ISOLDE: using deleted 'session' attribute of dead Structure

[jliu321@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.9 (2019-06-06)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /data2/users/jliu/ccpem_project/Flex-EM_3/1_MD/final1_mdcg.pdb

Chain information for final1_mdcg.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 /data2/users/jliu/Documents/J79/J79_map_invert.mrc

Opened J79_map_invert.mrc, grid size 288,288,288, pixel 1.06, shown at level
0.294, step 2, values float32  

> ui mousemode rightMode "rotate selected models"

> select #1

10404 atoms, 10542 bonds selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> fitmap #1 inMap #2

Fit molecule final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404
atoms  
average map value = 0.4909, steps = 116  
shifted from previous position = 9.65  
rotated from previous position = 6.16 degrees  
atoms outside contour = 3741, contour level = 0.29422  
  
Position of final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.96239600 -0.04256905 0.26829437 274.52001913  
-0.17241686 -0.66748987 -0.72438233 356.81491917  
0.20992005 -0.74340112 0.63504992 133.05039824  
Axis -0.13241463 0.40642003 -0.90404044  
Axis point 134.70529547 202.88620204 0.00000000  
Rotation angle (degrees) 175.88174344  
Shift along axis -11.61667520  
  

> addh

Summary of feedback from adding hydrogens to final1_mdcg.pdb #1  
---  
warning | Unknown hybridization for atoms (C8, C3, C4, O4, C1, C7, O3, O6, C5,
O5, C6, O7, C2) of residue type NAG; not adding hydrogens to them  
notes | No usable SEQRES records for final1_mdcg.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for final1_mdcg.pdb (#1) chain B; guessing termini
instead  
No usable SEQRES records for final1_mdcg.pdb (#1) chain C; guessing termini
instead  
No usable SEQRES records for final1_mdcg.pdb (#1) chain D; guessing termini
instead  
No usable SEQRES records for final1_mdcg.pdb (#1) chain E; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLU 190, /B PRO 37, /C
GLN 1, /D LYS 289, /E LEU 40  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 287, /B GLN 273, /C SER
189, /D GLN 389, /E ALA 713  
Chain-final residues that are not actual C termini:  
676 hydrogen bonds  
10265 hydrogens added  
  

> show selAtoms

> hide selAtoms

> hide selAtoms

> show selAtoms ribbons

> hide selAtoms

> show selAtoms

> hide selAtoms

> hide

> hide HC

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for final1_mdcg.pdb  
---  
Chain | Description  
1.3/A | No description available  
1.3/B | No description available  
1.3/C | No description available  
1.3/D | No description available  
1.3/E | No description available  
  
Done loading forcefield  

> select #1.3.1

2 models selected  

> select #1.3.2

2 models selected  

> ~select #1.3.3

2 models selected  

> ~select #1.3

Nothing selected  

> select #1

20669 atoms, 20807 bonds, 7 models selected  

> hide #!2 models

> hide #!2.1 models

> hide #!1.3.1 models

> hide #!1.3.2 models

> hide #!1.3.3 models

> hide #!1.1 models

> show #!1.2 models

> hide #!1 models

> show #!1 models

> hide #!1.3 models

> show #!1.3 models

> select #1.3

20669 atoms, 20807 bonds, 5 models selected  

> clipper associate #2 toModel #1.3

> clipper spotlight radius 20.00

Setting spotlight mode for model 1.3 to True  

> clipper spotlight radius 20.00

Setting spotlight mode for model 1.3 to True  

> clipper associate #2 toModel #1.3

Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1552, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Invoked getPositions() on a State which does not contain
positions.  
  
Error processing trigger "new frame": Invoked getPositions() on a State which
does not contain positions.:  
RuntimeError: Invoked getPositions() on a State which does not contain
positions.  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  

QWidget::repaint: Recursive repaint detected  

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1552, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Invoked getPositions() on a State which does not contain
positions.  
  
Error processing trigger "new frame": Invoked getPositions() on a State which
does not contain positions.:  
RuntimeError: Invoked getPositions() on a State which does not contain
positions.  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  

> ~select #1.2

14 atoms, 13 bonds, 1 model selected  

> hide #!1.2 models

> hide #!1.1.1 models

> close #1.3

> close

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1015, in _update_model_list  
self._update_sim_control_button_states()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1117, in
_update_sim_control_button_states  
self._selection_changed()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1052, in _selection_changed  
self._clear_rotamer()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 2074, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/session_extensions.py", line 110, in
get_rotamer_restraint_mgr  
return Rotamer_Restraint_Mgr(model)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/molobject.py", line 3189, in __init__  
session=model.session  
File "/programs/x86_64-linux/chimerax/0.9/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 "/programs/x86_64-linux/chimerax/0.9/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 "/programs/x86_64-linux/chimerax/0.9/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 "remove models": 'Structure' object has no attribute
'session':  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/programs/x86_64-linux/chimerax/0.9/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 0x7f06f4229378>  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1086, in __del__  
if not self.was_deleted:  
AttributeError: 'Rotamer_Restraint_Mgr' object has no attribute 'was_deleted'  

