Opened 6 years ago

Closed 5 years ago

#2785 closed defect (duplicate)

Nucleotides saving deleted Residue

Reported by: lynnettj@… 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:        Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-21)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warnings | 'clip' is a prefix of an existing command 'clipper'  
'rota' is a prefix of an existing command 'rotamers'  
  
UCSF ChimeraX version: 0.91 (2019-09-21)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/postprocess_cl2_5p9_B176_flip.mrc"

Opened postprocess_cl2_5p9_B176_flip.mrc, grid size 256,256,256, pixel 1.06,
shown at level 0.0142, step 1, values float32  

> open "/Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.1.pdb"

Summary of feedback from opening /Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.1.pdb  
---  
warnings | Ignored bad PDB record found on line 3713  
N_BS 123  
  
Ignored bad PDB record found on line 3714  
N_NWC 1  
  
Ignored bad PDB record found on line 3715  
N_WC 48  
  
Ignored bad PDB record found on line 3716  
score -2513.84  
  
Ignored bad PDB record found on line 3717  
silent_score -2513.84  
  
1 messages similar to the above omitted  
  
Chain information for anticodon_tRNA_model.out.1.pdb #2  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> open "/Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.2.pdb"

Summary of feedback from opening /Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.2.pdb  
---  
warnings | Ignored bad PDB record found on line 3713  
N_BS 120  
  
Ignored bad PDB record found on line 3714  
N_NWC 2  
  
Ignored bad PDB record found on line 3715  
N_WC 47  
  
Ignored bad PDB record found on line 3716  
score -2510.54  
  
Ignored bad PDB record found on line 3717  
silent_score -2510.54  
  
1 messages similar to the above omitted  
  
Chain information for anticodon_tRNA_model.out.2.pdb #3  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> open "/Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.3.pdb"

Summary of feedback from opening /Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.3.pdb  
---  
warnings | Ignored bad PDB record found on line 3713  
N_BS 124  
  
Ignored bad PDB record found on line 3714  
N_NWC 2  
  
Ignored bad PDB record found on line 3715  
N_WC 45  
  
Ignored bad PDB record found on line 3716  
score -2503.31  
  
Ignored bad PDB record found on line 3717  
silent_score -2503.31  
  
1 messages similar to the above omitted  
  
Chain information for anticodon_tRNA_model.out.3.pdb #4  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> open "/Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.4.pdb"

Summary of feedback from opening /Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.4.pdb  
---  
warnings | Ignored bad PDB record found on line 3713  
N_BS 125  
  
Ignored bad PDB record found on line 3714  
N_NWC 1  
  
Ignored bad PDB record found on line 3715  
N_WC 48  
  
Ignored bad PDB record found on line 3716  
score -2495.55  
  
Ignored bad PDB record found on line 3717  
silent_score -2495.55  
  
1 messages similar to the above omitted  
  
Chain information for anticodon_tRNA_model.out.4.pdb #5  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> open "/Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.5.pdb"

Summary of feedback from opening /Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.5.pdb  
---  
warnings | Ignored bad PDB record found on line 3713  
N_BS 120  
  
Ignored bad PDB record found on line 3714  
N_NWC 2  
  
Ignored bad PDB record found on line 3715  
N_WC 47  
  
Ignored bad PDB record found on line 3716  
score -2493.67  
  
Ignored bad PDB record found on line 3717  
silent_score -2493.67  
  
1 messages similar to the above omitted  
  
Chain information for anticodon_tRNA_model.out.5.pdb #6  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> open "/Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.6.pdb"

Summary of feedback from opening /Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.6.pdb  
---  
warnings | Ignored bad PDB record found on line 3713  
N_BS 115  
  
Ignored bad PDB record found on line 3714  
N_NWC 1  
  
Ignored bad PDB record found on line 3715  
N_WC 45  
  
Ignored bad PDB record found on line 3716  
score -2493  
  
Ignored bad PDB record found on line 3717  
silent_score -2493  
  
1 messages similar to the above omitted  
  
Chain information for anticodon_tRNA_model.out.6.pdb #7  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> open "/Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.7.pdb"

Summary of feedback from opening /Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.7.pdb  
---  
warnings | Ignored bad PDB record found on line 3713  
N_BS 122  
  
