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

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\LocalAdmin\Desktop\Pol I script ChimeraX\4c2m_2_monomers.cif"
> format mmcif

Chain information for 4c2m_2_monomers.cif #1  
---  
Chain | Description  
A | DNA-directed RNA polymerase I subunit RPA190  
B | DNA-directed RNA polymerase I subunit RPA135  
C | DNA-directed RNA polymerases I and III subunit RPAC1  
D | DNA-directed RNA polymerase I subunit RPA14  
E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1  
F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2  
G O | DNA-directed RNA polymerase I subunit RPA43  
H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3  
I | DNA-directed RNA polymerase I subunit RPA12  
J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5  
K | DNA-directed RNA polymerases I and III subunit RPAC2  
L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4  
M | DNA-directed RNA polymerase I subunit RPA49  
N | DNA-directed RNA polymerase I subunit RPA34  
  
4c2m_2_monomers.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> open "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/mono-WT.mrc"

Opened mono-WT.mrc, grid size 128,128,128, pixel 2.16, shown at level 0.121,
step 1, values float32  

> fitmap #1 inMap #2 search 50

Found 40 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).  
  
Average map values and times found:  
0.1059 (4), 0.0706 (2), 0.07023 (2), 0.0674 (1), 0.06721 (1), 0.06671 (2),
0.06649 (1), 0.06645 (2), 0.0664 (1), 0.06561 (1), 0.06554 (1), 0.06542 (1),
0.06527 (1), 0.06522 (1), 0.06522 (1), 0.06515 (1), 0.06488 (1), 0.06452 (1),
0.06451 (1), 0.06441 (3), 0.06436 (1), 0.06422 (1), 0.06401 (2), 0.06387 (1),
0.06377 (1), 0.06353 (1), 0.06317 (1), 0.06301 (1), 0.06267 (1), 0.06252 (1),
0.06232 (1), 0.06185 (1), 0.06169 (1), 0.06158 (1), 0.06142 (1), 0.0612 (1),
0.06059 (1), 0.06011 (1), 0.05999 (1), 0.05882 (1)  
  
Best fit found:  
Fit molecule 4c2m_2_monomers.cif (#1) to map mono-WT.mrc (#2) using 34700
atoms  
average map value = 0.1059, steps = 404  
shifted from previous position = 63.8  
rotated from previous position = 79.8 degrees  
atoms outside contour = 21910, contour level = 0.12128  
Position of 4c2m_2_monomers.cif (#1) relative to mono-WT.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.08208368 -0.11788364 0.98962907 223.83194517  
-0.14338191 0.98404673 0.10532605 205.57661288  
-0.98625751 -0.13324934 -0.09767656 254.56479204  
Axis -0.11986298 0.99270779 -0.01281062  
Axis point 241.57292821 0.00000000 16.89073036  
Rotation angle (degrees) 95.61576609  
Shift along axis 173.98720927  
  
Found 40 fits. List window not yet implemented.  

> volume #2 level 0.06169

> view

> open "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/script-
> domainssattributionpolI-030720envoyeMichael.cxc"

> hide atoms

> show cartoons

> select all

34700 atoms, 35175 bonds, 42 pseudobonds, 5 models selected  

> color sel grey

> select clear

> name rpa190 #1/A

> name rpa135 #1/B

> name rpb5 #1/E

> name rpb6 #1/F

> name rpb8 #1/H

> name rpb10 #1/J

> name rpb12 #1/L

> name ac40 #1/C

> name ac19 #1/K

> name rpa12 #1/I

> name rpa14 #1/D

> name rpa43 #1/G

> name rpa34 #1/N

> name rpa49 #1/M

> name a++clamp #1/A:01-90 #1/A:356-477 #1/A:1608-1664 #1/A:126-303
> #1/B:1170-1203

> name a++jaw #1/A:1285-1320 #1/A:1456-1500 #1/E:1-145 #1/I:1-39

> name a++stalk #1/D #1/G

> name a++shelf #1/A:477-506 #1/A:581-654 #1/A:506-581 #1/A:1060-1137
> #1/A:991-1053 #1/A:1180-1261 #1/A:1514-1608 #1/E #1/F #1/B:1068-1092

