Opened 6 years ago

Closed 6 years ago

#2331 closed defect (fixed)

Better session error reporting

Reported by: sfeng-08@… Owned by: Greg Couch
Priority: normal Milestone: 1.0
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.91 (2019-08-16)
Description
RuntimeError: Error while saving session data for "": Residue already deleted

File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 258, in process
raise RuntimeError(msg)

Log:
UCSF ChimeraX version: 0.91 (2019-08-16)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/asus/Desktop/chromatin/fig2/N10_interaction_with_DNA.cxs

opened ChimeraX session  

> open C:/Users/asus/Desktop/chromatin/N1-N12/PDB/N1_N10_compare/N1.pdb

Summary of feedback from opening
C:/Users/asus/Desktop/chromatin/N1-N12/PDB/N1_N10_compare/N1.pdb  
---  
warnings | Ignored bad PDB record found on line 14737  
END  
  
Start residue of secondary structure not found: HELIX 1 1 VAL l 27 LYS l 36 1
10  
Start residue of secondary structure not found: HELIX 2 2 GLY l 46 ASP l 72 1
27  
Start residue of secondary structure not found: HELIX 3 3 PRO l 80 ASN l 89 1
10  
Start residue of secondary structure not found: HELIX 4 4 GLU l 91 LEU l 96 1
6  
Start residue of secondary structure not found: HELIX 5 5 SER l 113 LEU l 115
1 3  
40 messages similar to the above omitted  
  
Chain information for N1.pdb  
---  
Chain | Description  
7.7/B | No description available  
7.3/D | No description available  
7.5/E | No description available  
7.9/E | No description available  
7.2/Y | No description available  
7.4/e | No description available  
7.8/j | No description available  
7.1/l | No description available  
7.6/q | No description available  
7.10/s | No description available  
7.10/t | No description available  
  

> toolshed show "Fit in Map"

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!7 models

> show #!7 models

> select #1

8210 atoms, 9106 bonds, 3 models selected  

> select #2

1448 atoms, 1464 bonds, 3 models selected  

> select #1

8210 atoms, 9106 bonds, 3 models selected  

> ~select #1

Nothing selected  

> select #7

14608 atoms, 15543 bonds, 2 pseudobonds, 12 models selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode translate

> ui mousemode rightMode translate

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> select clear

> cartoon style protein modeHelix tube radius 2 sides 24

> select clear

> hide #!7.10 models

> show #!7.10 models

> hide #!7.10 models

> show #!7.10 models

> show #!6 models

> hide #!6 models

> hide #!7.10 models

> show #!7.10 models

> hide #!7.9 models

> show #!7.9 models

> hide #!7.9 models

> show #!7.9 models

> hide #!7 models

> ~colordef #1.2/A:227-230 medium blue target r

Expected fewer arguments  

> ~colordef #1.2/A:227-230 medium blue target r

Expected fewer arguments  

> ~colordef #1.2/A:227-230 medium blue target r

Expected fewer arguments  

> hide #!1.2 models

> show #!1.2 models

> toolshed show "Side View"

> lighting simple

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

Unknown command: lightiing gentle  

> lighting gentle

> lighting gentle

> lighting gentle

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting gentle

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting simple

> lighting simple

> lighting simple

> hide #!1.1 models

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> show sel surfaces

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> style sel stick

Changed 61 atom styles  

> style sel sphere

Changed 61 atom styles  

> hide sel surfaces

> show sel atoms

> show sel surfaces

> style sel stick

Changed 61 atom styles  

> hide sel atoms

> color sel byhetero

> show #!1.1 models

> hide sel atoms

> hide sel surfaces

> select clear

> select #5.1/U:4123

6 atoms, 5 bonds, 1 model selected  

> color sel byhetero

> show sel surfaces

> hide sel surfaces

> show sel atoms

> select clear

> select clear

> hide sel atoms

> show sel surfaces

> select #5

1837 atoms, 1857 bonds, 3 models selected  

> ~select #5

1 model selected  

> hide #1.1-2 #2.1-2 #3.1-2 #4.1-2 #5.1,2 surfaces

> show #1.1-2 #2.1-2 #3.1-2 #4.1-2 #5.1,2 cartoons

> select clear

> show sel atoms

> style sel sphere

Changed 12 atom styles  

> style sel ball

Changed 12 atom styles  

> style sel sphere

Changed 12 atom styles  

> style sel ball

Changed 37 atom styles  

> style sel sphere

Changed 37 atom styles  

> show sel atoms

> style sel sphere

Changed 37 atom styles  

> select clear

> save session
C:/Users/asus/Desktop/chromatin/fig2/N1_N10_H2A-H5_interaction_compare.cxs

