Problem updating parameters

[ym337@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.93 (2020-04-03)
Description
I was just simulating about 30 amino acids (a helix), and residues around it, for a while, using ISOLDE. The software just crashed and refused to run any more simulations with the following error (screenshot attached).


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  

> open
> C:/Users/yai25/OneDrive/Desktop/Pendrive_March2020/Kraken_20March_2020/Maps_Models_suffolk_/CIII_cytC_job1613/375_box_0Bfactor_1048pix_postprocess_job1613.mrc

Opened 375_box_0Bfactor_1048pix_postprocess_job1613.mrc, grid size
375,375,375, pixel 1.05, shown at level 0.0119, step 2, values float32  

> open
> C:/Users/yai25/OneDrive/Desktop/Pendrive_March2020/Kraken_20March_2020/Maps_Models_suffolk_/CIII_cytC_job1613/375_box_Default_Bfactor_1048pix_postprocess_job1613.mrc

Opened 375_box_Default_Bfactor_1048pix_postprocess_job1613.mrc, grid size
375,375,375, pixel 1.05, shown at level 0.0163, step 2, values float32  

> open
> C:/Users/yai25/OneDrive/Desktop/Pendrive_March2020/Kraken_20March_2020/Maps_Models_suffolk_/CIII_cytC_job1613/RealSpaceRefined/RealSpaceRefined_44/CIII_NoSecStructure_real_space_refined.cif

Summary of feedback from opening
C:/Users/yai25/OneDrive/Desktop/Pendrive_March2020/Kraken_20March_2020/Maps_Models_suffolk_/CIII_cytC_job1613/RealSpaceRefined/RealSpaceRefined_44/CIII_NoSecStructure_real_space_refined.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 152  
Missing entity information. Treating each chain as a separate entity.  
Missing first residue in struct_conn "C00001"  
Missing first residue in struct_conn "C00002"  
Missing first residue in struct_conn "C00003"  
Missing first residue in struct_conn "C00004"  
Missing first residue in struct_conn "C00005"  
26 messages similar to the above omitted  
Atom H1 is not in the residue template for ALA #212 in chain b  
Atom H1 is not in the residue template for GLY #3 in chain d  
Atom H1 is not in the residue template for ALA #212 in chain e  
Atom H1 is not in the residue template for ASP #22 in chain f  
Atom H1 is not in the residue template for PHE #2 in chain o  
1 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 29829  
Skipping chem_comp category: Missing column 'type' near line 30694  
Skipping chem_comp category: Missing column 'type' near line 31437  
Skipping chem_comp category: Missing column 'type' near line 31996  
Skipping chem_comp category: Missing column 'type' near line 32023  
2 messages similar to the above omitted  
notes | Fetching CCD HEM from http://ligand-
expo.rcsb.org/reports/H/HEM/HEM.cif  
Fetching CCD PC1 from http://ligand-expo.rcsb.org/reports/P/PC1/PC1.cif  
Fetching CCD 3PH from http://ligand-expo.rcsb.org/reports/3/3PH/3PH.cif  
Fetching CCD HEC from http://ligand-expo.rcsb.org/reports/H/HEC/HEC.cif  
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif  
Fetching CCD FES from http://ligand-expo.rcsb.org/reports/F/FES/FES.cif  
Fetching CCD 3PE from http://ligand-expo.rcsb.org/reports/3/3PE/3PE.cif  
  
Chain information for CIII_NoSecStructure_real_space_refined.cif #3  
---  
Chain | Description  
a | No description available  
b e | No description available  
c | No description available  
d | No description available  
f | No description available  
o | No description available  
p | No description available  
y z | No description available  
  

> isolde start

> set selectionWidth 4

Chain information for CIII_NoSecStructure_real_space_refined.cif  
---  
Chain | Description  
3.2/a | No description available  
3.2/b 3.2/e | No description available  
3.2/c | No description available  
3.2/d | No description available  
3.2/f | No description available  
3.2/o | No description available  
3.2/p | No description available  
3.2/y 3.2/z | No description available  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
Done loading forcefield  