> name a++core #1/B:647-698 #1/H #1/A:709-827 #1/A:827-991 #1/B:469-553
> #1/B:698-800 #1/C #1/J #1/K #1/B:43-209 #1/B:400-469 #1/L #1/B:800-910

> name rpa190++clampcore++engel #1/A:01-90 #1/A:356-477 #1/A:1608-1664

> name rpa190++clampcore++tornero #1/A:01-90 #1/A:350-477 #1/A:1608-1664

> name rpa190++clamphead++engel #1/A:126-303

> name rpa190++clamphead++tornero #1/A:90-350

> name rpa190++activesite #1/A:477-506 #1/A:581-654

> name rpa190++dock #1/A:506-581

> name rpa190++pore++engel #1/A:709-827

> name rpa190++pore++tornero #1/A:654-828

> name rpa190++funnel #1/A:827-991

> name rpa190++cleft++engel #1/A:991-1053 #1/A:1180-1261 #1/A:1514-1608

> name rpa190++cleft++tornero #1/A:991-1051 #1/A:1180-1260 #1/A:1499-1607

> name rpa190++foot #1/A:1060-1137

> name rpa190++jaw++engel #1/A:1285-1320 #1/A:1456-1500

> name rpa190++jaw++tornero #1/A:1260-1360 #1/A:1400-1499

> name rpa190++expander++engel #1/A:1337-1440

> name rpa190++mimickingloop++tornero #1/A:1360-1400

> name rpa190++BH++engel #1/A:991-1051

> name rpa190++BH++Darriere #1/A:1012-1016

> name rpa135++extendedprotrusion #1/B:1-43

> name rpa135++nter #1/B:1-42

> name rpa135++protrusion++engel #1/B:43-209 #1/B:400-469

> name rpa135++protrusion++tornero #1/B:42-210 #1/B:399-470

> name rpa135++lobe++engel #1/B:209-400

> name rpa135++lobe++tornero #1/B:210-399

> name rpa135++fork++engel #1/B:469-553

> name rpa135++fork++tornero #1/B:470-553

> name rpa135++external1++engel #1/B:647-698

> name rpa135++external1++tornero #1/B:649-697

> name rpa135++external2++engel #1/B:553-647

> name rpa135++external2++tornero #1/B:553-649

> name rpa135++hybridbinding++engel #1/B:698-800

> name rpa135++hybridbinding++tornero #1/B:697-800

> name rpa135++wall++engel #1/B:800-910

> name rpa135++wall++tornero #1/B:800-911

> name rpa135++anchor++engel #1/B:1068-1092

> name rpa135++anchor++tornero #1/B:1069-1095

> name rpa135++stalkbinding++tornero #1/B:1095-1170

> name rpa135++clamp++engel #1/B:1092-1203

> name rpa135++clamp++tornero #1/B:1170-1203

> name rpb5++jaw #1/E:1-145

> name rpb5++assembly #1/E:145-215

> name rpb6++tail #1/F:01-72

> name rpb6++assembly #1/F:72-155

> name rpb6++nter++tornero #1/F:55-71

> name rpb8++betabarrel #1/H:01-63 #1/H:96-146

> name rpb8++loop #1/H:63-96

> name rpb10++zincbundle #1/J:1-53

> name rpb10++tail #1/J:53-70

> name rpb12++zincribbon #1/L:1-60

> name rpb12++tail #1/L:60-70

> name ac19++tail #1/K:1-48

> name ac19++dimerization #1/K:49-142

> name ac40++nterextension #1/C:1-31

> name ac40++dimerization #1/C:31-75 #1/C:220-230 #1/C:297-335

> name ac40++domain2 #1/C:75-143 #1/C:168-220

> name ac40++zincloop #1/C:143-168