> lighting simple

> lighting soft

> lighting full

> lighting soft

> save image
C:/Users/asus/Desktop/染色质相关/fig2/N10_H2A-H5_interaction_compare.tif width 2000
height 1500 supersample 3

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> show #!7 models

> select #7.10/t:2207

21 atoms, 23 bonds, 1 model selected  

> select up

3472 atoms, 3889 bonds, 1 model selected  

> show sel cartoons

> select clear

> toolshed show "Side View"

> open C:/Users/asus/Desktop/chromatin/N1-N12/PDB/N1_DNA.pdb

Summary of feedback from opening
C:/Users/asus/Desktop/chromatin/N1-N12/PDB/N1_DNA.pdb  
---  
warning | Ignored bad PDB record found on line 15193  
END  
  
N1_DNA.pdb title:  
\--- [more info...]  
  
Chain information for N1_DNA.pdb #8  
---  
Chain | Description  
s | No description available  
t | No description available  
  

> toolshed show "Fit in Map"

> color #7.1-9,10 #8 bynucleotide

> close #8

> open C:/Users/asus/Desktop/chromatin/N1-N12/PDB/N1_DNA.pdb

Summary of feedback from opening
C:/Users/asus/Desktop/chromatin/N1-N12/PDB/N1_DNA.pdb  
---  
warning | Ignored bad PDB record found on line 14126  
END  
  
N1_DNA.pdb title:  
\--- [more info...]  
  
Chain information for N1_DNA.pdb #8  
---  
Chain | Description  
s | No description available  
t | No description available  
  

> hide #!7.10 models

> show #!7.10 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> close #7

> open C:/Users/asus/Desktop/chromatin/N1-N12/PDB/N1_N10_compare/N1.pdb

Summary of feedback from opening
C:/Users/asus/Desktop/chromatin/N1-N12/PDB/N1_N10_compare/N1.pdb  
---  
warnings | Ignored bad PDB record found on line 14737  
END  
  
Start residue of secondary structure not found: HELIX 1 1 VAL l 27 LYS l 36 1
10  
Start residue of secondary structure not found: HELIX 2 2 GLY l 46 ASP l 72 1
27  
Start residue of secondary structure not found: HELIX 3 3 PRO l 80 ASN l 89 1
10  
Start residue of secondary structure not found: HELIX 4 4 GLU l 91 LEU l 96 1
6  
Start residue of secondary structure not found: HELIX 5 5 SER l 113 LEU l 115
1 3  
40 messages similar to the above omitted  
  
Chain information for N1.pdb  
---  
Chain | Description  
7.7/B | No description available  
7.3/D | No description available  
7.5/E | No description available  
7.9/E | No description available  
7.2/Y | No description available  
7.4/e | No description available  
7.8/j | No description available  
7.1/l | No description available  
7.6/q | No description available  
7.10/s | No description available  
7.10/t | No description available  
  

> hide #!7.10 models

> show #!7.10 models

> select #7.10

6921 atoms, 7759 bonds, 2 pseudobonds, 2 models selected  

> close #7.10

> cartoon style protein modeHelix tube radius 2 sides 24

> hide #!7.1 models

> show #!7.1 models

> select clear

> toolshed show "Side View"

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting flat

> lighting shadows true intensity 0.5

> set silhouettes false

> lighting full

> lighting soft

> lighting simple

> lighting soft

> save session
C:/Users/asus/Desktop/chromatin/fig2/N1_N10_H2A-H5_interaction_compare.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 631, in take_snapshot  
data = {'structure': self.structure,  
File "cymol.pyx", line 1378, 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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 769, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 532, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 631, in take_snapshot  
data = {'structure': self.structure,  
File "cymol.pyx", line 1378, 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 "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 871, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 601, in file_save_cb  
self.save_dialog.display(self, session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 138, in display  
fmt.save(session, filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 1062, in save  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 956, in save_session  
save(session, filename, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 213, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 769, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 532, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\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 431.60
OpenGL renderer: GeForce 930MX/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by pett, 6 years ago

Component: Unassigned → Sessions
Milestone: → 1.0
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Better session error reporting

Greg,

Despite the fact that there is a dead residue in the session data being saved, there is no good indication in the session error message exactly _what_ was trying to save that residue in its session data, making debugging this problem much, much harder.

comment:2 by Greg Couch, 6 years ago

Resolution: → fixed
Status: assigned → closed

Added code to keep track of where data is saved from in a session, and to print the stack when an error occurs.

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