Ignored bad PDB record found on line 3714  
N_NWC 4  
  
Ignored bad PDB record found on line 3715  
N_WC 44  
  
Ignored bad PDB record found on line 3716  
score -2492.93  
  
Ignored bad PDB record found on line 3717  
silent_score -2492.93  
  
1 messages similar to the above omitted  
  
Chain information for anticodon_tRNA_model.out.7.pdb #8  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> open "/Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.8.pdb"

Summary of feedback from opening /Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.8.pdb  
---  
warnings | Ignored bad PDB record found on line 3713  
N_BS 122  
  
Ignored bad PDB record found on line 3714  
N_NWC 2  
  
Ignored bad PDB record found on line 3715  
N_WC 44  
  
Ignored bad PDB record found on line 3716  
score -2490.84  
  
Ignored bad PDB record found on line 3717  
silent_score -2490.84  
  
1 messages similar to the above omitted  
  
Chain information for anticodon_tRNA_model.out.8.pdb #9  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> open "/Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.9.pdb"

Summary of feedback from opening /Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.9.pdb  
---  
warnings | Ignored bad PDB record found on line 3713  
N_BS 120  
  
Ignored bad PDB record found on line 3714  
N_NWC 1  
  
Ignored bad PDB record found on line 3715  
N_WC 44  
  
Ignored bad PDB record found on line 3716  
score -2490.68  
  
Ignored bad PDB record found on line 3717  
silent_score -2490.68  
  
1 messages similar to the above omitted  
  
Chain information for anticodon_tRNA_model.out.9.pdb #10  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> open "/Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.10.pdb"

Summary of feedback from opening /Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus6/anticodon_tRNA_model_class5/models_06-24-19/anticodon_tRNA_model.out.10.pdb  
---  
warnings | Ignored bad PDB record found on line 3713  
N_BS 117  
  
Ignored bad PDB record found on line 3714  
N_NWC 2  
  
Ignored bad PDB record found on line 3715  
N_WC 47  
  
Ignored bad PDB record found on line 3716  
score -2490.47  
  
Ignored bad PDB record found on line 3717  
silent_score -2490.47  
  
1 messages similar to the above omitted  
  
Chain information for anticodon_tRNA_model.out.10.pdb #11  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> set bgColor white

> hide #!2 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> hide #!11 models

> hide #!8 models

> hide #!4 models

> hide #!5 models

> hide #!7 models

> hide #!3 models

> hide #!1 models

> show #!1 models

> hide #!6 models

> show #!6 models

> hide #!9 models

> show #!2 models

> hide #!6 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> show #!5 models

> hide #!4 models

> show #!6 models

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> hide #!7 models

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> show #!11 models

> hide #!11 models

> close #2-4

> close #7-11

> hide #!6 models

> nucleotides #5 fill

> style nucleic & #5 stick

Changed 3710 atom styles  

> save image "/Users/lynnettj/Documents/Grad School/Research/Figures/KK
anticodon tRNA plus6 model.png" width 864 height 698

> save session "/Users/lynnettj/Documents/Grad School/Research/Slide
decks/2020-01-29_LNJ_Group_Meeting_plus6_KKmodels.cxs"

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 794, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 278, in process  
msg = 'Error while saving session data for %s: %s' % (_obj_chain(parents,
obj), e)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 199, in _obj_chain  
if hasattr(o, 'name'):  
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 601, in file_save_cb  
self.save_dialog.display(self, session)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 138, in display  
fmt.save(session, filename)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1089, in save  
run(session, cmd)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 981, in save_session  
save(session, filename, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 220, in export  
result = self.export_func(session, path, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 794, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 278, in process  
msg = 'Error while saving session data for %s: %s' % (_obj_chain(parents,
obj), e)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 199, in _obj_chain  
if hasattr(o, 'name'):  
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.3.9
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

Change History (2)

comment:1 by pett, 6 years ago

Component: Unassigned → Sessions
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Nucleotides saving deleted Residue

Reproducible with a somewhat simpler recipe, namely:

open 1bna
open 1bna
open 1bna
close #1
close #3
nucleotides #2 fill
style nucleic & #2 stick
save ~/Desktop/out.cxs

Might be possible to reduce that even further. Anyway, that results in the error:

RuntimeError: Error while saving session data for 'nucleotides' -> <chimerax.atomic.nucleotides._data.NucleotideState object at 0x12bca9450> -> <chimerax.atomic.molobject.Residue object at 0x136bdd0f0>

Bug reported by Lynette Jackson

comment:2 by Greg Couch, 5 years ago

Resolution: → duplicate
Status: assigned → closed

Duplicate of #2955. And fixed!

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