Model is None after sim stop, and then things go pear-shaped

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-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  

> ui tool show ISOLDE

> set selectionWidth 4

Forcefield cache not found or out of date.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  

Populating font family aliases took 361 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

> open "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5.pdb"

Summary of feedback from opening /Users/brendanfarrell/OneDrive -
Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5.pdb  
---  
warnings | Cannot find LINK/SSBOND residue CYS (282 )  
Cannot find LINK/SSBOND residue CYS (288 )  
Cannot find LINK/SSBOND residue CYS (293 )  
Cannot find LINK/SSBOND residue CYS (308 )  
  
Chain information for rcr3_build2_coot_newmap_5.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/cryosparc/J500/cryosparc_P32_J500_005_volume_map_deep_standard.mrc"

Opened cryosparc_P32_J500_005_volume_map_deep_standard.mrc as #2, grid size
416,416,416, pixel 0.832, shown at level 0.000138, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.07301

> style stick

Changed 12672 atom styles  

> color #2 #b2b2b2a4 models

> volume #2 level 0.133

> volume #2 level 0.0773

> open "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/cryosparc/J499/cryosparc_P32_J499_004_volume_map_deep_standard.mrc"

Opened cryosparc_P32_J499_004_volume_map_deep_standard.mrc as #3, grid size
416,416,416, pixel 0.832, shown at level 0.000106, step 2, values float32  

> volume #3 level 0.05274

> volume #3 step 1

> volume #3 color #ffffb2b4

> volume #3 color #ffffb287

> ui mousemode right zoom

> volume #3 level 0.0163

> volume #3 level 0.06894

> volume #3 level 0.0163

> volume #3 level 0.01225

> volume #2 level 0.02157

> volume #2 level 0.004425

> volume #3 level 0.08109

> volume #2 level 0.06444

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 67 residues in model #1 to IUPAC-IUB
standards.  
Chain information for rcr3_build2_coot_newmap_5.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
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  

> clipper associate #2 toModel #1

Opened cryosparc_P32_J500_005_volume_map_deep_standard.mrc as #1.1.1.1, grid
size 416,416,416, pixel 0.832, shown at step 1, values float32  

> open "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/CombineFocusedMaps_4/deep_rcr3_composite_map.ccp4"

Opened deep_rcr3_composite_map.ccp4 as #2, grid size 416,416,416, pixel 0.832,
shown at level -0.0203, step 2, values float32  

> volume #2 level 5.2

> volume #2 step 1

> volume #2 level 3.373

> clipper associate #2 toModel #1

Opened deep_rcr3_composite_map.ccp4 as #1.1.1.2, grid size 416,416,416, pixel
0.832, shown at step 1, values float32  

> select clear

> volume #1.1.1.2 level 13.63

> volume #1.1.1.2 level 18.56

> volume #1.1.1.2 level 4.531

> volume #1.1.1.2 level 0.8966

> volume #1.1.1.2 level 0.3105

> volume #1.1.1.2 level 0.6231

> volume #1.1.1.2 level 3.588

> volume #1.1.1.2 level 4.127

> volume #1.1.1.2 level 31.89

> volume #1.1.1.2 level 24.57

> volume #1.1.1.2 level 19.34

> volume #1.1.1.2 level 16.72

> volume #1.1.1.2 level 7.163

> volume #1.1.1.2 level 8.679

> volume #1.1.1.1 level 0.1333

> addh

Summary of feedback from adding hydrogens to rcr3_build2_coot_newmap_5.pdb
#1.2  
---  
notes | No usable SEQRES records for rcr3_build2_coot_newmap_5.pdb (#1.2)
chain A; guessing termini instead  
No usable SEQRES records for rcr3_build2_coot_newmap_5.pdb (#1.2) chain B;
guessing termini instead  
No usable SEQRES records for rcr3_build2_coot_newmap_5.pdb (#1.2) chain C;
guessing termini instead  
No usable SEQRES records for rcr3_build2_coot_newmap_5.pdb (#1.2) chain D;
guessing termini instead  
No usable SEQRES records for rcr3_build2_coot_newmap_5.pdb (#1.2) chain E;
guessing termini instead  
Chain-initial residues that are actual N termini: /A LEU 54, /B VAL 33, /C ILE
157, /D ALA 23, /E ALA 20  
Chain-initial residues that are not actual N termini: /A LYS 137, /A ALA 311,
/A PRO 314, /A LYS 345, /A ASN 559, /C MET 304, /E GLY 165  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A VAL 715, /A PRO 123, /A
LYS 274, /A LEU 312, /A ILE 340, /A ASN 477, /B TYR 358, /C GLN 516, /C PRO
241, /D ARG 229, /E PRO 245, /E PRO 155  
975 hydrogen bonds  
Adding 'H' to /A LYS 137  
Adding 'H' to /A ALA 311  
Adding 'H' to /A LYS 345  
Adding 'H' to /A ASN 559  
Adding 'H' to /C MET 304  
1 messages similar to the above omitted  
/A VAL 715 is not terminus, removing H atom from 'C'  
/B TYR 358 is not terminus, removing H atom from 'C'  
/C GLN 516 is not terminus, removing H atom from 'C'  
/D ARG 229 is not terminus, removing H atom from 'C'  
/E PRO 245 is not terminus, removing H atom from 'C'  
12328 hydrogens added  
  

