![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 years ago
Closed 5 years ago
#3971 closed defect (fixed)
'OpenMM_Thread_Handler' object has no attribute '_c_pointer'
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core 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 > /home/kartikmanne/Documents/DH851p3-refine/Repreocess/Repreocess-C1maps/DH851-J575.pdb Chain information for DH851-J575.pdb #1 --- Chain | Description a | No description available b c | No description available d e f | No description available g n r | No description available h m q | No description available i l p | No description available j k o | No description available > set bgColor white > addh Summary of feedback from adding hydrogens to DH851-J575.pdb #1 --- notes | No usable SEQRES records for DH851-J575.pdb (#1) chain a; guessing termini instead No usable SEQRES records for DH851-J575.pdb (#1) chain b; guessing termini instead No usable SEQRES records for DH851-J575.pdb (#1) chain c; guessing termini instead No usable SEQRES records for DH851-J575.pdb (#1) chain d; guessing termini instead No usable SEQRES records for DH851-J575.pdb (#1) chain e; guessing termini instead 13 messages similar to the above omitted Chain-initial residues that are actual N termini: /a ILE 515, /b ALA 512, /c ALA 512, /d GLU 32, /e GLU 32, /f GLU 32, /g ALA 3, /h GLN 1, /i GLN 1, /j ALA 3, /k ALA 3, /l GLN 1, /m GLN 1, /n ALA 3, /o ALA 3, /p GLN 1, /q GLN 1, /r ALA 3 Chain-initial residues that are not actual N termini: /a HIS 564, /b GLN 563, /c GLN 563 Chain-final residues that are actual C termini: /a ASP 664, /b ASP 664, /c ASP 664, /d VAL 505, /e VAL 505, /f VAL 505, /g CYS 211, /h GLY 228, /i GLU 222, /j PRO 208, /k PRO 208, /l GLU 222, /m GLY 228, /n CYS 211, /o PRO 208, /p GLU 222, /q GLY 228, /r CYS 211 Chain-final residues that are not actual C termini: /a LEU 544, /b LEU 544, /c LEU 544 4419 hydrogen bonds Adding 'H' to /a HIS 564 Adding 'H' to /b GLN 563 Adding 'H' to /c GLN 563 /a LEU 544 is not terminus, removing H atom from 'C' /b LEU 544 is not terminus, removing H atom from 'C' /c LEU 544 is not terminus, removing H atom from 'C' 33668 hydrogens added > open > /home/kartikmanne/Documents/DH851p3-refine/Repreocess/Repreocess-C1maps/cryosparc_P56_J575_007_volume_map_sharp.mrc Opened cryosparc_P56_J575_007_volume_map_sharp.mrc, grid size 384,384,384, pixel 1.07, shown at level 0.728, step 2, values float32 > clipper associate #2 toModel #1 Chain information for DH851-J575.pdb --- Chain | Description 1.2/a | No description available 1.2/b 1.2/c | No description available 1.2/d 1.2/e 1.2/f | No description available 1.2/g 1.2/n 1.2/r | No description available 1.2/h 1.2/m 1.2/q | No description available 1.2/i 1.2/l 1.2/p | No description available 1.2/j 1.2/k 1.2/o | No description available > ui tool show ISOLDE > set selectionWidth 4 Done loading forcefield > clipper spotlight radius 32.00 > clipper spotlight radius 32.00 > select #1 67913 atoms, 68764 bonds, 6 pseudobonds, 13 models selected Deleted the following atoms from residue NAG e517: H12, H11 Deleted the following atoms from residue NAG d524: H12, HO4, H11 Deleted the following atoms from residue NAG d506: H12, H11 Deleted the following atoms from residue NAG c667: H12, H11, HO4 Deleted the following atoms from residue NAG c665: H11, H12 Deleted the following atoms from residue NAG b665: H11, HO4, H12 Deleted the following atoms from residue NAG a665: H11, H12 > select #1 67903 atoms, 68754 bonds, 6 pseudobonds, 19 models selected > select #1 67906 atoms, 68757 bonds, 6 pseudobonds, 19 models selected Map is too large for fast cubic interpolation on the GPU! Switching to slower, more memory-efficient implementation. > show sel cartoons > hide sel atoms > set bgColor black > set bgColor white > set bgColor white > show sel cartoons > hide sel atoms > style sel sphere Changed 67906 atom styles > show sel atoms > style sel stick Changed 67906 atom styles > style sel ball Changed 67906 atom styles > style sel stick Changed 67906 atom styles > show sel cartoons > hide sel atoms > select clear > show sel atoms > volume #1.1.1.1 level 1.662 > volume #1.1.1.1 level 0.9393 > volume #1.1.1.1 level 0.2828 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > show sel cartoons > hide sel atoms > volume #1.1.1.1 level 0.8727 > show sel atoms > hide sel atoms > select clear > volume #1.1.1.1 level 1.03 > volume #1.1.1.1 level 0.8509 > volume #1.1.1.1 level 1.91 > close session Deleting atomic symmetry model... > open > /home/kartikmanne/Documents/DH851p3-refine/Repreocess/Reprocess-C3maps/RealSpaceRefine_22/DH851-J576-isolde1-delH.pdb- > rsr21_real_space_refined.pdb Chain information for DH851-J576-isolde1-delH.pdb-rsr21_real_space_refined.pdb #1 --- Chain | Description a | No description available b c | No description available d e f | No description available g n r | No description available h m q | No description available i l p | No description available j k o | No description available > set bgColor