> name ac40++looptoe #1/C:230-297

> name rpa12++jaw++zincbindingribbon1 #1/I:1-40

> name rpa12++linkerflexible #1/I:40-65

> name rpa12++zincbindingribbon2 #1/I:65-125

> name rpa43++nter #1/G:1-37

> name rpa43++tipdomain #1/G:38-91

> name rpa43++tiploop #1/G:92-113

> name rpa43++obdomain #1/G:114-248

> name rpa43++ctail #1/G:249-326

> name rpa43++connector #1/G:270-313

> name rpa14++nter #1/D:1-21

> name rpa14++tipassociateddomain #1/D:22-96

> name rpa14++linker #1/D:97-137

> name rpa49++nterdimerization #1/M:1-101

> name rpa49++linkerdomain #1/M:102-184

> name rpa49++twh #1/M:185-403

> name rpa49++wh1 #1/M:255-320

> name rpa49++wh2 #1/M:321-403

> name rpa49++cter #1/M:403-415

> name rpa34++nter #1/N:1-22

> name rpa34++dimerizationdomain #1/N:23-144

> name rpa34++ctail #1/N:145-233

executed script-domainssattributionpolI-030720envoyeMichael.cxc  

> isolde start

> set selectionWidth 4

Chain information for 4c2m_2_monomers.cif  
---  
Chain | Description  
1.2/A | DNA-directed RNA polymerase I subunit RPA190  
1.2/B | DNA-directed RNA polymerase I subunit RPA135  
1.2/C | DNA-directed RNA polymerases I and III subunit RPAC1  
1.2/D | DNA-directed RNA polymerase I subunit RPA14  
1.2/E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1  
1.2/F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2  
1.2/G 1.2/O | DNA-directed RNA polymerase I subunit RPA43  
1.2/H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3  
1.2/I | DNA-directed RNA polymerase I subunit RPA12  
1.2/J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5  
1.2/K | DNA-directed RNA polymerases I and III subunit RPAC2  
1.2/L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4  
1.2/M | DNA-directed RNA polymerase I subunit RPA49  
1.2/N | DNA-directed RNA polymerase I subunit RPA34  
  
4c2m_2_monomers.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Done loading forcefield  

> clipper associate #2 toModel #1

> clipper spotlight radius 12.00

> ui tool show "Basic Actions"

> select a++core

11985 atoms, 12201 bonds, 10 pseudobonds, 3 models selected  

> select a++stalk

1989 atoms, 2029 bonds, 2 pseudobonds, 2 models selected  

> view sel

> select #1.2

34700 atoms, 35175 bonds, 42 pseudobonds, 7 models selected  

> select #1.2

34700 atoms, 35175 bonds, 42 pseudobonds, 7 models selected  

> select #1

34700 atoms, 35175 bonds, 42 pseudobonds, 14 models selected  

> select #1

34700 atoms, 35175 bonds, 42 pseudobonds, 14 models selected  

> select #1.2

34700 atoms, 35175 bonds, 42 pseudobonds, 7 models selected  

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> clipper spotlight radius 16.00

