ISOLDE: add real-space map: structure is None

[andrey.malyutin@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Attempted to associate a map with model in Isolde. Have not had success using it in version 1.3. Version 1.2 tends to work. 

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-macosx_10_13_x86_64.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/andrey.malyutin/Library/Application
Support/ChimeraX/1.3/site-packages  
sysconfig: /Users/andrey.malyutin/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/andrey.malyutin/Library/Application
Support/ChimeraX/1.3/site-packages  
sysconfig: /Users/andrey.malyutin/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/andrey.malyutin/Library/Application
Support/ChimeraX/include/python3.9/ChimeraX-Clipper  
sysconfig: /Users/andrey.malyutin/Library/Python/3.9/include/ChimeraX-Clipper  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/andrey.malyutin/Library/Application Support/ChimeraX/bin  
sysconfig: /Users/andrey.malyutin/Library/Python/3.9/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/andrey.malyutin/Library/Application Support/ChimeraX  
sysconfig: /Users/andrey.malyutin/Library/Python/3.9  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/andrey.malyutin/Library/Application
Support/ChimeraX/include/python3.9/ChimeraX-ISOLDE  
sysconfig: /Users/andrey.malyutin/Library/Python/3.9/include/ChimeraX-ISOLDE  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/andrey.malyutin/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /Users/andrey.malyutin/Library/Python/3.9/include/UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 22.0.2 is
available.  
You should consider upgrading via the
'/Applications/ChimeraX-1.3.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/Users/andrey.malyutin/Downloads/ChimeraX_ISOLDE-1.3-cp39-cp39-macosx_10_13_x86_64.whl  
Collecting ChimeraX-Clipper~=0.17.0  
Using cached
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.17.0/ChimeraX_Clipper-0.17.0-cp39-cp39-macosx_10_13_x86_64.whl
(37.5 MB)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=4.2 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ISOLDE==1.3) (4.2)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ISOLDE==1.3) (1.0)  
Requirement already satisfied: ChimeraX-Core~=1.3rc202112010000 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ISOLDE==1.3) (1.3)  
Requirement already satisfied: ChimeraX-Atomic~=1.31 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ISOLDE==1.3) (1.31)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.6.5)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.4)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0.2)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.1)  
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.2.2)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.0.2)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.5)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.7)  
Requirement already satisfied: ChimeraX-IO~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.13.7)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.1)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.1)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-MapSeries~=2.0->ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)  
Installing collected packages: ChimeraX-Clipper, ChimeraX-ISOLDE  
Successfully installed ChimeraX-Clipper-0.17.0 ChimeraX-ISOLDE-1.3  
\---  

Successfully installed ChimeraX-Clipper-0.17.0 ChimeraX-ISOLDE-1.3  
Installed ChimeraX-Clipper (0.17.0)  
Installed ChimeraX-ISOLDE (1.3)  

> ui tool show ISOLDE

> set selectionWidth 4

Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> open "/Users/andrey.malyutin/OneDrive -
> Takeda/Documents/Projects/SARS_FABS/DansMaps/Krios_0921-22/Fab1/Final/Fab1_final.pdb"
> format pdb

Chain information for Fab1_final.pdb #1  
---  
Chain | Description  
E | No description available  
H | No description available  
L | No description available  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1050, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2525, in _change_selected_model  
correct_pseudosymmetric_sidechain_atoms(session, m.residues)  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/util.py", line 28, in
correct_pseudosymmetric_sidechain_atoms  
if flip_if_necessary(r, ('CD','NE','CZ',('NH2','NH1'))):  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/util.py", line 66, in flip_if_necessary  
if swap_equivalent_atoms(residue):  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/util.py", line 118, in swap_equivalent_atoms  
pair[0].coords, pair[1].coords = pair[1].coords, pair[0].coords  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 3 does not match objects array length 1  
  
Error processing trigger "add models":  
ValueError: Values array length 3 does not match objects array length 1  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  

> open "/Users/andrey.malyutin/OneDrive -
> Takeda/Documents/Projects/SARS_FABS/DansMaps/Krios_0921-22/Fab1/Fab1_local_sharp_krios.mrc"
> format mrc

Opened Fab1_local_sharp_krios.mrc as #2, grid size 300,300,300, pixel 1.24,
shown at level 0.0977, step 2, values float32  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1050, in _update_model_list  
self._change_selected_model(model=current_model)  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2525, in _change_selected_model  
correct_pseudosymmetric_sidechain_atoms(session, m.residues)  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/util.py", line 28, in
correct_pseudosymmetric_sidechain_atoms  
if flip_if_necessary(r, ('CD','NE','CZ',('NH2','NH1'))):  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/util.py", line 66, in flip_if_necessary  
if swap_equivalent_atoms(residue):  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/atomic/util.py", line 118, in swap_equivalent_atoms  
pair[0].coords, pair[1].coords = pair[1].coords, pair[0].coords  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 3 does not match objects array length 1  
  
Error processing trigger "add models":  
ValueError: Values array length 3 does not match objects array length 1  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1496, in
_add_real_space_map_from_gui  
self.add_real_space_map(existing_volume=v, to_model=self.selected_model)  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1386, in add_real_space_map  
map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True)  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 183, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
AttributeError: 'NoneType' object has no attribute 'parent'  
  
File "/Users/andrey.malyutin/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 166, in _get_symmetry_handler  
p = structure.parent  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 4 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 11.6.2 (20G314)
      Kernel Version: Darwin 20.6.0
      Time since boot: 2 days 7:08

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Resolution: 3360 x 2100
          UI Looks like: 1680 x 1050 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    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-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
    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
    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: 21.0
    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
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Tristan Croll]

Looks like the error in #6087 broke the assignment of the model to isolde.selected_model, which in turn broke the next step. Does seem like two separate bugs, so I'll keep this ticket open - but if you correct the hydrogens on the model, then everything should work correctly.

[Tristan Croll]

This should all be fixed now.