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#2989 closed defect (duplicate)

ISOLDE referencing a Structure that's been deleted

Reported by:	chimerax-bug-report@…	Owned by:	Tristan Croll
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-5.0.0-32-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.92 (2020-03-08)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.92 (2020-03-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/paola/PhD_studies/Interactions_analysis/Current_models/630/CD630_slpa_new-
> folder_refine_104.pdb

Summary of feedback from opening
/home/paola/PhD_studies/Interactions_analysis/Current_models/630/CD630_slpa_new-
folder_refine_104.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2020-02-24 Time 15:07:12 GMT +0000 (1582556832.77 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name :
/home/CAMPUS/b7055280/slpa/012/dls_280918/CCP4_i2/CCP4_JOBS/job_100/job_4/hklout.mtz  
  
41 messages similar to the above omitted  
  
Chain information for CD630_slpa_new-folder_refine_104.pdb #1  
---  
Chain | Description  
A | No description available  
B D | No description available  
C | No description available  
  

> addh

Summary of feedback from adding hydrogens to CD630_slpa_new-
folder_refine_104.pdb #1  
---  
warnings | Not adding hydrogens to /B LYS 320 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /B GLU 321 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /C TYR 87 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /D LYS 107 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /D ASP 108 CB because it is missing heavy-atom bond
partners  
1 messages similar to the above omitted  
notes | No usable SEQRES records for CD630_slpa_new-folder_refine_104.pdb (#1)
chain A; guessing termini instead  
No usable SEQRES records for CD630_slpa_new-folder_refine_104.pdb (#1) chain
B; guessing termini instead  
No usable SEQRES records for CD630_slpa_new-folder_refine_104.pdb (#1) chain
C; guessing termini instead  
No usable SEQRES records for CD630_slpa_new-folder_refine_104.pdb (#1) chain
D; guessing termini instead  
Chain-initial residues that are actual N termini: /A ALA 1, /B ASN 2, /C ALA
1, /D ASN 2  
Chain-initial residues that are not actual N termini: /A THR 220, /C ASN 137,
/C LEU 237  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLU 318, /A GLY 217, /B
MET 374, /C GLU 318, /C LYS 129, /C THR 231, /D MET 374  
1195 hydrogen bonds  
Adding 'H' to /A THR 220  
Adding 'H' to /C ASN 137  
Adding 'H' to /C LEU 237  
/A GLU 318 is not terminus, removing H atom from 'C'  
/A GLY 217 is not terminus, removing H atom from 'C'  
/B MET 374 is not terminus, removing H atom from 'C'  
/C GLU 318 is not terminus, removing H atom from 'C'  
/C LYS 129 is not terminus, removing H atom from 'C'  
2 messages similar to the above omitted  
10346 hydrogens added  
  

> style stick

Changed 20577 atom styles  

> select #1

20577 atoms, 20616 bonds, 6 pseudobonds, 2 models selected  

> addh

Summary of feedback from adding hydrogens to CD630_slpa_new-
folder_refine_104.pdb #1  
---  
warnings | Not adding hydrogens to /B LYS 320 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /B GLU 321 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /C TYR 87 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /D LYS 107 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /D ASP 108 CB because it is missing heavy-atom bond
partners  
1 messages similar to the above omitted  
notes | No usable SEQRES records for CD630_slpa_new-folder_refine_104.pdb (#1)
chain A; guessing termini instead  
No usable SEQRES records for CD630_slpa_new-folder_refine_104.pdb (#1) chain
B; guessing termini instead  
No usable SEQRES records for CD630_slpa_new-folder_refine_104.pdb (#1) chain
C; guessing termini instead  
No usable SEQRES records for CD630_slpa_new-folder_refine_104.pdb (#1) chain
D; guessing termini instead  
Chain-initial residues that are actual N termini: /A ALA 1, /B ASN 2, /C ALA
1, /D ASN 2  
Chain-initial residues that are not actual N termini: /A THR 220, /C ASN 137,
/C LEU 237  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLU 318, /A GLY 217, /B
MET 374, /C GLU 318, /C LYS 129, /C THR 231, /D MET 374  
1108 hydrogen bonds  
/A GLU 318 is not terminus, removing H atom from 'C'  
/A GLY 217 is not terminus, removing H atom from 'C'  
/B MET 374 is not terminus, removing H atom from 'C'  
/C GLU 318 is not terminus, removing H atom from 'C'  
/C LYS 129 is not terminus, removing H atom from 'C'  
2 messages similar to the above omitted  
0 hydrogens added  
  

