'OpenMM_Thread_Handler' object has no attribute '_c_pointer'

[mks131@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
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/Manoj/Documents/phenix_lin28/sharpened_map3.3.ccp4

Opened sharpened_map3.3.ccp4, grid size 376,376,376, pixel 0.649, shown at
level 3.05, step 2, values float32  

> volume #1 level 5.819

QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: "data"  

> open2
> C:/Users/Manoj/Downloads/Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb

Summary of feedback from opening <_io.textiowrapper
name="C:/Users/Manoj/Downloads/Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb"
mode="rt" encoding="utf-8">  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 22  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 23  
BOND : 0.006 0.070 12495  
  
Ignored bad PDB record found on line 24  
ANGLE : 0.827 8.410 18038  
  
18 messages similar to the above omitted  
  
Chain information for Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb #2  
---  
Chain | Description  
A E | No description available  
B | No description available  
C G | No description available  
D H | No description available  
F | No description available  
I | No description available  
J | No description available  
  

> style sphere

Changed 11849 atom styles  

> style sphere

Changed 11849 atom styles  

> show atoms

> nucleotides atoms

> style nucleic stick

Changed 5614 atom styles  

> volume style mesh

> volume style surface

> transparency 50

> volume hide

Expected a density maps specifier or a keyword  

Expected a density maps specifier or a keyword  

Expected a density maps specifier or a keyword  

> show #!1 models

> volume showOutlineBox true

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb  
---  
Chain | Description  
2.2/A 2.2/E | No description available  
2.2/B | No description available  
2.2/C 2.2/G | No description available  
2.2/D 2.2/H | No description available  
2.2/F | No description available  
2.2/I | No description available  
2.2/J | No description available  
  
Done loading forcefield  

> select /A

823 atoms, 819 bonds, 1 model selected  

> select /J

2840 atoms, 3199 bonds, 1 model selected  

No template found for residue A52 (ARG)  

Adding hydrogens  
Summary of feedback from adding hydrogens to
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb #2.2  
---  
notes | No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain A; guessing
termini instead  
No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain B; guessing
termini instead  
No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain C; guessing
termini instead  
No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain D; guessing
termini instead  
No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain E; guessing
termini instead  
5 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A PRO 38, /B VAL 21, /C LYS
13, /D ARG 28, /E PRO 38, /F LYS 16, /G LYS 13, /H ARG 28, /I DT -64, /J DG
-72  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ALA 135, /B GLY 102, /D LYS
122, /F GLY 102, /H LYS 122, /I DC 72, /J DA 64  
Chain-final residues that are not actual C termini: /C LYS 119, /E ALA 135, /G
LYS 119  
1298 hydrogen bonds  
/C LYS 119 is not terminus, removing H atom from 'C'  
/E ALA 135 is not terminus, removing H atom from 'C'  
/G LYS 119 is not terminus, removing H atom from 'C'  
9813 hydrogens added  
  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 2 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 2 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 188 atom styles  

> show sel atoms

> volume style mesh

> volume #2.1.1.1 level 6.512

Drag select of 3 atoms, 3 bonds  
Drag select of 2 atoms, 1 residues, 3 bonds  
Drag select of 1 atoms, 6 bonds  

> volume #2.1.1.1 level 9.32

> volume #2.1.1.1 level 7.779

> volume #2.1.1.1 level 7.173

> volume #2.1.1.1 level 5.907

Drag select of 13 atoms, 2 residues, 14 bonds  

> volume #2.1.1.1 level 6.871

Drag select of 13 atoms, 1 residues, 15 bonds  
Drag select of  
Drag select of 12 atoms, 2 residues, 16 bonds  
Drag select of 12 atoms, 3 residues, 17 bonds  

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

reverting to start  

No template found for residue I-64 (DT)  

Adding hydrogens  
Summary of feedback from adding hydrogens to
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb #2.2  
---  
notes | No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain A; guessing
termini instead  
No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain B; guessing
termini instead  
No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain C; guessing
termini instead  
No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain D; guessing
termini instead  
No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain E; guessing
termini instead  
5 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A PRO 38, /B VAL 21, /C LYS
13, /D ARG 28, /E PRO 38, /F LYS 16, /G LYS 13, /H ARG 28, /I DT -64, /J DG
-72  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ALA 135, /B GLY 102, /D LYS
122, /F GLY 102, /H LYS 122, /I DC 72, /J DA 64  
Chain-final residues that are not actual C termini: /C LYS 119, /E ALA 135, /G
LYS 119  
1200 hydrogen bonds  
/C LYS 119 is not terminus, removing H atom from 'C'  
/E ALA 135 is not terminus, removing H atom from 'C'  
/G LYS 119 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  

No template found for residue I-64 (DT)  

Adding hydrogens  
Summary of feedback from adding hydrogens to
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb #2.2  
---  
notes | No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain A; guessing
termini instead  
No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain B; guessing
termini instead  
No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain C; guessing
termini instead  
No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain D; guessing
termini instead  
No usable SEQRES records for
Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb (#2.2) chain E; guessing
termini instead  
5 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A PRO 38, /B VAL 21, /C LYS
13, /D ARG 28, /E PRO 38, /F LYS 16, /G LYS 13, /H ARG 28, /I DT -64, /J DG
-72  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ALA 135, /B GLY 102, /D LYS
122, /F GLY 102, /H LYS 122, /I DC 72, /J DA 64  
Chain-final residues that are not actual C termini: /C LYS 119, /E ALA 135, /G
LYS 119  
1200 hydrogen bonds  
/C LYS 119 is not terminus, removing H atom from 'C'  
/E ALA 135 is not terminus, removing H atom from 'C'  
/G LYS 119 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  

No template found for residue I-64 (DT)  

Excluding residue  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> volume region all imageMode "full region"

> mousemode right "crop volume"

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\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\delayed_reaction.py", line 64, in callback  
if self.tf is None or self.tf():  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\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 "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 241, in
thread_finished  
return f(self._c_pointer)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.4531
OpenGL renderer: Intel(R) HD Graphics 5500
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Inspiron 7348
OS: Microsoft Windows 10 Home (Build 18362)
Memory: 8,501,149,696
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-5500U CPU @ 2.40GHz"

[Tristan Croll]

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