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Opened 6 years ago
Closed 6 years ago
#2792 closed defect (can't reproduce)
Attempt to save dead Residue in session
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.4.0-173-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.91 (2019-06-29)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.91 (2019-06-29)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /data/disk3/modeling/Figure4-20200115.cxs format session
Summary of feedback from opening /data/disk3/modeling/Figure4-20200115.cxs
---
notes | 2 headers
opened ChimeraX session
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!21 models
> hide #!21 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!11 models
> show #!11 models
> hide #!13 models
> show #!13 models
> select #13
7998 atoms, 8118 bonds, 1 model selected
> select clear
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> show #!6 models
> select #6
2 models selected
> save /data/disk3/modeling/gp12/genome-inside-channel.mrc models #6
> hide #!16 models
> show #!16 models
> hide #!16.1 models
> hide #!16 models
> show #!16 models
> show #!16.1 models
> select #16
566 atoms, 544 bonds, 3 models selected
> select #18
566 atoms, 544 bonds, 3 models selected
> hide #!16 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> hide #!18 models
> show #!19 models
> show #!18 models
> show #!16 models
Unknown command: combine #16 #18 #19 #24
> hide #!24 models
> show #!24 models
> save pdb #16 #18 #19 #24 /data/disk3/modeling/gp12
Missing filename suffix pdb
Expected a keyword
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> show #!16 models
> select clear
Expected a keyword
Expected a keyword
Invalid "models" argument: only initial part "/data/disk3/modeling/gp12/dsDNA-
model" of atom specifier valid
Invalid "displayedOnly" argument: Expected true or false (or 1 or 0)
Invalid "displayedOnly" argument: Expected true or false (or 1 or 0)
Invalid "displayedOnly" argument: Expected true or false (or 1 or 0)
Invalid "displayedOnly" argument: Expected true or false (or 1 or 0)
Expected a keyword
Invalid "displayedOnly" argument: Expected true or false (or 1 or 0)
Expected a models specifier or a keyword
Expected a models specifier or a keyword
Expected a models specifier or a keyword
Expected a models specifier or a keyword
Expected a models specifier or a keyword
> show #!11 models
> show #!12 models
> open /data/disk3/modeling/gp12/gp12-dim-chan.pdb
Chain information for gp12-dim-chan.pdb #25
---
Chain | Description
b f | No description available
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!12 models
> show #!12 models
> matchmaker #25 to #12
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker gp12-dimmer.pdb, chain c (#12) with gp12-dim-chan.pdb, chain b
(#25), sequence alignment score = 3705.4
RMSD between 783 pruned atom pairs is 0.485 angstroms; (across all 784 pairs:
0.496)
> hide #!12 models
> select #25
12504 atoms, 12824 bonds, 2 pseudobonds, 2 models selected
> select clear
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!8 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!13 models
> show #!14 models
> show #!15 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!10 models
> hide #!10 models
> open /data/disk3/modeling/gp8/gp8-6R21-C2.pdb
Chain information for gp8-6R21-C2.pdb #26
---
Chain | Description
F L | No description available
> hide #!26 models
> show #!26 models
> hide #!13 models
> show #!13 models
> matchmaker #26 to #13
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker gp8-dimmer.pdb, chain A (#13) with gp8-6R21-C2.pdb, chain F (#26),
sequence alignment score = 2210
RMSD between 369 pruned atom pairs is 0.691 angstroms; (across all 482 pairs:
5.378)
> hide #!15 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> open /data/disk3/modeling/gp8/gp8-6R21-C2.pdb
Chain information for gp8-6R21-C2.pdb #28
---
Chain | Description
F L | No description available
> hide #!28 models
> show #!28 models
> matchmaker #28 to #26
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker gp8-6R21-C2.pdb, chain F (#26) with gp8-6R21-C2.pdb, chain F (#28),
sequence alignment score = 2443.9
RMSD between 483 pruned atom pairs is 0.000 angstroms; (across all 483 pairs:
0.000)
> hide #!28 models
> show #!28 models
> hide #!26 models
> select #28
7560 atoms, 7680 bonds, 1 model selected
> show selAtoms surfaces
> hide #!24 models
> show #!24 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> open /data/disk3/modeling/gp12/gp12-dim-chan.pdb
Chain information for gp12-dim-chan.pdb #31
---
Chain | Description
b f | No description available
> hide #!28 models
> show #!28 models
> hide #!28 models
> show #!28 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> matchmaker #31 to #25
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker gp12-dim-chan.pdb, chain b (#25) with gp12-dim-chan.pdb, chain b
(#31), sequence alignment score = 3980.2
RMSD between 784 pruned atom pairs is 0.000 angstroms; (across all 784 pairs:
0.000)
> select #31
12504 atoms, 12824 bonds, 2 pseudobonds, 2 models selected
> show selAtoms surfaces
> transparency #31 80
> hide #!25 models
> show #!25 models
> hide #!25 models
> transparency #31 80
> show #!25 models
> select clear
> transparency #31 70
> select clear
> transparency #31 70
> transparency #31 70
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> transparency #14 70
> transparency #31 70
> select clear
> show #!12 models
> hide #!12 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> show #!28 models
> transparency #28 70
> show #!26 models
> select clear
> show #!6 models
> select #6
2 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> open /data/disk3/modeling/gp12/genome-inside-channel.mrc
Opened genome-inside-channel.mrc, grid size 400,400,400, pixel 1.05, shown at
level -7.94e-18, step 2, values float32