> isolde restrain ligands #1

> ui tool show "Ramachandran Plot"

> clipper associate #3 toModel #1

Opened cryosparc_P32_J499_004_volume_map_deep_standard.mrc as #1.1.1.3, grid
size 416,416,416, pixel 0.832, shown at step 1, values float32  
3 models selected  

> set bgColor white

3 models selected  

> volume #1.1.1.2 level 9.632

> select add #1

25000 atoms, 25294 bonds, 8 pseudobonds, 1578 residues, 22 models selected  

> select add #1

25000 atoms, 25294 bonds, 8 pseudobonds, 1578 residues, 22 models selected  

> select add #1

25000 atoms, 25294 bonds, 8 pseudobonds, 1578 residues, 22 models selected  

> isolde sim start sel

ISOLDE: stopped sim  
Fetching CCD LEU_LL from http://ligand-
expo.rcsb.org/reports/L/LEU_LL/LEU_LL.cif  
Fetching CCD LEU_LEO2 from http://ligand-
expo.rcsb.org/reports/L/LEU_LEO2/LEU_LEO2.cif  
Fetching CCD LEU_LFZW from http://ligand-
expo.rcsb.org/reports/L/LEU_LFZW/LEU_LFZW.cif  
Fetching CCD LAY from http://ligand-expo.rcsb.org/reports/L/LAY/LAY.cif  

> isolde sim start sel

ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 176, in
_fix_button_clicked_cb  
data = item.data(0, USER_ROLE)  
AttributeError: 'NoneType' object has no attribute 'data'  
  
AttributeError: 'NoneType' object has no attribute 'data'  
  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 176, in
_fix_button_clicked_cb  
data = item.data(0, USER_ROLE)  
  
See log for complete Python traceback.  
  
Deleted the following atoms from residue SER E145: HN, H  
Deleted the following atoms from residue LEU D125: H, HN  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> isolde sim stop discardTo start

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

> clipper spotlight

> clipper isolate sel maskRadius 4.0 focus false

[Repeated 2 time(s)]

> clipper spotlight

> isolde sim start sel

ISOLDE: started sim  

> select down

149 atoms, 148 bonds, 9 residues, 1 model selected  

> select down

149 atoms, 148 bonds, 9 residues, 1 model selected  

> select up

8416 atoms, 8519 bonds, 527 residues, 1 model selected  

> select up

24998 atoms, 25292 bonds, 1578 residues, 1 model selected  

> select up

24998 atoms, 25292 bonds, 1578 residues, 3 models selected  

> select up

24998 atoms, 25292 bonds, 1578 residues, 4 models selected  

> select down

24998 atoms, 25292 bonds, 1578 residues, 3 models selected  

> select down

24998 atoms, 25292 bonds, 1578 residues, 1 model selected  

> select down

8416 atoms, 8519 bonds, 527 residues, 1 model selected  

> select down

149 atoms, 148 bonds, 9 residues, 1 model selected  

> select down

149 atoms, 148 bonds, 9 residues, 1 model selected  

> ui mousemode right "isolde tug residue"

> 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  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 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  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde stepto

[Repeated 2 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde stepto

[Repeated 6 time(s)]

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde stepto

[Repeated 5 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde stepto

[Repeated 4 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde stepto

[Repeated 4 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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 sim start sel

ISOLDE: started sim  

> isolde stepto

[Repeated 6 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> 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/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 sim start sel

ISOLDE: started sim  

> isolde stepto

[Repeated 10 time(s)]

> isolde sim stop

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 sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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 sim start sel

ISOLDE: started sim  

> isolde sim stop

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 sim start sel

ISOLDE: started sim  

> isolde stepto

[Repeated 6 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde stepto

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
Unable to flip peptide bond after 50 rounds. Giving up.  

> volume #1.1.1.2 level 4.761

> ui mousemode right "isolde tug selection"

> ui mousemode right "isolde tug residue"

> ui mousemode right "isolde tug atom"

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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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

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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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.  
  

> clipper isolate sel maskRadius 4.0 focus false

[Repeated 2 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> isolde stepto

[Repeated 9 time(s)]

> isolde sim pause

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> 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  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 19 does not match objects array length 11  
  
ValueError: Values array length 19 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 19 does not match objects array length 11  
  
ValueError: Values array length 19 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 19 does not match objects array length 11  
  
ValueError: Values array length 19 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 19 does not match objects array length 11  
  
ValueError: Values array length 19 does not match objects array length 11  
  
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.  
  

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 19 does not match objects array length 11  
  
ValueError: Values array length 19 does not match objects array length 11  
  
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.  
  

> select up

8416 atoms, 8519 bonds, 527 residues, 1 model selected  

> select down

19 atoms, 18 bonds, 1 residue, 1 model selected  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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.  
  