> isolde start

> set bgColor white

> open C:\Users\yai25/Downloads/ISOLDE_Related/preflight.py

Fetching CCD SF4 from http://ligand-expo.rcsb.org/reports/S/SF4/SF4.cif  

2 atoms were automatically renamed to match the template: O1A->O2A, O2A->O1A  

2 atoms were automatically renamed to match the template: O1A->O2A, O2A->O1A  

2 atoms were automatically renamed to match the template: O1A->O2A, O2A->O1A  

2 atoms were automatically renamed to match the template: O1A->O2A, O2A->O1A  

Fetching CCD HEA from http://ligand-expo.rcsb.org/reports/H/HEA/HEA.cif  
executed preflight.py  

> hide HC

> select /a

7666 atoms, 7813 bonds, 8 pseudobonds, 2 models selected  
Found iron-sulfur cysteine  
Found iron-sulfur cysteine  
Loading residue template for 3PH from internal database  
reverting to start  

> select clear

> volume #3.1.1.1 level 0.01095

> select clear

> volume #3.1.1.1 level 0.01002

> volume #3.1.1.2 level 0.0165

> volume #3.1.1.2 level 0.02273

> volume #3.1.1.1 level 0.01321

> volume #3.1.1.2 level 0.02533

> volume #3.1.1.2 level 0.01987

> volume #3.1.1.1 level 0.01493

> volume #3.1.1.2 level 0.02639

> volume #3.1.1.2 level 0.02322

> volume #3.1.1.2 level 0.01842

> volume #3.1.1.2 level 0.0261

> volume #3.1.1.1 level 0.01161

> select /a

7666 atoms, 7813 bonds, 8 pseudobonds, 2 models selected  
Found iron-sulfur cysteine  
Found iron-sulfur cysteine  

> select up

176 atoms, 178 bonds, 1 model selected  
Found iron-sulfur cysteine  
Found iron-sulfur cysteine  
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\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1642, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 301, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Error downloading array stepSize: clEnqueueReadBuffer (-5)  
  
Error processing trigger "new frame":  
RuntimeError: Error downloading array stepSize: clEnqueueReadBuffer (-5)  
  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\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.  
  
Traceback (most recent call last):  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2681, in _start_sim_or_toggle_pause  
self.pause_sim_toggle()  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2917, in pause_sim_toggle  
self.sim_manager.toggle_pause()  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 713, in
toggle_pause  
self.pause = not self.pause  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 692, in pause  
self.sim_handler.pause = flag  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1740, in pause  
self._resume()  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1628, in _resume  
self._update_forces_in_context_if_needed()  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1789, in
_update_forces_in_context_if_needed  
f.updateParametersInContext(context)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 9086, in updateParametersInContext  
return _openmm.CustomExternalForce_updateParametersInContext(self, context)  
Exception: Error uploading parameter set customExternalParams:
clEnqueueWriteBuffer (-5)  
  
Exception: Error uploading parameter set customExternalParams:
clEnqueueWriteBuffer (-5)  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 9086, in updateParametersInContext  
return _openmm.CustomExternalForce_updateParametersInContext(self, context)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2681, in _start_sim_or_toggle_pause  
self.pause_sim_toggle()  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2917, in pause_sim_toggle  
self.sim_manager.toggle_pause()  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 713, in
toggle_pause  
self.pause = not self.pause  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 692, in pause  
self.sim_handler.pause = flag  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1740, in pause  
self._resume()  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1628, in _resume  
self._update_forces_in_context_if_needed()  
File "C:\Users\yai25\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1789, in
_update_forces_in_context_if_needed  
f.updateParametersInContext(context)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 9086, in updateParametersInContext  
return _openmm.CustomExternalForce_updateParametersInContext(self, context)  
Exception: Error uploading parameter set customExternalParams:
clEnqueueWriteBuffer (-5)  
  
Exception: Error uploading parameter set customExternalParams:
clEnqueueWriteBuffer (-5)  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 9086, in updateParametersInContext  
return _openmm.CustomExternalForce_updateParametersInContext(self, context)  
  
See log for complete Python traceback.  
  

QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: "data"  




OpenGL version: 3.3.0 NVIDIA 431.94
OpenGL renderer: GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: OMEN by HP Laptop 17-cb0xxx
OS: Microsoft Windows 10 Home (Build 18363)
Memory: 17,050,947,584
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz"
File attachment: ChimeraX-093.jpg

ChimeraX-093.jpg​

[ym337@…]

Added by email2trac

[Tristan Croll]

Same bug as #3251. Will continue discussion there.