> view cofr false
> select #86
3 models selected
> show #!86 models
> select #32
2 models selected
> ~select #32
Nothing selected
> hide #!86 models
> select #32
2 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> select clear
> ui mousemode rightMode "translate selected models"
> select #32
2 models selected
> select clear
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> select #32
2 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> select clear
> select #6
2 models selected
> select clear
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> select #18
566 atoms, 544 bonds, 3 models selected
> ui mousemode rightMode "translate selected models"
> close #18
> open /data/disk3/modeling/gp12/dsDNA-model1.pdb
Chain information for dsDNA-model1.pdb
---
Chain | Description
18.3/A 18.19/A 18.19/D 18.19/E 18.19/F 18.19/G 18.19/H | No description
available
18.4/A 18.22/B 18.23/B | No description available
18.5/A 18.8/A 18.9/A 18.10/A 18.11/A 18.12/A 18.13/A 18.14/A 18.15/A 18.16/A
18.17/A 18.18/A | No description available
18.24/A 18.25/A 18.25/B 18.3/C 18.19/C 18.24/C 18.25/C 18.19/N 18.19/O 18.19/P
18.19/Q 18.19/R | No description available
18.26/A 18.28/A 18.30/A 18.32/A 18.27/B 18.29/B 18.31/B 18.33/B | No
description available
18.3/B 18.19/B 18.19/I 18.19/J 18.19/K 18.19/L 18.19/M | No description
available
18.6/B 18.8/B 18.9/B 18.10/B 18.11/B 18.12/B 18.13/B 18.14/B 18.15/B 18.16/B
18.17/B 18.18/B 18.7/C 18.8/C 18.9/C 18.10/C 18.11/C 18.12/C 18.13/C 18.14/C
18.15/C 18.16/C 18.17/C 18.18/C | No description available
18.24/B | No description available
18.24/D | No description available
18.1/T | No description available
18.1/U | No description available
18.2/a 18.20/a 18.20/b 18.21/b 18.20/c 18.20/d 18.20/e 18.20/f 18.21/f | No
description available
> hide #!18.28 models
> hide #!18.29 models
> show #!18.29 models
> hide #18.1,3,5-7,2,4 target m
> hide #18.8-19,20,21,22,23 target m
> hide #!18.24 models
> hide #!18.25 models
> hide #!18.26 models
> show #!18.26 models
> hide #!18.26 models
> show #!18.26 models
> show #!18.25 models
> hide #!18.25 models
> show #!18.28 models
> hide #18.1,3,5-19,25,2,4,20,21,22,23,24 target m
> close #18.1,3,5-19,25,2,4,20,21,22,23,24
> select #18
2264 atoms, 2176 bonds, 9 models selected
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> select #16
566 atoms, 544 bonds, 3 models selected
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!24 models
> show #!24 models
> select #24
566 atoms, 544 bonds, 3 models selected
> ui mousemode rightMode "translate selected models"
> select clear
> show #!19 models
> select #18
2264 atoms, 2176 bonds, 9 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "rotate selected models"
> select clear
> select clear
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> select #19
566 atoms, 544 bonds, 3 models selected
> ui mousemode rightMode "translate selected models"
> select #24
566 atoms, 544 bonds, 3 models selected
> select #16
566 atoms, 544 bonds, 3 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> select #19
566 atoms, 544 bonds, 3 models selected
> select #24
566 atoms, 544 bonds, 3 models selected
> ui mousemode rightMode "translate selected models"
> select clear
> select #32
2 models selected
> select clear
> save session /data/disk3/modeling/gp12/Figure7new-20200202-channel-open.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 631, in take_snapshot
data = {'structure': self.structure,
File "cymol.pyx", line 1355, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 763, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 532, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 234, in discovery
self.processed[key] = self.process(obj)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process
raise RuntimeError(msg)
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.molobject.Residue'>": Residue already deleted
RuntimeError: Error while saving session data for "": Residue already deleted
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process
raise RuntimeError(msg)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 631, in take_snapshot
data = {'structure': self.structure,
File "cymol.pyx", line 1355, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 855, in <lambda>
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 595, in file_save_cb
self.save_dialog.display(self, session)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 138, in display
fmt.save(session, filename)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 1056, in save
run(session, cmd)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2641, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 950, in save_session
save(session, filename, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save
fmt.export(session, filename, fmt.nicknames[0], **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/io.py", line 213, in export
result = self.export_func(session, path, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 763, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 532, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 234, in discovery
self.processed[key] = self.process(obj)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process
raise RuntimeError(msg)
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.molobject.Residue'>": Residue already deleted
RuntimeError: Error while saving session data for "": Residue already deleted
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process
raise RuntimeError(msg)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 384.130
OpenGL renderer: Quadro K2200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Attempt to save dead Residue in session |
comment:2 by , 6 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Bug from version before code to provide more extensive error information was added.