> select up

22 atoms, 21 bonds, 1 residue, 1 model selected  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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 pepflip sel

Flipping the peptide bond for 1 residues  
Residue does not have an N-terminal peptide bond!  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
Residue does not have an N-terminal peptide bond!  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 12 does not match objects array length 11  
  
ValueError: Values array length 12 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 12 does not match objects array length 11  
  
ValueError: Values array length 12 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 12 does not match objects array length 11  
  
ValueError: Values array length 12 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 12 does not match objects array length 11  
  
ValueError: Values array length 12 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 12 does not match objects array length 11  
  
ValueError: Values array length 12 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 12 does not match objects array length 11  
  
ValueError: Values array length 12 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 12 does not match objects array length 11  
  
ValueError: Values array length 12 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 12 does not match objects array length 11  
  
ValueError: Values array length 12 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 12 does not match objects array length 11  
  
ValueError: Values array length 12 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 12 does not match objects array length 11  
  
ValueError: Values array length 12 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 12 does not match objects array length 11  
  
ValueError: Values array length 12 does not match objects array length 11  
  
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 pepflip sel

Flipping the peptide bond for 1 residues  
ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 7 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 7 residues  

> 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  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
Unable to flip peptide bond after 50 rounds. Giving up.  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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 sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 22 does not match objects array length 11  
  
ValueError: Values array length 22 does not match objects array length 11  
  
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

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
Unable to flip peptide bond after 50 rounds. Giving up.  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
Unable to flip peptide bond after 50 rounds. Giving up.  

> 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  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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  

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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  

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> volume #1.1.1.2 level 9.51

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.2 level 12.55

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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  

> clipper isolate sel maskRadius 4.0 focus false

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> 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  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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  

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
Unable to flip peptide bond after 50 rounds. Giving up.  

> 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  

> volume #1.1.1.2 level 9.207

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde sim stop discardTo start

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

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.2 level 4.97

> isolde sim stop discardTo start

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

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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 sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> volume #1.1.1.2 level 3.521

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde stepto

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

[Repeated 1 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

[Repeated 1 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

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

> clipper isolate sel maskRadius 4.0 focus false

> volume #1.1.1.2 level 2.364

> volume #1.1.1.2 level 4.87

> volume #1.1.1.2 level 6.411

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> ui mousemode right "isolde tug selection"

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde stepto

> volume #1.1.1.2 level 4.082

> isolde sim start sel

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/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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 19 does not match objects array length 11  
  
ValueError: Values array length 19 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 19 does not match objects array length 11  
  
ValueError: Values array length 19 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 19 does not match objects array length 11  
  
ValueError: Values array length 19 does not match objects array length 11  
  
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/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 37, in toolbar_command  
_rota_command(session, name)  
File "/Users/brendanfarrell/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 63, in _rota_command  
rrmgr.next_preview(rota)  
File "/Users/brendanfarrell/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/brendanfarrell/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/brendanfarrell/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 19 does not match objects array length 11  
  
ValueError: Values array length 19 does not match objects array length 11  
  
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

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 sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> volume #1.1.1.3 level 0.04053

> clipper isolate sel maskRadius 4.0 focus false

> volume #1.1.1.3 level 0.01844

> volume #1.1.1.1 level 0.0306

3 models selected  

> volume #1.1.1.1 level 0.0306

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> volume #1.1.1.1 level 0.1594

> volume #1.1.1.1 level 0.1462

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

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  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> clipper isolate sel maskRadius 4.0 focus false

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
ISOLDE: started sim  

> isolde sim stop

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  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"

> isolde sim start sel

ISOLDE: started sim  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/brendanfarrell/OneDrive -
> Nexus365/Postdoc/LabBook/RCR/EM/20220712_RCR3_Krios/building/2/RealSpaceRefine_2/rcr3_build2_coot_newmap_5_isolde_1.pdb"




OpenGL version: 4.1 INTEL-14.7.28
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel 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: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1731.140.2.0.0 (iBridge: 19.16.16066.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2026)
      Kernel Version: Darwin 19.6.0
      Time since boot: 23 days 28 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LS24A600N:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: HNAR400167  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          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

[Tristan Croll]

Ah - now I see where these are coming from. Can reproduce the issue by
stopping a simulation while ISOLDE has a rotamer preview visible. The
rotamer preview is a subclass of `AtomicStructure`, and is meant to be very
temporary (destroyed upon assignment of the rotamer to the working model,
deselection of the target residue, or selection of any atom outside the
target residue). I made it a subclass to make it easier for ISOLDE to
distinguish it from "real" models when compiling its list of models
available to work on... but it appears I neglected to consider the full
implications for Clipper. Stopping a simulation runs the command "clipper
spotlight #{working model ID}", which captures the rotamer preview model
along with the working model. Not sure why things go quite *that*
pear-shaped from there... but it's a straightforward fix to limit the
spotlight command to strict `AtomicStructure`s excluding subclasses.



On Thu, Sep 22, 2022 at 6:56 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote: