Opened 6 years ago

Closed 6 years ago

Last modified 6 years ago

#2988 closed defect (duplicate)

Session save: 'NoneType' object has no attribute 'array'

Reported by: Fengwei.Zheng@… Owned by: Eric Pettersen
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-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-23)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warnings | No presets found in custom preset folder
/Users/fengwei.zheng/Documents/Draft_PolD/Figure  
No presets found in custom preset folder
/Users/fengwei.zheng/Documents/Draft_PolD/Session  
  
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2b_ystPolDcmplx-
> Pol.cxs format session

opened ChimeraX session  

Expected an objects specifier or a keyword  

> close #2

> name PIP #1/A:997-1003

> select PIP :< 4.5 & #1 & ~PIP

138 atoms, 134 bonds, 1 model selected  

> show sel cartoons

> view sel

> select PIP :< 4.5 & #1

187 atoms, 183 bonds, 1 model selected  

> show sel cartoons

> mlp sel

Map values for surface "409-ystPolDcplx_156-679.pdb_H SES surface": minimum
-28.01, mean -5.135, maximum 24.3  
Map values for surface "409-ystPolDcplx_156-679.pdb_A SES surface": minimum
-29.35, mean -4.544, maximum 25.07  

> undo

> select PIP :< 4.5 & #1 & ~PIP

138 atoms, 134 bonds, 1 model selected  

Expected an atoms specifier or a keyword  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

Unknown command: ~mlp  

> hide surfaces

> select PIP :< 4.5 & #1 & ~PIP

138 atoms, 134 bonds, 1 model selected  

> mlp sel

Map values for surface "409-ystPolDcplx_156-679.pdb_H SES surface": minimum
-28.01, mean -5.135, maximum 24.3  
Map values for surface "409-ystPolDcplx_156-679.pdb_A SES surface": minimum
-29.35, mean -4.544, maximum 25.07  

> close session

> open /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2e_PIP-PCNA.cxs
> format session

opened ChimeraX session  

> hide surfaces

> select PIP :< 4.5 & #1 & ~PIP

138 atoms, 134 bonds, 1 model selected  

> mlp sel

Map values for surface "409-ystPolDcplx_156-679.pdb_H SES surface": minimum
-28.01, mean -5.135, maximum 24.3  
Map values for surface "409-ystPolDcplx_156-679.pdb_A SES surface": minimum
-29.35, mean -4.544, maximum 25.07  

> hide sel

> hide surfaces

> select up

140 atoms, 134 bonds, 3 models selected  

> select PIP :< 4.5 & #1

187 atoms, 183 bonds, 1 model selected  

> open /Users/fengwei.zheng/Documents/Structures/PolD/cryosparc_P3_J409.mrc

Opened cryosparc_P3_J409.mrc, grid size 420,420,420, pixel 0.826, shown at
level 0.0788, step 2, values float32  

> volume #5 step 1

> volume #5 level 0.25

> volume zone #5 nearAtoms sel range 2

> volume #6 style mesh

> volume #6 color gold

> graphics silhouettes false

> undo

> undo

> redo

> redo

> redo

No redo action is available  

> show sel atoms

> style sel stick

Changed 187 atom styles  

> hide sel cartoons

> hide cartoons

> volume #6 level 0.2

> volume #6 level 0.1

> volume #6 level 0.15

Missing or invalid "surfaces" argument: invalid surfaces specifier  

Missing or invalid "surfaces" argument: invalid surfaces specifier  

Missing or invalid "surfaces" argument: empty atom specifier  

Missing or invalid "surfaces" argument: empty atom specifier  

> surface dust #1 size 5

> undo

> open /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2a_ystPolDcmplx-
> Exo.cxs format session

opened ChimeraX session  

> open /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2b_ystPolDcmplx-
> Pol.cxs format session

opened ChimeraX session  

> open /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2e_PIP-PCNA.cxs
> format session

opened ChimeraX session  

> hide surfaces

> name PIP #1/a:997-1003

> name PIP #1/a:997-1003

> select PIP :< 4.5 & #1

187 atoms, 183 bonds, 1 model selected  

> open /Users/fengwei.zheng/Documents/Structures/PolD/cryosparc_P3_J409.mrc

Opened cryosparc_P3_J409.mrc, grid size 420,420,420, pixel 0.826, shown at
level 0.0788, step 2, values float32  

> volume #5 level 0.15

> surface dust #5 size 5

> volume #5 step 1

> surface dust #5 size 5

> surface dust #5 size 5

> volume zone #5 nearAtoms sel range 2

> volume #6 style mesh

> hide cartoons

> surface dust #6

> select PIP :< 4.5 & #1

187 atoms, 183 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 187 atom styles  

> volume #6 color peru

> graphics silhouettes false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> select clear

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> graphics silhouettes false

> lighting simple

> lighting full

> lighting simple

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting simple

> lighting soft

> lighting soft

> lighting simple

> volume #6 level 0.2

> volume #6 level 0.25

> hide #1/H atoms

> close #6

Expected an objects specifier or a keyword  

> select @display

Nothing selected  

> select @@display

1938 atoms, 2095 bonds, 3 models selected  

> hide #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!4 models

> hide #!4 models

> show #!1 models

> select #4

8154 atoms, 7804 bonds, 28 pseudobonds, 3 models selected  

> ~select #4

Nothing selected  

> close #4

> close #3

> close #2

> select @@display

97 atoms, 95 bonds, 1 model selected  

> volume zone #5 nearAtoms sel range 2

> surface dust #2

> volume #2 level 0.25

> volume #2 style mesh

> select clear

> select /A:992@C

1 atom, 1 model selected  

> select up

7 atoms, 6 bonds, 2 models selected  

> select up

138 atoms, 138 bonds, 2 models selected  

> select clear

> select clear

> select up

2 atoms, 1 bond, 1 model selected  

> select up

7 atoms, 6 bonds, 2 models selected  

> select up

138 atoms, 138 bonds, 2 models selected  

> select clear

> hide #1/992-993

> hide #1/992-993 atoms

> hide #1/A:992-993

> close #2

> undo

> redo

> select @@disp

16769 atoms, 17166 bonds, 42 pseudobonds, 3 models selected  

> hide cartoons

> select @@disp

16769 atoms, 17166 bonds, 42 pseudobonds, 3 models selected  

> select clear

> select /A:1104@ZN

1 atom, 1 model selected  

> hide ions

> volume zone #5 nearAtoms sel range 2

> surface dust #2

> volume #2 style mesh

> volume #2 level 0.2

> volume #2 level 0.25

> volume #2 level 0.35

> volume #2 level 0.3

> volume #2 level 0.25

> volume #2 level 0.2

> select clear

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting simple

> color #2 #cd853f

> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2e_PIP-
> mesh.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2391, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 159, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-0.91.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-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12e0a49d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x137e871d0>
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2391, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 159, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 911, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 641, in file_save_cb  
self.save_dialog.display(self, session)  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 139, in display  
fmt.save(session, filename)  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1100, in save  
run(session, cmd)  
File
"/Applications/ChimeraX-0.91.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-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 992, in save_session  
save(session, filename, **kw)  
File
"/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 229, in export  
result = self.export_func(session, path, **kw)  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-0.91.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-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12e0a49d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x137e871d0>
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  

> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2e_PIP-
> mesh.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2391, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 159, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-0.91.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-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12e0a49d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x137e871d0>
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2391, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 159, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 911, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 641, in file_save_cb  
self.save_dialog.display(self, session)  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 139, in display  
fmt.save(session, filename)  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1100, in save  
run(session, cmd)  
File
"/Applications/ChimeraX-0.91.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-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 992, in save_session  
save(session, filename, **kw)  
File
"/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 229, in export  
result = self.export_func(session, path, **kw)  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-0.91.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-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12e0a49d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x137e871d0>
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  

> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2e_PIP-
> mesh.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2391, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 159, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-0.91.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-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12e0a49d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x137e871d0>
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2391, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 159, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 911, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 641, in file_save_cb  
self.save_dialog.display(self, session)  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 139, in display  
fmt.save(session, filename)  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1100, in save  
run(session, cmd)  
File
"/Applications/ChimeraX-0.91.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-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 992, in save_session  
save(session, filename, **kw)  
File
"/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 229, in export  
result = self.export_func(session, path, **kw)  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-0.91.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-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12e0a49d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x137e871d0>
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  

> save session
> /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2e_PIP_mesh.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2391, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 159, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-0.91.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-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12e0a49d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x137e871d0>
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2391, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 159, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 911, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 641, in file_save_cb  
self.save_dialog.display(self, session)  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 139, in display  
fmt.save(session, filename)  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1100, in save  
run(session, cmd)  
File
"/Applications/ChimeraX-0.91.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-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 992, in save_session  
save(session, filename, **kw)  
File
"/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 229, in export  
result = self.export_func(session, path, **kw)  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-0.91.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-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12e0a49d0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x137e871d0>
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array'  
  
File
"/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (4)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Sessions
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Reporter: changed from chimerax-bug-report@… to Fengwei.Zheng@…
Status: new → accepted
Summary: ChimeraX bug report submission → Session save: 'NoneType' object has no attribute 'array'

comment:2 by Eric Pettersen, 6 years ago

Resolution: → duplicate
Status: accepted → closed

Hi,

This problem was fixed awhile ago. Please upgrade to the 0.92 release.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by Fengwei.Zheng@…, 6 years ago 

Dear Eric,

Awesome, got it, many thanks! Have a good one and stay safe!

Best,

Fengwei
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Saturday, March 28, 2020 13:00
Cc: Zheng, Fengwei <Fengwei.Zheng@vai.org>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: [External] Re: [ChimeraX] #2988: Session save: 'NoneType' object has no attribute 'array'

#2988: Session save: 'NoneType' object has no attribute 'array'
--------------------------------------+----------------------------
          Reporter:  Fengwei.Zheng@…  |      Owner:  Eric Pettersen
              Type:  defect           |     Status:  closed
          Priority:  normal           |  Milestone:
         Component:  Sessions         |    Version:
        Resolution:  duplicate        |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => closed
 * resolution:   => duplicate


Comment:

 Hi,
         This problem was fixed awhile ago.  Please upgrade to the 0.92
 release.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2988#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
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comment:4 by Eric Pettersen, 6 years ago

You stay safe too!

--Eric

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