> style sel stick

Changed 20577 atom styles  

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for CD630_slpa_new-folder_refine_104.pdb  
---  
Chain | Description  
1.1/A | No description available  
1.1/B 1.1/D | No description available  
1.1/C | No description available  
  
Done loading forcefield  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  

QWidget::repaint: Recursive repaint detected  

> select clear

> volume #!1.2.1.2-8 appearance airways

> close session

Deleting (LIVE) 2mFo-DFc_sharp_21  
Deleting (LIVE) MDFF potential  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting Crystallographic maps (CD630_slpa_new-folder_refine_104.mtz)  

> open
> /home/paola/PhD_studies/Interactions_analysis/Current_models/630/CD630_slpa_new-
> folder_refine_104.pdb

Summary of feedback from opening
/home/paola/PhD_studies/Interactions_analysis/Current_models/630/CD630_slpa_new-
folder_refine_104.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2020-02-24 Time 15:07:12 GMT +0000 (1582556832.77 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name :
/home/CAMPUS/b7055280/slpa/012/dls_280918/CCP4_i2/CCP4_JOBS/job_100/job_4/hklout.mtz  
  
41 messages similar to the above omitted  
  
Chain information for CD630_slpa_new-folder_refine_104.pdb #1  
---  
Chain | Description  
A | No description available  
B D | No description available  
C | No description available  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1027, in _update_model_list  
self._update_sim_control_button_states()  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1127, in
_update_sim_control_button_states  
self._selection_changed()  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1062, in _selection_changed  
self._clear_rotamer()  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2092, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/session_extensions.py", line 81, in
get_rotamer_restraint_mgr  
return RotamerRestraintMgr(model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/molobject.py", line 3939, in __init__  
session=model.session  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7f866db6f050>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1111, in __del__  
if not self.was_deleted:  
AttributeError: 'RotamerRestraintMgr' object has no attribute 'was_deleted'  

> addh

Summary of feedback from adding hydrogens to CD630_slpa_new-
folder_refine_104.pdb #1  
---  
warnings | Not adding hydrogens to /B LYS 320 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /B GLU 321 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /C TYR 87 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /D LYS 107 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /D ASP 108 CB because it is missing heavy-atom bond
partners  
1 messages similar to the above omitted  
notes | No usable SEQRES records for CD630_slpa_new-folder_refine_104.pdb (#1)
chain A; guessing termini instead  
No usable SEQRES records for CD630_slpa_new-folder_refine_104.pdb (#1) chain
B; guessing termini instead  
No usable SEQRES records for CD630_slpa_new-folder_refine_104.pdb (#1) chain
C; guessing termini instead  
No usable SEQRES records for CD630_slpa_new-folder_refine_104.pdb (#1) chain
D; guessing termini instead  
Chain-initial residues that are actual N termini: /A ALA 1, /B ASN 2, /C ALA
1, /D ASN 2  
Chain-initial residues that are not actual N termini: /A THR 220, /C ASN 137,
/C LEU 237  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLU 318, /A GLY 217, /B
MET 374, /C GLU 318, /C LYS 129, /C THR 231, /D MET 374  
1195 hydrogen bonds  
Adding 'H' to /A THR 220  
Adding 'H' to /C ASN 137  
Adding 'H' to /C LEU 237  
/A GLU 318 is not terminus, removing H atom from 'C'  
/A GLY 217 is not terminus, removing H atom from 'C'  
/B MET 374 is not terminus, removing H atom from 'C'  
/C GLU 318 is not terminus, removing H atom from 'C'  
/C LYS 129 is not terminus, removing H atom from 'C'  
2 messages similar to the above omitted  
10346 hydrogens added  
  

> select #1

20577 atoms, 20616 bonds, 6 pseudobonds, 2 models selected  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1062, in _selection_changed  
self._clear_rotamer()  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2092, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/session_extensions.py", line 81, in
get_rotamer_restraint_mgr  
return RotamerRestraintMgr(model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/molobject.py", line 3939, in __init__  
session=model.session  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
Error processing trigger "selection changed":  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7f866db6f050>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1111, in __del__  
if not self.was_deleted:  
AttributeError: 'RotamerRestraintMgr' object has no attribute 'was_deleted'  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1062, in _selection_changed  
self._clear_rotamer()  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2092, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/session_extensions.py", line 81, in
get_rotamer_restraint_mgr  
return RotamerRestraintMgr(model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/molobject.py", line 3939, in __init__  
session=model.session  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
Error processing trigger "selection changed":  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7f866db6f050>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1111, in __del__  
if not self.was_deleted:  
AttributeError: 'RotamerRestraintMgr' object has no attribute 'was_deleted'  

