ISOLDE: matplotlib: 'box_aspect' and 'fig_aspect' must be positive + other errors

[mille153@…]

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/mille153/Downloads/FNV-asymmetic-unit-1/fnv-asymmetric-unit-1
> copy.pdb"

Chain information for fnv-asymmetric-unit-1 copy.pdb #1  
---  
Chain | Description  
A C E | No description available  
D F G | No description available  
  

> show atoms

> style stick

Changed 25203 atom styles  

> show atoms

> hide atoms

[Repeated 1 time(s)]

> show atoms

> show cartoons

> hide atoms

> open /Users/mille153/Downloads/cryosparc_P102_J43_008_volume_map.mrc format
> mrc

Opened cryosparc_P102_J43_008_volume_map.mrc as #2, grid size 600,600,600,
pixel 1.33, shown at level 0.108, step 4, values float32  

> volume #2 step 1

> transparency 50

> addh

Summary of feedback from adding hydrogens to fnv-asymmetric-unit-1 copy.pdb #1  
---  
notes | No usable SEQRES records for fnv-asymmetric-unit-1 copy.pdb (#1) chain
A; guessing termini instead  
No usable SEQRES records for fnv-asymmetric-unit-1 copy.pdb (#1) chain C;
guessing termini instead  
No usable SEQRES records for fnv-asymmetric-unit-1 copy.pdb (#1) chain D;
guessing termini instead  
No usable SEQRES records for fnv-asymmetric-unit-1 copy.pdb (#1) chain E;
guessing termini instead  
No usable SEQRES records for fnv-asymmetric-unit-1 copy.pdb (#1) chain F;
guessing termini instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ALA 1, /C ALA 1, /E ALA 1  
Chain-initial residues that are not actual N termini: /D LYS 18, /F LYS 18, /G
LYS 18  
Chain-final residues that are actual C termini: /A ALA 493, /C ALA 493, /D SER
75, /E ALA 493, /F SER 75, /G SER 75  
Chain-final residues that are not actual C termini:  
1387 hydrogen bonds  
38 hydrogens added  
  

> isolde start

> set selectionWidth 4

Populating font family aliases took 742 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 30 residues in model #1 to IUPAC-IUB
standards.  
Chain information for fnv-asymmetric-unit-1 copy.pdb  
---  
Chain | Description  
1.2/A 1.2/C 1.2/E | No description available  
1.2/D 1.2/F 1.2/G | No description available  
  
ISOLDE: created disulfide bonds between the following residues:  
C60-C121; C74-C105; A182-A283; E74-E105; E60-E121; A3-A30; E182-E283;
A74-A105; C182-C283; C300-C330; E300-E330; A300-A330; E92-E116; C92-C116;
E3-E30; A60-A121; A92-A116; C3-C30  

> cofr sel

> clipper associate #2 toModel #1

Opened cryosparc_P102_J43_008_volume_map.mrc as #1.1.1.1, grid size
600,600,600, pixel 1.33, shown at step 1, values float32  

> volume #1.1.1.1 level 0.1121

> ui tool show "Ramachandran Plot"

> addh

Summary of feedback from adding hydrogens to fnv-asymmetric-unit-1 copy.pdb
#1.2  
---  
notes | No usable SEQRES records for fnv-asymmetric-unit-1 copy.pdb (#1.2)
chain A; guessing termini instead  
No usable SEQRES records for fnv-asymmetric-unit-1 copy.pdb (#1.2) chain C;
guessing termini instead  
No usable SEQRES records for fnv-asymmetric-unit-1 copy.pdb (#1.2) chain D;
guessing termini instead  
No usable SEQRES records for fnv-asymmetric-unit-1 copy.pdb (#1.2) chain E;
guessing termini instead  
No usable SEQRES records for fnv-asymmetric-unit-1 copy.pdb (#1.2) chain F;
guessing termini instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ALA 1, /C ALA 1, /E ALA 1  
Chain-initial residues that are not actual N termini: /D LYS 18, /F LYS 18, /G
LYS 18  
Chain-final residues that are actual C termini: /A ALA 493, /C ALA 493, /D SER
75, /E ALA 493, /F SER 75, /G SER 75  
Chain-final residues that are not actual C termini:  
1363 hydrogen bonds  
0 hydrogens added  
  

> select clear

[Repeated 1 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> ui mousemode right "isolde tug selection"

> select clear

> volume #1.1.1.1 level 0.09672

> isolde sim pause

> view orient

> ui mousemode right "isolde tug selection"

