0635

> view matrix models
> #3,-0.58423,-0.55499,-0.59216,383.64,-0.70689,0.70644,0.035333,127.13,0.39872,0.43924,-0.80504,190.77

> view matrix models
> #3,-0.86567,-0.47659,0.15322,287.16,-0.44637,0.87339,0.19478,43.951,-0.22665,0.10022,-0.96881,345.98

> view matrix models
> #3,-0.52467,-0.81052,0.26033,266.34,-0.69716,0.58459,0.41501,78.189,-0.48856,0.03625,-0.87178,373.32

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.52467,-0.81052,0.26033,310.08,-0.69716,0.58459,0.41501,85.091,-0.48856,0.03625,-0.87178,359.23

> view matrix models
> #3,-0.52467,-0.81052,0.26033,310.85,-0.69716,0.58459,0.41501,104.07,-0.48856,0.03625,-0.87178,368.43

> ui tool show "Fit in Map"

Fit molecule 7m69 (#3) to map J80_011_volume_map.mrc (#2) using 21795 atoms  
average map value = 0.0494, steps = 224  
shifted from previous position = 6.51  
rotated from previous position = 21.6 degrees  
atoms outside contour = 11298, contour level = 0.045011  
  
Position of 7m69 (#3) relative to J80_011_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.28543274 -0.78664689 0.54746215 223.70014673  
-0.71610042 0.55469760 0.42368708 108.71592070  
-0.63696807 -0.27110372 -0.72164703 400.76826640  
Axis -0.50530761 0.86141268 0.05130705  
Axis point 236.36972585 0.00000000 145.29578403  
Rotation angle (degrees) 136.56802234  
Shift along axis 1.17412522  
  

> select clear

> volume #2 color #40bfbf36

> select #2

2 models selected  

> color sel 80,80,80,50

> color sel 80,80,80,70

> select clear

> select /A:1222

14 atoms, 13 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select /A:1221

17 atoms, 16 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide H

> ui mousemode right "bond rotation"

> select /A:1221@CG

1 atom, 1 residue, 1 model selected  

> select add /A:1221@CB

2 atoms, 1 residue, 1 model selected  

> torsion /A:1221@OE1,CD,CG,CB -16.24

> select #2

2 models selected  

> torsion /A:1221@CG,CB,CA,N -151.72

> torsion /A:1221@CG,CB,CA,N -117.72

> torsion /A:1221@CG,CB,CA,N -93.72

> ui mousemode right "translate selected models"

> select /A:1228

24 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide H

> select /A:1225

24 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 57 residues in model #3 to IUPAC-IUB
standards.  
7m69 title:  
E1435Q Ycf1 mutant in inward-facing wide conformation [more info...]  
  
Chain information for 7m69  
---  
Chain | Description | UniProt  
3.2/A | Metal resistance protein YCF1 | YCFI_YEAST  
  
Done loading forcefield  
Opened J80_011_volume_map.mrc as #3.1.1.1, grid size 440,440,440, pixel 0.684,
shown at step 1, values float32  

> volume #3.1.1.1 level 0.001057

> volume #3.1.1.1 level -0.00144

> volume #3.1.1.1 level 0.0003134

ISOLDE: started sim  

> volume #3.1.1.1 level 0.03578

> isolde start

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> select clear

ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> volume #3.1.1.1 level 0.02836

ISOLDE: started sim  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /data/tsoong/project/Ycf1/cryosparc/Chimerax/7M69_isolde1.pdb

> select clear

> isolde add ligand gds

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/building/cmd.py", line 69, in add_ligand  
place_ligand(session, *args, **kwargs)  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/building/place_ligand.py", line 114, in
place_ligand  
tmpl = mmcif.find_template_residue(session, ligand_id)  
File "src/mmcif.pyx", line 385, in chimerax.mmcif.mmcif.find_template_residue  
ValueError: No template for residue type gds  
  
ValueError: No template for residue type gds  
  
File "src/mmcif.pyx", line 385, in chimerax.mmcif.mmcif.find_template_residue  
  
See log for complete Python traceback.  
  

