Save RMF in session: _RMFProvenance class not handled by get_class()

[gorbea@…]

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)
Hi, 

I received this error message when attempting to save a Chimera X session of a multiscale model. If there's any way I can help solve this issue, let me know!

Best,
Jose

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/jose/Desktop/Final
> Files/TFIIK_Mediator_PIC_Modeling/results/clustering/kmeans_run1_m500/cluster.0/localization_probability_density_envelopes/Ccl1.mrc"
> "/Users/jose/Desktop/Final
> Files/TFIIK_Mediator_PIC_Modeling/results/clustering/kmeans_run1_m500/cluster.0/localization_probability_density_envelopes/Kin28.mrc"
> "/Users/jose/Desktop/Final
> Files/TFIIK_Mediator_PIC_Modeling/results/clustering/kmeans_run1_m500/cluster.0/localization_probability_density_envelopes/Tfb3.mrc"

Opened Ccl1.mrc, grid size 99,99,105, pixel 3, shown at level 0.0221, step 1,
values float32  

> open "/Users/jose/Desktop/Final
> Files/TFIIK_Mediator_PIC_Modeling/results/clustering/kmeans_run1_m500/cluster.0/representative_model/0.rmf3"

Opened RMF file produced with IMP 2.13.0, with 1 frame. Representation read at
the following resolutions: 1.0, 5.0, 10.0.  

> volume #1.1 color #33cccc

> volume #1.1 color #33cccc40

> volume #1.2 color #0066ff

> volume #1.2 color #0066ff40

> volume #1.3 color red

> volume #1.3 color #cc0000

> volume #1.3 color red

> volume #1.3 color #ff3300

> volume #1.3 color #ff330040

> volume #1.3 level 0.075

> volume #1.2 level 0.16

> volume #1.1 level 0.16

4361 atoms, 4361 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel white

2994 atoms, 2994 residues, 1 model selected  

> color sel forest green

1579 atoms, 1579 residues, 1 model selected  

> color sel dark gray

2817 atoms, 2817 residues, 1 model selected  

> color sel gold

419 atoms, 419 residues, 1 model selected  

> color sel cyan

395 atoms, 395 residues, 1 model selected  

> color sel dodger blue

173 atoms, 173 residues, 1 model selected  

> color sel deep pink

251 atoms, 251 residues, 1 model selected  

> color sel orange red

> lighting soft

> set bgColor white

> select clear

> select minimumLength 50

96 pseudobonds, 1 model selected  

> hide sel

> select maximumLength 50

1014 pseudobonds, 1 model selected  

> size sel pseudobondRadius 1

Changed 1014 pseudobond radii  

> ui tool show "Color Actions"

> color sel gold

> select clear

Drag select of 41 atoms, 10 pseudobonds  

> select clear

> select ::resolution=10

1168 atoms, 1168 residues, 1 model selected  

> hide sel

> select ::resolution=20

Nothing selected  

> select clear

> save "/Users/jose/Desktop/Final
> Files/TFIIK_Mediator_PIC_Modeling/results/clustering/kmeans_run1_m500/cluster.0/representative_model/chiemraXsession.cxs"

Traceback (most recent call last):  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 292, in process  
return copy_state(data, convert=convert)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 215, in copy_state  
return _copy(data)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 213, in _copy  
return convert(data)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 291, in convert  
return add_obj(obj, parents)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 265, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 141, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 438, in get_class  
return f(class_name)  
File "/Users/jose/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/rmf/__init__.py", line 71, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name '_RMFProvenance'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x10dc96790> -> <chimerax.atomic.pbgroup.PseudobondGroup object at
0x158119510> 'Features' -> <chimerax.rmf.io._RMFState object at 0x129e29190>
'State_0' -> <chimerax.rmf.io._RMFModel object at 0x129e0be10> '0': Unknown
class name '_RMFProvenance'  
  
ValueError: error processing: 'models' -> -> 'Features' -> 'State_0' -> '0':
Unknown class name '_RMFProvenance'  
  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 292, in process  
return copy_state(data, convert=convert)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 215, in copy_state  
return _copy(data)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 213, in _copy  
return convert(data)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 291, in convert  
return add_obj(obj, parents)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 265, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 141, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 438, in get_class  
return f(class_name)  
File "/Users/jose/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/rmf/__init__.py", line 71, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name '_RMFProvenance'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display  
run(session, cmd)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/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
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/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
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/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
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x10dc96790> -> <chimerax.atomic.pbgroup.PseudobondGroup object at
0x158119510> 'Features' -> <chimerax.rmf.io._RMFState object at 0x129e29190>
'State_0' -> <chimerax.rmf.io._RMFModel object at 0x129e0be10> '0': Unknown
class name '_RMFProvenance'  
  
ValueError: error processing: 'models' -> -> 'Features' -> 'State_0' -> '0':
Unknown class name '_RMFProvenance'  
  
File
"/private/var/folders/q7/t99ws1x97wgf3mxfglktzfkr0000gn/T/AppTranslocation/594E9856-F97A-460C-B295-E11518C14103/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3.7 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 8 GB
      Boot ROM Version: 1554.60.15.0.0
      SMC Version (system): 2.46f12

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H114)
      Kernel Version: Darwin 19.6.0
      Time since boot: 2:03

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          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: 2.1.1
    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-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: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 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-RMF: 0.9
    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
    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
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[Eric Pettersen]

Reported by Jose Gorbea