ISOLDE: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-23)
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: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/srehan/Documents/Coot_Session/RNC_Sec61_445/sharpened_focused_class_map_box.ccp4

Opened sharpened_focused_class_map_box.ccp4, grid size 103,89,89, pixel 0.83,
shown at level 11.5, step 1, values float32  

> open /Users/srehan/Desktop/1.cif

Summary of feedback from opening /Users/srehan/Desktop/1.cif  
---  
warnings | Unknown polymer entity '1' near line 134  
Unknown polymer entity '2' near line 6328  
Unknown polymer entity '3' near line 7283  
Unable to fetch template for 'KZC': might be missing bonds  
Atom H2 is not in the residue template for PRO #11 in chain B  
Atom H1 is not in the residue template for PHE #7 in chain C  
Atom H1 is not in the residue template for ALA #24 in chain D  
Unable to fetch template for 'KZC': might be missing bonds  
Missing or invalid residue template for KZC #1 in chain A  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
notes | Combining 2 symmetry atoms into KZC /A:1 HH  
Combining 2 symmetry atoms into KZC /A:1 HH8  
  
Chain information for 1.cif #2  
---  
Chain | Description  
B | ?  
C | ?  
D | ?  
  

> set bgColor white

> volume #1 level 9.147

> clipper associate #1 toModel #2

Chain information for 1.cif  
---  
Chain | Description  
1.1/B | ?  
1.1/C | ?  
1.1/D | ?  
  

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to 1.cif #1.1  
---  
warning | Unknown hybridization for atoms (C5, C6) of residue type KZC; not
adding hydrogens to them  
notes | No usable SEQRES records for 1.cif (#1.1) chain B; guessing termini
instead  
No usable SEQRES records for 1.cif (#1.1) chain C; guessing termini instead  
No usable SEQRES records for 1.cif (#1.1) chain D; guessing termini instead  
Chain-initial residues that are actual N termini: /B PRO 11, /C PHE 7, /D ALA
24  
Chain-initial residues that are not actual N termini: /B TYR 63, /B THR 105,
/B VAL 147, /B ALA 229, /B PRO 337, /D ALA 46  
Chain-final residues that are actual C termini: /B SER 466, /D ALA 52  
Chain-final residues that are not actual C termini: /B CYS 46, /B ALA 97, /B
GLY 135, /B LEU 220, /B PHE 312, /C ASN 63, /D ALA 44  
358 hydrogen bonds  
/B CYS 46 is not terminus, removing H atom from 'C'  
/B ALA 97 is not terminus, removing H atom from 'C'  
/B LEU 220 is not terminus, removing H atom from 'C'  
/C ASN 63 is not terminus, removing H atom from 'C'  
/D ALA 44 is not terminus, removing H atom from 'C'  
7 hydrogens added  
  

> hide HC

QWidget::repaint: Recursive repaint detected  

No template found for residue A1 (KZC)  

Excluding residue  
reverting to start  

> select clear

> select clear

Alignment identifier is 1.1.B  
Destroying pre-existing alignment with identifier 1.1.B  
Alignment identifier is 1.1.B  
reverting to start  

> select clear

reverting to start  
reverting to start  
reverting to start  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/delayed_reaction.py", line 64, in callback  
if self.tf is None or self.tf():  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 241, in
thread_finished  
return f(self._c_pointer)  
AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer'  
  
Error processing trigger "new frame":  
AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer'  
  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 241, in
thread_finished  
return f(self._c_pointer)  
  
See log for complete Python traceback.  
  

> select clear

Not saving entity_poly_seq for non-authoritative sequences  

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

QWidget::repaint: Recursive repaint detected  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  

[deleted quite a few of these]

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/Users/srehan/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.17
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.

[Tristan Croll]

Finally tracked down and squished. Will be fixed in the next release.