> isolde add ligand GDS

Fetching CCD GDS from http://ligand-expo.rcsb.org/reports/G/GDS/GDS.cif  
Loading residue template for GDS from internal database  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/building/cmd.py", line 69, in add_ligand  
place_ligand(session, *args, **kwargs)  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/building/place_ligand.py", line 125, in
place_ligand  
tdict = find_residue_templates(Residues([r]), ff, ligand_db=ligand_db,
logger=session.logger)  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3143, in
find_residue_templates  
forcefield.loadFile(xf)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/openmm/app/forcefield.py", line 331, in loadFile  
self.registerResidueTemplate(template)  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 256, in
registerResidueTemplate  
template.graph = self.template_graph(template)  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 280, in template_graph  
labels = [a.element.atomic_number for a in atoms]  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 280, in <listcomp>  
labels = [a.element.atomic_number for a in atoms]  
AttributeError: 'NoneType' object has no attribute 'atomic_number'  
  
AttributeError: 'NoneType' object has no attribute 'atomic_number'  
  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 280, in  
labels = [a.element.atomic_number for a in atoms]  
  
See log for complete Python traceback.  
  

> select up

72 atoms, 71 bonds, 1 residue, 1 model selected  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2784, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 619, in __init__  
raise e  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 597, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc,  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1350, in __init__  
system = self._system = self._create_openmm_system(ff, top,  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1433, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2798, in start_sim  
self._unparam_mgr._sim_unparam_res_cb()  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 228, in
_sim_unparam_res_cb  
self._show_main_frame()  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 50, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 107, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 353, in
find_possible_templates  
tgraph = template.graph  
AttributeError: '_TemplateData' object has no attribute 'graph'  
  
AttributeError: '_TemplateData' object has no attribute 'graph'  
  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 353, in
find_possible_templates  
tgraph = template.graph  
  
See log for complete Python traceback.  
  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2784, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 619, in __init__  
raise e  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 597, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc,  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1350, in __init__  
system = self._system = self._create_openmm_system(ff, top,  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1433, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2798, in start_sim  
self._unparam_mgr._sim_unparam_res_cb()  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 228, in
_sim_unparam_res_cb  
self._show_main_frame()  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 50, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 107, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 353, in
find_possible_templates  
tgraph = template.graph  
AttributeError: '_TemplateData' object has no attribute 'graph'  
  
AttributeError: '_TemplateData' object has no attribute 'graph'  
  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 353, in
find_possible_templates  
tgraph = template.graph  
  
See log for complete Python traceback.  
  

> select clear

> select up

72 atoms, 71 bonds, 1 residue, 1 model selected  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2784, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 619, in __init__  
raise e  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 597, in __init__  
sh = self.sim_handler = Sim_Handler(session, sim_params, sc,  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1350, in __init__  
system = self._system = self._create_openmm_system(ff, top,  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1433, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2798, in start_sim  
self._unparam_mgr._sim_unparam_res_cb()  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 228, in
_sim_unparam_res_cb  
self._show_main_frame()  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 50, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/unparameterised.py", line 107, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 353, in
find_possible_templates  
tgraph = template.graph  
AttributeError: '_TemplateData' object has no attribute 'graph'  
  
AttributeError: '_TemplateData' object has no attribute 'graph'  
  
File "/home/tsoong/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/forcefields.py", line 353, in
find_possible_templates  
tgraph = template.graph  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 510.39.01
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 128 AMD Ryzen Threadripper 3990X 64-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           251G         11G         50G        144M        189G        239G
	Swap:            9G        4.7G        5.3G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2204] (rev a1)	
	Subsystem: ZOTAC International (MCO) Ltd. Device [19da:1625]	
	Kernel driver in use: nvidia
Locale: ('en_US', '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
    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

[Eric Pettersen]

Reported by Thomas Tomasiak