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#3950 closed defect (duplicate)

After closing some models from restored session, session save fails

Reported by:	claudia.mueller@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Sessions	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description (last modified by Eric Pettersen)

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.dev202011140750 (2020-11-14 07:50:08 UTC)
Description
Dear ChimeraX-Team,

I've closed the respective pdb and subsequent saving gives me following error message:
ValueError: error processing: 'named views' -> -> -> 'cap near' -> '5mdv.pdb_z SES surface': Error while saving session data for 'named views' -> -> -> 'cap near' -> '5mdv.pdb_z SES surface'

Is this because of the Intel graphics problem? Can I circumvent this somehow without leaving the pdb(s) open?

Thanks for your help!
Best,
Claudia

Log:
UCSF ChimeraX version: 1.2.dev202011140750 (2020-11-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "C:\Users\claud\Documents\Reviews\FrontiersReview-Translation
> regulation\Figures\CimeraSessions\ChmX_Figure4_ArfB.cxs" format session

Log from Fri Nov 13 02:10:38 2020UCSF ChimeraX version: 1.2.dev202011040611
(2020-11-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "C:\Users\claud\Documents\Reviews\FrontiersReview-Translation
> regulation\Figures\CimeraSessions\ChmX_Figure3_ArfA-BrfA.cxs" format session

[had to deleted embedded logs due to length]

opened ChimeraX session  

> surface gridSpacing 2

> view 2

> ui tool show "Side View"

> show #!14 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!14 models

> surface gridSpacing 2.5

> show #!14 models

> hide #!15 models

> show #!16 models

> hide #!14 models

> hide #!16 models

> show #!14 models

> hide #!14 models

> show #!1 models

> view 7

> show #!1 cartoons

> hide #!1 surfaces

> view 7

Drag select of 10 residues  

> select up

1772 atoms, 1978 bonds, 83 residues, 3 models selected  

> select clear

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!1,4 surfaces

> show #!1,4 cartoons

> hide #!4 models

> save C:\Users\claud\Desktop\image16.png supersample 3

> view 6

> view 5

> show #!3 models

> hide #!1,3 surfaces

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> hide #!1 models

> show #!4 models

> view 5

Drag select of 21 residues  

> select up

1731 atoms, 1933 bonds, 81 residues, 3 models selected  

> hide sel cartoons

Drag select of 3 residues  

> select up

125 atoms, 126 bonds, 16 residues, 2 models selected  

> select up

261 atoms, 265 bonds, 32 residues, 2 models selected  

> hide sel cartoons

Drag select of 37 residues  

> select up

530 atoms, 537 bonds, 64 residues, 2 models selected  

> select up

2706 atoms, 2741 bonds, 341 residues, 2 models selected  

> color (#!4 & sel) gray

> transparency #4/7 70 cartoons

> select clear

> show #!1 models

Drag select of 1 residues  

> select up

125 atoms, 126 bonds, 16 residues, 2 models selected  

> select up

369 atoms, 375 bonds, 45 residues, 2 models selected  

> hide sel cartoons

> save C:\Users\claud\Desktop\image17.png supersample 3

> hide #!4 models

> show sel cartoons

> select clear

Drag select of 18 residues  

> select up

1772 atoms, 1978 bonds, 83 residues, 3 models selected  

> hide sel cartoons

> view 6

> view 7

> select #1/w:45

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #1/w:44

19 atoms, 18 bonds, 2 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 19 atom styles  