> ui mousemode right select

> isolde sim stop

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

> select clear

> select add #1.2

25205 atoms, 25478 bonds, 1653 residues, 11 models selected  

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> ui tool show "Ramachandran Plot"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process  
func(*args, **kwargs)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize  
c.draw()  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw  
self.figure.draw(self.renderer)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper  
result = draw(artist, renderer, *args, **kwargs)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper  
return draw(artist, renderer)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw  
artists = self._get_draw_artists(renderer)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists  
ax.apply_aspect()  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect  
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect  
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")  
ValueError: 'box_aspect' and 'fig_aspect' must be positive  

> isolde sim stop discardTo start

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

> isolde sim start sel

ISOLDE: started sim  

> ui mousemode right "isolde tug selection"

> ui mousemode right "isolde tug residue"

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
Peptide bond must be mobile in the simulation!  

> isolde sim stop

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.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/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 1009, in _sim_end_cb  
run(self.session, f'clipper spot #{self.selected_model.id_string}', log=False)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/cmd.py", line 109, in spotlight  
sh = get_symmetry_handler(m, create=create, auto_add_to_session=True)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 594, in __init__  
self.add_model(model, ignore_model_symmetry=ignore_model_symmetry,  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 649, in add_model  
self.set_default_atom_display(mode=self._hydrogen_mode)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 922, in set_default_atom_display  
atoms = model.atoms  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "sim terminated":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/clipper/symmetry.py", line 922, in set_default_atom_display  
atoms = model.atoms  
  
See log for complete Python traceback.  
  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  
ISOLDE: started sim  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process  
func(*args, **kwargs)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize  
c.draw()  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw  
self.figure.draw(self.renderer)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper  
result = draw(artist, renderer, *args, **kwargs)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper  
return draw(artist, renderer)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw  
artists = self._get_draw_artists(renderer)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists  
ax.apply_aspect()  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect  
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect  
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")  
ValueError: 'box_aspect' and 'fig_aspect' must be positive  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4490, in next_preview  
return self._incr_preview(rotamer, 1)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4474, in _incr_preview  
self._create_preview(rotamer, target_def, new_target)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4583, in _create_preview  
pm.atoms.coords = master_atoms.coords  
File
"/Applications/ChimeraX-1.4.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 24 does not match objects array length 22  
  
ValueError: Values array length 24 does not match objects array length 22  
  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4490, in next_preview  
return self._incr_preview(rotamer, 1)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4474, in _incr_preview  
self._create_preview(rotamer, target_def, new_target)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4583, in _create_preview  
pm.atoms.coords = master_atoms.coords  
File
"/Applications/ChimeraX-1.4.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 24 does not match objects array length 22  
  
ValueError: Values array length 24 does not match objects array length 22  
  
File
"/Applications/ChimeraX-1.4.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.  
  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4490, in next_preview  
return self._incr_preview(rotamer, 1)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4474, in _incr_preview  
self._create_preview(rotamer, target_def, new_target)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4583, in _create_preview  
pm.atoms.coords = master_atoms.coords  
File
"/Applications/ChimeraX-1.4.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 24 does not match objects array length 22  
  
ValueError: Values array length 24 does not match objects array length 22  
  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4490, in next_preview  
return self._incr_preview(rotamer, 1)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4474, in _incr_preview  
self._create_preview(rotamer, target_def, new_target)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4583, in _create_preview  
pm.atoms.coords = master_atoms.coords  
File
"/Applications/ChimeraX-1.4.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 24 does not match objects array length 22  
  
ValueError: Values array length 24 does not match objects array length 22  
  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4490, in next_preview  
return self._incr_preview(rotamer, 1)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4474, in _incr_preview  
self._create_preview(rotamer, target_def, new_target)  
File "/Users/mille153/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4583, in _create_preview  
pm.atoms.coords = master_atoms.coords  
File
"/Applications/ChimeraX-1.4.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 24 does not match objects array length 22  
  
ValueError: Values array length 24 does not match objects array length 22  
  
File
"/Applications/ChimeraX-1.4.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.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 575X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 220.270.93.0.0
      SMC Version (system): 2.46f12

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G95)
      Kernel Version: Darwin 18.7.0
      Time since boot: 30 days 8:31

Graphics/Displays:

    Radeon Pro 575X:

      Chipset Model: Radeon Pro 575X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c4
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A14GP-003
      EFI Driver Version: 01.01.042
      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
          Rotation: Supported
          Automatically Adjust Brightness: No


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[Eric Pettersen]

Reported by Andrew Miller