![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7642 closed defect (can't reproduce)
Hang in cview
| 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-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
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Hang in cview |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