white > addh Summary of feedback from adding hydrogens to DH851-J576-isolde1-delH.pdb- rsr21_real_space_refined.pdb #1 --- notes | No usable SEQRES records for DH851-J576-isolde1-delH.pdb- rsr21_real_space_refined.pdb (#1) chain a; guessing termini instead No usable SEQRES records for DH851-J576-isolde1-delH.pdb- rsr21_real_space_refined.pdb (#1) chain b; guessing termini instead No usable SEQRES records for DH851-J576-isolde1-delH.pdb- rsr21_real_space_refined.pdb (#1) chain c; guessing termini instead No usable SEQRES records for DH851-J576-isolde1-delH.pdb- rsr21_real_space_refined.pdb (#1) chain d; guessing termini instead No usable SEQRES records for DH851-J576-isolde1-delH.pdb- rsr21_real_space_refined.pdb (#1) chain e; guessing termini instead 13 messages similar to the above omitted Chain-initial residues that are actual N termini: /a ILE 515, /b ALA 512, /c ALA 512, /d GLU 32, /e GLU 32, /f GLU 32, /g ALA 3, /h GLN 1, /i GLN 1, /j ALA 3, /k ALA 3, /l GLN 1, /m GLN 1, /n ALA 3, /o ALA 3, /p GLN 1, /q GLN 1, /r ALA 3 Chain-initial residues that are not actual N termini: /a HIS 564, /b GLN 563, /c GLN 563 Chain-final residues that are actual C termini: /a ASP 664, /b ASP 664, /c ASP 664, /d VAL 505, /e VAL 505, /f VAL 505, /g CYS 211, /h GLY 228, /i GLU 222, /j PRO 208, /k PRO 208, /l GLU 222, /m GLY 228, /n CYS 211, /o PRO 208, /p GLU 222, /q GLY 228, /r CYS 211 Chain-final residues that are not actual C termini: /a LEU 544, /b LEU 544, /c LEU 544 4420 hydrogen bonds Adding 'H' to /a HIS 564 Adding 'H' to /b GLN 563 Adding 'H' to /c GLN 563 /a LEU 544 is not terminus, removing H atom from 'C' /b LEU 544 is not terminus, removing H atom from 'C' /c LEU 544 is not terminus, removing H atom from 'C' 33668 hydrogens added > open > /home/kartikmanne/Documents/DH851p3-refine/Repreocess/Reprocess-C3maps/cryosparc_P56_J576_005_volume_map_sharp.mrc Opened cryosparc_P56_J576_005_volume_map_sharp.mrc, grid size 384,384,384, pixel 1.07, shown at level 0.71, step 2, values float32 > clipper associate #2 toModel #1 Chain information for DH851-J576-isolde1-delH.pdb-rsr21_real_space_refined.pdb --- Chain | Description 1.2/a | No description available 1.2/b 1.2/c | No description available 1.2/d 1.2/e 1.2/f | No description available 1.2/g 1.2/n 1.2/r | No description available 1.2/h 1.2/m 1.2/q | No description available 1.2/i 1.2/l 1.2/p | No description available 1.2/j 1.2/k 1.2/o | No description available > ui tool show ISOLDE > set selectionWidth 4 Done loading forcefield > select #1 67913 atoms, 68764 bonds, 6 pseudobonds, 13 models selected Deleted the following atoms from residue NAG e517: H12, H11 Deleted the following atoms from residue NAG d524: HO4, H12, H11 Deleted the following atoms from residue NAG d506: H12, H11 Deleted the following atoms from residue NAG c667: HO4, H12, H11 Deleted the following atoms from residue NAG c665: H11, H12 Deleted the following atoms from residue NAG b665: HO4, H12, H11 Deleted the following atoms from residue NAG a665: H12, H11 > select #1 67903 atoms, 68754 bonds, 6 pseudobonds, 19 models selected > select #1 67906 atoms, 68757 bonds, 6 pseudobonds, 19 models selected Map is too large for fast cubic interpolation on the GPU! Switching to slower, more memory-efficient implementation. Map is too large for fast cubic interpolation on the GPU! Switching to slower, more memory-efficient implementation. Traceback (most recent call last): File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/delayed_reaction.py", line 79, in callback if self.tf is None or self.tf(): File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/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. Traceback (most recent call last): File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/delayed_reaction.py", line 79, in callback if self.tf is None or self.tf(): File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/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 NVIDIA 430.40 OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: TYAN Model: B7105F48TV8HR-2T-G OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 64 Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz Cache Size: 22528 KB Memory: total used free shared buff/cache available Mem: 187G 13G 165G 173M 8.4G 173G Swap: 9G 0B 9G Graphics: 04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41) Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] Kernel driver in use: ast PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8
Change History (3)
comment:1 by , 5 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'OpenMM_Thread_Handler' object has no attribute '_c_pointer' |
comment:2 by , 5 years ago
comment:3 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Finally tracked down and squished. Will be fixed in the next release.
Note:
See TracTickets
for help on using tickets.
This traceback has been reported a few times now, but I've never been able to reproduce it. Could you provide any extra information on what you did that triggered it?