Opened 3 years ago

Closed 3 years ago

#7504 closed defect (fixed)

ISOLDE Deleting symmetry model: 'AtomicStructure' object has no attribute '_c_pointer_ref'

Reported by: lp212@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc: Eric Pettersen, Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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  

> open "/Users/luca/Dropbox (Cambridge University)/RAD51 Structures/RAD51 Hi-
> Res/Coot/ADP-filament.pdb" format pdb

Chain information for ADP-filament.pdb #1  
---  
Chain | Description  
A B C D E F G | No description available  
  

> show cartoons

> hide atoms

> open "/Users/luca/Dropbox (Cambridge University)/RAD51 Structures/RAD51 +
> ADP + dsDNA/RAD51 ADP Final Maps/RAD51_ADP_Resolve.ccp4" format ccp4

Opened RAD51_ADP_Resolve.ccp4 as #2, grid size 85,86,150, pixel 1.3, shown at
level 0.522, step 1, values float32  

> 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Forcefield cache not found or out of date.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 242 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

Removed all altlocs in #1 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 168 residues in model #1 to IUPAC-IUB
standards.  
Chain information for ADP-filament.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G | 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 RAD51_ADP_Resolve.ccp4 as #1.1.1.1, grid size 85,86,150, pixel 1.3,
shown at step 1, values float32  

> ui tool show "Ramachandran Plot"

Loading residue template for ATP from internal database  

> isolde tutorial

> select clear

> select ::name="HOH"

126 atoms, 126 residues, 1 model selected  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> addh

Summary of feedback from adding hydrogens to ADP-filament.pdb #1.2  
---  
notes | No usable SEQRES records for ADP-filament.pdb (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for ADP-filament.pdb (#1.2) chain B; guessing termini
instead  
No usable SEQRES records for ADP-filament.pdb (#1.2) chain C; guessing termini
instead  
No usable SEQRES records for ADP-filament.pdb (#1.2) chain D; guessing termini
instead  
No usable SEQRES records for ADP-filament.pdb (#1.2) chain E; guessing termini
instead  
2 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A PRO 22, /B PRO 22, /C PRO
22, /D PRO 22, /E PRO 22, /F PRO 22, /G PRO 22  
Chain-initial residues that are not actual N termini: /A PRO 283, /B PRO 283,
/C PRO 283, /D PRO 283, /E PRO 283, /F PRO 283, /G PRO 283  
Chain-final residues that are actual C termini: /A ASP 339, /B ASP 339, /C ASP
339, /D ASP 339, /E ASP 339, /F ASP 339, /G ASP 339  
Chain-final residues that are not actual C termini: /A ASP 274, /B ASP 274, /C
ASP 274, /D ASP 274, /E ASP 274, /F ASP 274, /G ASP 274  
1890 hydrogen bonds  
16891 hydrogens added  
  

> volume #1.1.1.1 level 0.01819

> open "/Users/luca/Dropbox (Cambridge University)/RAD51 Structures/RAD51 +
> ADP + dsDNA/RAD51 ADP Final Maps/RAD51_ADP_Resolve.ccp4" format ccp4

Opened RAD51_ADP_Resolve.ccp4 as #2, grid size 85,86,150, pixel 1.3, shown at
level 0.522, step 1, values float32  

> clipper associate #2 toModel #1

Opened RAD51_ADP_Resolve.ccp4 as #1.1.1.2, grid size 85,86,150, pixel 1.3,
shown at step 1, values float32  

> open "/Users/luca/Dropbox (Cambridge University)/RAD51 Structures/RAD51 +
> ADP + dsDNA/RAD51 ADP Final Maps/RAD51_ADP_Resolve.ccp4" format ccp4

Opened RAD51_ADP_Resolve.ccp4 as #2, grid size 85,86,150, pixel 1.3, shown at
level 0.522, step 1, values float32  

> clipper associate #2 toModel #1

Opened RAD51_ADP_Resolve.ccp4 as #1.1.1.3, grid size 85,86,150, pixel 1.3,
shown at step 1, values float32  

> hide #!1.2 models

> show #!1.2 models

> isolde restrain ligands #1

> ui tool show "Ramachandran Plot"

> select #1

33782 atoms, 34020 bonds, 21 pseudobonds, 2191 residues, 23 models selected  

> 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 66 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: 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 0.2196

> volume #1.1.1.3 style surface

> transparency (#!1.2 & sel) 30

> ui tool show "Model Panel"

