id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7642 Hang in cview chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-5.4.0-121-generic-x86_64-with-debian-bullseye-sid ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Errors --- error | Bundle 'ChimeraX-Registration' custom initialization failed warning | Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 342, in initialize api._api_caller.initialize(api, session, self) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1599, in initialize return cls._get_func(api, ""initialize"")(session, bi) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/registration/__init__.py"", line 41, in initialize nag(session) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/registration/nag.py"", line 28, in nag if not check_registration(logger=session.logger): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/registration/nag.py"", line 49, in check_registration return _check_expiration(param, logger) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/registration/nag.py"", line 135, in _check_expiration logger.warning(""Registration file %r has expired"" % reg_file) NameError: name 'reg_file' is not defined 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 rmsf.pdb Summary of feedback from opening rmsf.pdb --- warning | Ignored bad PDB record found on line 2 REMARK THIS IS A SIMULATION BOX rmsf.pdb title: Title [more info...] Chain information for rmsf.pdb #1 --- Chain | Description A E F | No description available B C D | No description available Non-standard residues in rmsf.pdb #1 --- HSD — (HSD) > color bfactor #1 range 1,150 2268 atoms, 2268 residues, atom bfactor range 16.4 to 2.9e+03 > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > show cartoons > color bfactor #1 range 1,300 2268 atoms, 2268 residues, atom bfactor range 16.4 to 2.9e+03 > color bfactor #1 range 1,10 2268 atoms, 2268 residues, atom bfactor range 16.4 to 2.9e+03 > color bfactor #1 range 1,100 2268 atoms, 2268 residues, atom bfactor range 16.4 to 2.9e+03 > open /mnt/sdc1/karunakar/CD4-Gp120-PGT145/MD/C1/gromacs/core-rmsf.pdb Summary of feedback from opening /mnt/sdc1/karunakar/CD4-Gp120-PGT145/MD/C1/gromacs/core-rmsf.pdb --- warning | Ignored bad PDB record found on line 2 REMARK THIS IS A SIMULATION BOX core-rmsf.pdb title: Title [more info...] Chain information for core-rmsf.pdb #2 --- Chain | Description A B C | No description available Non-standard residues in core-rmsf.pdb #2 --- HSD — (HSD) > color bfactor #2 range 1,100 21225 atoms, 1359 residues, atom bfactor range 14.2 to 1.16e+03 > hide #!1 models > color bfactor #2 range 1,150 21225 atoms, 1359 residues, atom bfactor range 14.2 to 1.16e+03 > open /mnt/sdc1/karunakar/CD4-Gp120-PGT145/MD/C2/gromacs/core-rmsf.pdb Summary of feedback from opening /mnt/sdc1/karunakar/CD4-Gp120-PGT145/MD/C2/gromacs/core-rmsf.pdb --- warning | Ignored bad PDB record found on line 2 REMARK THIS IS A SIMULATION BOX core-rmsf.pdb title: Title [more info...] Chain information for core-rmsf.pdb #3 --- Chain | Description A B C | No description available Non-standard residues in core-rmsf.pdb #3 --- HSD — (HSD) > hide #2 models > color bfactor #3 range 1,150 21225 atoms, 1359 residues, atom bfactor range 15.5 to 1.07e+03 > select #2 21225 atoms, 21453 bonds, 1 model selected > show #2 models > ui mousemode right ""translate selected models"" > cview > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > cview > hide #2 models > hide #3 models > show #2 models > ~select #2 Nothing selected > show #3 models > cview > show #!1 models > select #1 2268 atoms, 2196 pseudobonds, 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > cview > ~select #1 Nothing selected > cview > cview > hide #!1 models > cview > cview Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): KeyboardInterrupt KeyboardInterrupt File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): KeyboardInterrupt KeyboardInterrupt File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): KeyboardInterrupt KeyboardInterrupt File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 470.129.06 OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Supermicro Model: SYS-7048GR-TR OS: Ubuntu 20.04 focal Architecture: 64bit ELF CPU: 64 Intel(R) Xeon(R) CPU E5-2683 v4 @ 2.10GHz Cache Size: 40960 KB Memory: total used free shared buff/cache available Mem: 503Gi 4.0Gi 400Gi 52Mi 99Gi 496Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation GP102 [TITAN Xp] [10de:11df] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Third Party can't reproduce all ChimeraX