> clipper spotlight radius 17.00

> clipper spotlight radius 18.00

> clipper spotlight radius 19.00

> clipper spotlight radius 20.00

> clipper spotlight radius 21.00

> clipper spotlight radius 22.00

> clipper spotlight radius 23.00

> clipper spotlight radius 5.00

> clipper spotlight radius 50.00

> clipper spotlight radius 50.00

> clipper spotlight radius 49.00

> clipper spotlight radius 48.00

> clipper spotlight radius 47.00

> clipper spotlight radius 46.00

> clipper spotlight radius 45.00

> clipper spotlight radius 44.00

> clipper spotlight radius 43.00

> clipper spotlight radius 42.00

> clipper spotlight radius 41.00

> clipper spotlight radius 40.00

> volume #1.1.1.1 level 0.1109

> select a++stalk

1989 atoms, 2029 bonds, 2 pseudobonds, 2 models selected  

> addh

Summary of feedback from adding hydrogens to 4c2m_2_monomers.cif #1.2  
---  
notes | Termini for 4c2m_2_monomers.cif (#1.2) chain A determined from SEQRES
records  
Termini for 4c2m_2_monomers.cif (#1.2) chain B determined from SEQRES records  
Termini for 4c2m_2_monomers.cif (#1.2) chain C determined from SEQRES records  
Termini for 4c2m_2_monomers.cif (#1.2) chain D determined from SEQRES records  
Termini for 4c2m_2_monomers.cif (#1.2) chain E determined from SEQRES records  
10 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A MET 1, /J MET 1  
Chain-initial residues that are not actual N termini: /A SER 174, /A SER 312,
/A ALA 1213, /A ALA 1286, /A PRO 1342, /A ASN 1361, /A ASN 1440, /B PRO 8, /B
ASN 87, /B ILE 1151, /C TRP 31, /D THR 12, /D THR 80, /E GLU 4, /F PRO 55, /G
ALA 14, /G GLY 215, /H ASN 3, /H SER 78, /I SER 2, /K PRO 42, /L LEU 27, /M
SER 8, /N SER 24, /N LYS 49, /N THR 78, /O SER 265  
Chain-final residues that are actual C termini: /A ALA 1664, /B LYS 1203, /C
GLN 335, /E MET 215, /H ARG 146, /I ASN 125, /K MET 142, /L ARG 70  
Chain-final residues that are not actual C termini: /A LEU 141, /A ASP 273, /A
PHE 1205, /A THR 1276, /A THR 1339, /A PRO 1349, /A MET 1395, /B SER 81, /B
LEU 1141, /D GLU 48, /D PRO 100, /F ASP 154, /G HIS 170, /G ILE 250, /H ASN
64, /J ARG 69, /M SER 115, /N ASN 41, /N VAL 72, /N PHE 180, /O GLU 316  
Missing OXT added to C-terminal residue /A ALA 1664  
4575 hydrogen bonds  
Adding 'H' to /A SER 174  
Adding 'H' to /A SER 312  
Adding 'H' to /A ALA 1213  
Adding 'H' to /A ALA 1286  
Adding 'H' to /A ASN 1361  
18 messages similar to the above omitted  
/A LEU 141 is not terminus, removing H atom from 'C'  
/A ASP 273 is not terminus, removing H atom from 'C'  
/A PHE 1205 is not terminus, removing H atom from 'C'  
/A THR 1276 is not terminus, removing H atom from 'C'  
/A THR 1339 is not terminus, removing H atom from 'C'  
16 messages similar to the above omitted  
34911 hydrogens added  
  
Loading residue template for SO4 from internal database  

> select a++stalk

4003 atoms, 4043 bonds, 2 pseudobonds, 2 models selected  

> select a++stalk

4003 atoms, 4043 bonds, 2 pseudobonds, 2 models selected  

> volume #1.1.1.1 level 0.09704

> select rpa14

932 atoms, 935 bonds, 1 pseudobond, 2 models selected  

> select rpa14++linker

62 atoms, 62 bonds, 1 model selected  

> select rpa14++nter

145 atoms, 145 bonds, 1 model selected  

> select rpa14++tipassociateddomain

716 atoms, 720 bonds, 1 pseudobond, 2 models selected  

> select rpa43

3071 atoms, 3108 bonds, 1 pseudobond, 2 models selected  

> select rpa43++ctail

38 atoms, 37 bonds, 1 model selected  

> select rpa43++ctail

38 atoms, 37 bonds, 1 model selected  

> select rpa43++nter

392 atoms, 394 bonds, 1 model selected  

> select rpa43++obdomain

1420 atoms, 1442 bonds, 1 pseudobond, 2 models selected  

> select rpa190++clampcore++engel

4213 atoms, 4246 bonds, 1 model selected  

> select a++clamp

6642 atoms, 6690 bonds, 1 pseudobond, 2 models selected  

> select a++core

23995 atoms, 24211 bonds, 10 pseudobonds, 3 models selected  

> select a++shelf

13213 atoms, 13329 bonds, 1 pseudobond, 2 models selected  

> select a++shelf

13213 atoms, 13329 bonds, 1 pseudobond, 2 models selected  

> select a++jaw

4161 atoms, 4200 bonds, 1 model selected  

> volume #1.1.1.1 level 0.03237

> view sel

> view sel

> view

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.1 models

reverting to start  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\delayed_reaction.py", line 79, in callback  
if self.tf is None or self.tf():  
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.0\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\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.0\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 23.20.16.4973
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: HP
Model: HP EliteBook 850 G5
OS: Microsoft Windows 10 Education (Build 18363)
Memory: 8,425,529,344
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Tristan Croll]

I managed to trigger this myself the other day, but I still have no idea how it happens (I wasn't doing anything unusual). It's clearly a very rare occurrence... seems there's some sort of race condition in my logic. Will dig into it when time permits.

[pett]

Race conditions -- always fun! :-)