> select add #1.1

107 atoms, 106 bonds, 7 residues, 12 models selected  

> transparency (#!1.2 & sel) 30

> select add #1

33782 atoms, 34020 bonds, 21 pseudobonds, 2191 residues, 26 models selected  

> select add #1

33782 atoms, 34020 bonds, 21 pseudobonds, 2191 residues, 26 models selected  

> select add #1

33782 atoms, 34020 bonds, 21 pseudobonds, 2191 residues, 26 models selected  

> select add #1.2

33782 atoms, 34020 bonds, 21 pseudobonds, 2191 residues, 26 models selected  

> select add #1

33782 atoms, 34020 bonds, 21 pseudobonds, 2191 residues, 26 models selected  

> select subtract #1.1

33782 atoms, 34020 bonds, 21 pseudobonds, 2191 residues, 15 models selected  

> select subtract #1.3

33782 atoms, 34020 bonds, 21 pseudobonds, 2191 residues, 14 models selected  

> select add #1

33782 atoms, 34020 bonds, 21 pseudobonds, 2191 residues, 26 models selected  

> select subtract #1.3

33782 atoms, 34020 bonds, 21 pseudobonds, 2191 residues, 25 models selected  

> select add #1.2.13

33782 atoms, 34020 bonds, 21 pseudobonds, 2191 residues, 25 models selected  

> volume #1.1.1.2 style image

> volume #1.1.1.2 style surface

> transparency (#!1.2 & sel) 30

> volume #1.1.1.3 style mesh

> select clear

> ui tool show "Side View"

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.2 change image level -0.3595,0 level 1.031,0.8 level 1.478,1

> volume #1.1.1.2 level 0.262

> isolde release distances #1.2&sel groupName "Reference Distance Restraints"

> isolde release torsions #1.2&sel

[Repeated 2 time(s)]

> select clear

> ui mousemode right "isolde tug selection"

> volume #1.1.1.3 level 0.1053

> isolde sim stop discardTo start

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

> close #1.1.1.1

> close #1.1.1.2

> close #1.1.1.3

> ui tool show "Model Panel"

> close #1

> open "/Users/luca/Dropbox (Cambridge University)/RAD51 Structures/RAD51 Hi-
> Res/Coot/ADP-filament.pdb" format pdb

Chain information for ADP-filament.pdb #1  
---  
Chain | Description  
A B C D E F G | No description available  
  

> hide atoms

> show cartoons

> open "/Users/luca/Dropbox (Cambridge University)/RAD51 Structures/RAD51 +
> ADP + dsDNA/RAD51 ADP Final Maps/RAD51_ADP_Resolve.ccp4" format ccp4

Opened RAD51_ADP_Resolve.ccp4 as #2, grid size 85,86,150, pixel 1.3, shown at
level 0.522, step 1, values float32  

> volume #2 level 0.2556

> transparency 30

> select up

48 atoms, 48 bonds, 7 residues, 1 model selected  

> select up

73 atoms, 73 bonds, 10 residues, 1 model selected  

> select up

429 atoms, 436 bonds, 57 residues, 1 model selected  

> select down

73 atoms, 73 bonds, 10 residues, 1 model selected  

> select up

85 atoms, 86 bonds, 12 residues, 1 model selected  

> volume #2 level 0.1508

Removed all altlocs in #1 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 168 residues in model #1 to IUPAC-IUB
standards.  
Chain information for ADP-filament.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G | No description available  
  

> select clear

> select ::name="HOH"

126 atoms, 126 residues, 1 model selected  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> isolde restrain ligands #1

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> isolde sim start sel

> addh

Summary of feedback from adding hydrogens to ADP-filament.pdb #1.2  
---  
notes | No usable SEQRES records for ADP-filament.pdb (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for ADP-filament.pdb (#1.2) chain B; guessing termini
instead  
No usable SEQRES records for ADP-filament.pdb (#1.2) chain C; guessing termini
instead  
No usable SEQRES records for ADP-filament.pdb (#1.2) chain D; guessing termini
instead  
No usable SEQRES records for ADP-filament.pdb (#1.2) chain E; guessing termini
instead  
2 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A PRO 22, /B PRO 22, /C PRO
22, /D PRO 22, /E PRO 22, /F PRO 22, /G PRO 22  
Chain-initial residues that are not actual N termini: /A PRO 283, /B PRO 283,
/C PRO 283, /D PRO 283, /E PRO 283, /F PRO 283, /G PRO 283  
Chain-final residues that are actual C termini: /A ASP 339, /B ASP 339, /C ASP
339, /D ASP 339, /E ASP 339, /F ASP 339, /G ASP 339  
Chain-final residues that are not actual C termini: /A ASP 274, /B ASP 274, /C
ASP 274, /D ASP 274, /E ASP 274, /F ASP 274, /G ASP 274  
1890 hydrogen bonds  
16891 hydrogens added  
  

