ISOLDE's self.selected_model is dead

[gyadav@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.93 (2020-04-03)
Description
Error processing trigger "add models":
AttributeError: 'Structure' object has no attribute 'session'

File "C:\Program Files\ChimeraX\bin\lib\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.


(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: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2
> C:/Users/jianglab/Documents/Gaya/PRMT5/06292020/Realspace_july/RealSpaceRefine_14_pix110/rrealspace_aftercoot07062020_pix110_real_space_refined.pdb

Chain information for
rrealspace_aftercoot07062020_pix110_real_space_refined.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open2
> C:/Users/jianglab/Documents/Gaya/PRMT5/06292020/Realspace_july/local_vol65_90_zflip_pix110.mrc

Opened local_vol65_90_zflip_pix110.mrc, grid size 256,256,256, pixel 1.1,
shown at level 2.48, step 1, values float32  

> volume #2 level 3.054

> addh

Summary of feedback from adding hydrogens to
rrealspace_aftercoot07062020_pix110_real_space_refined.pdb #1  
---  
notes | No usable SEQRES records for
rrealspace_aftercoot07062020_pix110_real_space_refined.pdb (#1) chain A;
guessing termini instead  
No usable SEQRES records for
rrealspace_aftercoot07062020_pix110_real_space_refined.pdb (#1) chain B;
guessing termini instead  
Chain-initial residues that are actual N termini: /A ARG 13, /B PRO 21  
Chain-initial residues that are not actual N termini: /B CYS 247  
Chain-final residues that are actual C termini: /A LEU 637  
Chain-final residues that are not actual C termini: /B THR 329, /B ALA 245  
539 hydrogen bonds  
Adding 'H' to /B CYS 247  
/B THR 329 is not terminus, removing H atom from 'C'  
/B ALA 245 is not terminus, removing H atom from 'C'  
7 hydrogens added  
  

> clipper associate #2 toModel #1

Chain information for
rrealspace_aftercoot07062020_pix110_real_space_refined.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
  

> addh

Summary of feedback from adding hydrogens to
rrealspace_aftercoot07062020_pix110_real_space_refined.pdb #1.2  
---  
notes | No usable SEQRES records for
rrealspace_aftercoot07062020_pix110_real_space_refined.pdb (#1.2) chain A;
guessing termini instead  
No usable SEQRES records for
rrealspace_aftercoot07062020_pix110_real_space_refined.pdb (#1.2) chain B;
guessing termini instead  
Chain-initial residues that are actual N termini: /A ARG 13, /B PRO 21  
Chain-initial residues that are not actual N termini: /B CYS 247  
Chain-final residues that are actual C termini: /A LEU 637  
Chain-final residues that are not actual C termini: /B THR 329, /B ALA 245  
539 hydrogen bonds  
/B THR 329 is not terminus, removing H atom from 'C'  
/B ALA 245 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  

> hide HC

> select #1

14583 atoms, 14780 bonds, 2 pseudobonds, 8 models selected  

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> volume #1.1.1.1 level 5.205

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

QWidget::repaint: Recursive repaint detected  

> set bgColor white

Unable to flip peptide bond after 50 rounds. Giving up.  

No rotamer preview selected! Ignoring command.  

> select #1

14583 atoms, 14780 bonds, 2 pseudobonds, 19 models selected  

> close session

Deleting atomic symmetry model...  

> open2
> C:/Users/jianglab/Documents/Gaya/PRMT5/06292020/Realspace_july/RealSpaceRefine_14_pix110/rrealspace_aftercoot07062020_pix110_real_space_refined.pdb

Chain information for
rrealspace_aftercoot07062020_pix110_real_space_refined.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\jianglab\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 1027, in _update_model_list  
self._update_sim_control_button_states()  
File "C:\Users\jianglab\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 1127, in
_update_sim_control_button_states  
self._selection_changed()  
File "C:\Users\jianglab\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 1062, in _selection_changed  
self._clear_rotamer()  
File "C:\Users\jianglab\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2092, in _clear_rotamer  
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)  
File "C:\Users\jianglab\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\session_extensions.py", line 81, in
get_rotamer_restraint_mgr  
return RotamerRestraintMgr(model)  
File "C:\Users\jianglab\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\molobject.py", line 3937, in __init__  
session=model.session  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\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 0x000001C2F95794C8>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\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 442.53
OpenGL renderer: GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: CyberPowerPC
Model: TRACER IV GK7MR0R
OS: Microsoft Windows 10 Home (Build 18363)
Memory: 17,008,533,504
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz"

[Tristan Croll]

Well, I've *finally* gotten around to making ISOLDE gracefully recover when the working model is closed during a simulation. :)