> select #1

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1062, in _selection_changed  
self._clear_rotamer()  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2092, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/session_extensions.py", line 81, in
get_rotamer_restraint_mgr  
return RotamerRestraintMgr(model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/molobject.py", line 3939, in __init__  
session=model.session  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
Error processing trigger "selection changed":  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7f866db6f050>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1111, in __del__  
if not self.was_deleted:  
AttributeError: 'RotamerRestraintMgr' object has no attribute 'was_deleted'  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1062, in _selection_changed  
self._clear_rotamer()  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2092, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/session_extensions.py", line 81, in
get_rotamer_restraint_mgr  
return RotamerRestraintMgr(model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/molobject.py", line 3939, in __init__  
session=model.session  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
Error processing trigger "selection changed":  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7f866db6f050>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1111, in __del__  
if not self.was_deleted:  
AttributeError: 'RotamerRestraintMgr' object has no attribute 'was_deleted'  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1062, in _selection_changed  
self._clear_rotamer()  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2092, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/session_extensions.py", line 81, in
get_rotamer_restraint_mgr  
return RotamerRestraintMgr(model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/molobject.py", line 3939, in __init__  
session=model.session  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
Error processing trigger "selection changed":  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7f866db6f050>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1111, in __del__  
if not self.was_deleted:  
AttributeError: 'RotamerRestraintMgr' object has no attribute 'was_deleted'  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1062, in _selection_changed  
self._clear_rotamer()  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2092, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/session_extensions.py", line 81, in
get_rotamer_restraint_mgr  
return RotamerRestraintMgr(model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/molobject.py", line 3939, in __init__  
session=model.session  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
Error processing trigger "selection changed":  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7f866db6f050>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1111, in __del__  
if not self.was_deleted:  
AttributeError: 'RotamerRestraintMgr' object has no attribute 'was_deleted'  
20577 atoms, 20616 bonds, 6 pseudobonds, 2 models selected  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1062, in _selection_changed  
self._clear_rotamer()  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2092, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/session_extensions.py", line 81, in
get_rotamer_restraint_mgr  
return RotamerRestraintMgr(model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/molobject.py", line 3939, in __init__  
session=model.session  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
Error processing trigger "selection changed":  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7f866db6f050>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1111, in __del__  
if not self.was_deleted:  
AttributeError: 'RotamerRestraintMgr' object has no attribute 'was_deleted'  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1062, in _selection_changed  
self._clear_rotamer()  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2092, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/session_extensions.py", line 81, in
get_rotamer_restraint_mgr  
return RotamerRestraintMgr(model)  
File "/home/paola/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/molobject.py", line 3939, in __init__  
session=model.session  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
Error processing trigger "selection changed":  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x7f866db6f050>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1111, in __del__  
if not self.was_deleted:  
AttributeError: 'RotamerRestraintMgr' object has no attribute 'was_deleted'  




OpenGL version: 3.3.0 NVIDIA 390.116
OpenGL renderer: GeForce MX250/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (6)

comment:1 by Eric Pettersen, 6 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ISOLDE referencing a Structure that's been deleted

Structure's 'delete' method deletes the "session" attribute, so "self.selected_model" must be referencing a dead Structure (which could be checked via the Structure's "deleted" property).

comment:2 by Tristan Croll, 6 years ago

Hmm... will try to track that one down when I get the chance (very focused right now on checking/fixing all the new COVID-19 related structures coming out). I'm a bit surprised, though... isn't that the Ubuntu ChimeraX build? How the heck is anything working at all?

comment:3 by Eric Pettersen, 6 years ago

Well, probably In most use cases people aren't closing models, so they don't run into this.

in reply to: 4 ; follow-up: 4 comment:4 by Tristan Croll, 6 years ago

That's not what surprised me. I'm pretty sure I know what's happened 
here: they closed the model while they still had a rotamer preview 
active (I open and close models with ISOLDE active all the time without 
trouble, but I guess I didn't account for that particular possibility). 
It's more that the Ubuntu builds are binary-incompatible with ISOLDE... 
at least they were...

On 2020-03-30 17:52, ChimeraX wrote:

comment:5 by Eric Pettersen, 6 years ago

Ah, I see.

comment:6 by Eric Pettersen, 6 years ago

Resolution:	→ duplicate
Status:	assigned → closed

Seems like a duplicate of #2992 (although that one's Mac) and #2992 has a reporter contact.

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