> isolde sim start sel

> isolde restrain distances

Missing or invalid "atoms" argument: empty atom specifier  

> isolde restrain distances #1

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

> isolde sim start sel

> select #1

33782 atoms, 34020 bonds, 21 pseudobonds, 2191 residues, 14 models selected  

> isolde sim start sel

[Repeated 1 time(s)]ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 22 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> ui tool show "Model Panel"

> hide #!1 models

> hide #1.1 models

> hide #1.3 models

> hide #!2 models

> show #!1.2 target m

> close #1.2

Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/position.py", line 118, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
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/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/distance.py", line 150, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
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/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/secondary_structure.py", line 79,
in _selection_changed_cb  
sel = self.isolde.selected_atoms.unique_residues  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
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/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/register_shift.py", line 105, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  

> open "/Users/luca/Dropbox (Cambridge University)/RAD51 Structures/RAD51 Hi-
> Res/Coot/ADP-filament.pdb" format pdb

Chain information for ADP-filament.pdb #3  
---  
Chain | Description  
A B C D E F G | No description available  
  
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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7fa970472b80>  
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/graphics/drawing.py", line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  

> show cartoons

> hide atoms

> open "/Users/luca/Dropbox (Cambridge University)/RAD51 Structures/RAD51 +
> ADP + dsDNA/RAD51 ADP Final Maps/RAD51_ADP_Resolve.ccp4" format ccp4

Opened RAD51_ADP_Resolve.ccp4 as #4, grid size 85,86,150, pixel 1.3, shown at
level 0.522, step 1, values float32  
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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7fa970472b80>  
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/graphics/drawing.py", line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7fa970472b80>  
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/graphics/drawing.py", line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7fa970472b80>  
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/graphics/drawing.py", line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  

> volume #4 level 0.3937

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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7fa970472b80>  
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/graphics/drawing.py", line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7fa970472b80>  
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/graphics/drawing.py", line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "remove models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7fa970472b80>  
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/graphics/drawing.py", line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Deleting atomic symmetry model...  
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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "remove models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7fa970472b80>  
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/graphics/drawing.py", line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Deleting atomic symmetry model...  
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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "remove models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7fa970472b80>  
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/graphics/drawing.py", line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Deleting atomic symmetry model...  
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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "remove models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7fa970472b80>  
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/graphics/drawing.py", line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Deleting atomic symmetry model...  
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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7fa970472b80>  
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/graphics/drawing.py", line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
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/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "/Users/luca/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7fa970472b80>  
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/graphics/drawing.py", line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  




OpenGL version: 4.1 ATI-3.10.23
OpenGL renderer: AMD Radeon Pro Vega 48 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1731.100.125.0.0
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1824)
      Kernel Version: Darwin 19.6.0
      Time since boot: 2 days 20:16

Graphics/Displays:

    Radeon Pro Vega 48:

      Chipset Model: Radeon Pro Vega 48
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6869
      Revision ID: 0x0000
      ROM Revision: 113-D0650E-072
      VBIOS Version: 113-D05001A1XG-011
      Option ROM Version: 113-D05001A1XG-011
      EFI Driver Version: 01.01.072
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Cc: Eric Pettersen Tom Goddard added
Component: Unassigned → Structure Editing
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE Deleting symmetry model: 'AtomicStructure' object has no attribute '_c_pointer_ref'

Reported by Luca Pelligrini

in reply to:  2 ; comment:2 by Tristan Croll, 3 years ago 

Yes, I’m afraid that closing the working model while ISOLDE has a
simulation running (or paused, in this case) will currently cause various
flavours of Bad Thing to happen. A bit of effort needed on my part to make
ISOLDE recover gracefully in that scenario - lots of different bits to
unwind.

On Thu, 25 Aug 2022 at 18:44, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:3 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

As of the next release, ISOLDE will now recover gracefully when the working model is deleted with a simulation running.

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