> open /data2/users/jliu/ccpem_project/Flex-EM_3/1_MD/final1_mdcg.pdb

Chain information for final1_mdcg.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1015, in _update_model_list  
self._update_sim_control_button_states()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1117, in
_update_sim_control_button_states  
self._selection_changed()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1052, in _selection_changed  
self._clear_rotamer()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 2074, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/session_extensions.py", line 110, in
get_rotamer_restraint_mgr  
return Rotamer_Restraint_Mgr(model)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/molobject.py", line 3189, in __init__  
session=model.session  
File "/programs/x86_64-linux/chimerax/0.9/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 "/programs/x86_64-linux/chimerax/0.9/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 "/programs/x86_64-linux/chimerax/0.9/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": 'Structure' object has no attribute
'session':  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/programs/x86_64-linux/chimerax/0.9/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 0x7f06f4229378>  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1086, in __del__  
if not self.was_deleted:  
AttributeError: 'Rotamer_Restraint_Mgr' object has no attribute 'was_deleted'  

> hide selAtoms

> show selAtoms ribbons

> open /data2/users/jliu/Documents/J79/J79_map_invert.mrc

Opened J79_map_invert.mrc, grid size 288,288,288, pixel 1.06, shown at level
0.294, step 2, values float32  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1015, in _update_model_list  
self._update_sim_control_button_states()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1117, in
_update_sim_control_button_states  
self._selection_changed()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1052, in _selection_changed  
self._clear_rotamer()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 2074, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/session_extensions.py", line 110, in
get_rotamer_restraint_mgr  
return Rotamer_Restraint_Mgr(model)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/molobject.py", line 3189, in __init__  
session=model.session  
File "/programs/x86_64-linux/chimerax/0.9/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 "/programs/x86_64-linux/chimerax/0.9/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 "/programs/x86_64-linux/chimerax/0.9/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": 'Structure' object has no attribute
'session':  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/programs/x86_64-linux/chimerax/0.9/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 0x7f06f4229378>  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1086, in __del__  
if not self.was_deleted:  
AttributeError: 'Rotamer_Restraint_Mgr' object has no attribute 'was_deleted'  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1015, in _update_model_list  
self._update_sim_control_button_states()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1117, in
_update_sim_control_button_states  
self._selection_changed()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1052, in _selection_changed  
self._clear_rotamer()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 2074, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/session_extensions.py", line 110, in
get_rotamer_restraint_mgr  
return Rotamer_Restraint_Mgr(model)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/molobject.py", line 3189, in __init__  
session=model.session  
File "/programs/x86_64-linux/chimerax/0.9/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 "/programs/x86_64-linux/chimerax/0.9/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 "/programs/x86_64-linux/chimerax/0.9/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": 'Structure' object has no attribute
'session':  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/programs/x86_64-linux/chimerax/0.9/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 0x7f06f4229378>  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1086, in __del__  
if not self.was_deleted:  
AttributeError: 'Rotamer_Restraint_Mgr' object has no attribute 'was_deleted'  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1015, in _update_model_list  
self._update_sim_control_button_states()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1117, in
_update_sim_control_button_states  
self._selection_changed()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 1052, in _selection_changed  
self._clear_rotamer()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 2074, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/session_extensions.py", line 110, in
get_rotamer_restraint_mgr  
return Rotamer_Restraint_Mgr(model)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/molobject.py", line 3189, in __init__  
session=model.session  
File "/programs/x86_64-linux/chimerax/0.9/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 "/programs/x86_64-linux/chimerax/0.9/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 "/programs/x86_64-linux/chimerax/0.9/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": 'Structure' object has no attribute
'session':  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/programs/x86_64-linux/chimerax/0.9/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 0x7f06f4229378>  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1086, in __del__  
if not self.was_deleted:  
AttributeError: 'Rotamer_Restraint_Mgr' object has no attribute 'was_deleted'  




OpenGL version: 3.3.0 NVIDIA 410.79
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

First comment: you shouldn't need to downgrade to ChimeraX 0.9 / ISOLDE 1.0b3 to get up and running - just follow my instructions in #2647 to upgrade to the correct version of ISOLDE in the ChimeraX daily build. There are many bug fixes in the newer version, and you should find that most common ligands just work.

The traceback you got here happened because you closed the model while ISOLDE was running (or trying to start) a simulation. That's something that will still happen in the development builds, I'm afraid - due to the asynchronous nature of everything that's going on during simulations, trying to catch and gracefully handle that particular event is a bit of a nightmare. I will eventually tackle it, but it's not an immediate priority.

[Tristan Croll]

From the next ISOLDE release onwards, closing the working model with a simulation running should no longer cause errors.