> color (#!1 & sel) byhetero

> select clear

> view 7

> save C:\Users\claud\Desktop\image18.png supersample 3

> hide #!1 models

> show #!14 models

> view 9

> show #!17 models

> hide #!14 models

> surface gridSpacing 2.5

> surface gridSpacing auto

Invalid "gridSpacing" argument: Expected a number  

> surface cap subdevision 2

Expected true or false or a keyword  

> surface cap subdevision s

Expected true or false or a keyword  

> surface cap subdevision factor 2

Expected true or false or a keyword  

> Cap subdivision 2

Unknown command: Cap subdivision 2  

> Cap subdivision factor 2

Unknown command: Cap subdivision factor 2  

> cap subdivision factor 2

Unknown command: cap subdivision factor 2  

> show #!14 models

> hide #!17 models

> show #!17 models

> hide #!14 models

> show #!14 models

> hide #!17 models

> save C:\Users\claud\Desktop\image19.png supersample 3

> show #!1 models

> hide #!1 models

> show #!6 models

> hide #!6 models

> view 2

> show #!15 models

> show #!16 models

> hide #!14 models

> view 2

> hide #!15 models

> surface cap true subdivision 2

> surface cap subdivision 2.0

> surface cap true subdivision 3

> surface cap subdivision 3.0

> surface cap true subdivision 4

> surface cap subdivision 4.0

> hide #!16 models

> show #!16 models

> show #!17 models

> hide #!16 models

> show #!16 models

> hide #!17 models

> surface cap true subdivision 1

> surface cap subdivision 1.0

> show #!14 models

> hide #!16 models

> hide #!14 models

> show #!16 models

Drag select of 5mdw.pdb_1 SES surface, 721834 of 739660 triangles, 5mdw.pdb_2
SES surface, 384492 of 395818 triangles, 5mdw.pdb_3 SES surface, 12063 of
34666 triangles, 5mdw.pdb_B SES surface, 5mdw.pdb_C SES surface, 5mdw.pdb_D
SES surface, 5mdw.pdb_E SES surface, 3691 of 16744 triangles, 5mdw.pdb_F SES
surface, 5mdw.pdb_G SES surface, 5mdw.pdb_H SES surface, 5mdw.pdb_I SES
surface, 5mdw.pdb_J SES surface, 5mdw.pdb_K SES surface, 5mdw.pdb_L SES
surface, 16383 of 17410 triangles, 5mdw.pdb_M SES surface, 5mdw.pdb_N SES
surface, 5mdw.pdb_P SES surface, 5mdw.pdb_Q SES surface, 5mdw.pdb_R SES
surface, 5mdw.pdb_S SES surface, 5mdw.pdb_T SES surface, 5mdw.pdb_U SES
surface, 5mdw.pdb_V SES surface, 17130 of 17652 triangles, 5mdw.pdb_W SES
surface, 6511 of 8332 triangles, 5mdw.pdb_X SES surface, 5mdw.pdb_Y SES
surface, 5mdw.pdb_Z SES surface, 5mdw.pdb_a SES surface, 869 of 9286
triangles, 5mdw.pdb_b SES surface, 5mdw.pdb_c SES surface, 4695 of 6148
triangles, 5mdw.pdb_d SES surface, 5mdw.pdb_e SES surface, 5mdw.pdb_f SES
surface, 5mdw.pdb_g SES surface, 5mdw.pdb_h SES surface, 5mdw.pdb_i SES
surface, 5mdw.pdb_j SES surface, 5mdw.pdb_k SES surface, 5mdw.pdb_l SES
surface, 13975 of 14702 triangles, 5mdw.pdb_m SES surface, 5mdw.pdb_n SES
surface, 10372 of 12622 triangles, 5mdw.pdb_o SES surface, 5mdw.pdb_p SES
surface, 5mdw.pdb_q SES surface, 5mdw.pdb_r SES surface, 6163 of 12270
triangles, 5mdw.pdb_s SES surface, 11341 of 12338 triangles, 5mdw.pdb_t SES
surface, 5mdw.pdb_u SES surface, 5mdw.pdb_v SES surface, 5mdw.pdb_w SES
surface, 5mdw.pdb_x SES surface, 9419 of 9536 triangles, 5mdw.pdb_y SES
surface, 5mdw.pdb_z SES surface  

> hide #!16.59 models

> show #!16.59 models

> select clear

> select #16

144909 atoms, 156838 bonds, 10972 residues, 36 models selected  

> surface gridSpacing 2

> surface gridSpacing 1

> surface gridSpacing 2.7

> surface gridSpacing 2.8

> surface gridSpacing 2.9

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 165, in <lambda>  
lambda *args, ft=self._fill_tree, ar=always_rebuild: ft(always_rebuild=ar))  
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 201, in _fill_tree  
self._get_info(model, all_selected_models, part_selected_models)  
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 274, in _get_info  
bg_color = self._model_color(obj)  
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 297, in _model_color  
return model.single_color  
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 385, in _get_single_color  
return self.color if vc is None else most_common_color(vc)  
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\core\colors.py", line 759, in most_common_color  
max_index = argmax(counts)  
File "<__array_function__ internals>", line 5, in argmax  
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\numpy\core\fromnumeric.py", line 1188, in argmax  
return _wrapfunc(a, 'argmax', axis=axis, out=out)  
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\numpy\core\fromnumeric.py", line 58, in _wrapfunc  
return bound(*args, **kwds)  
ValueError: attempt to get argmax of an empty sequence  
  
Error processing trigger "new frame":  
ValueError: attempt to get argmax of an empty sequence  
  
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\numpy\core\fromnumeric.py", line 58, in _wrapfunc  
return bound(*args, **kwds)  
  
See log for complete Python traceback.  
  

> surface gridSpacing 2.8

> surface gridSpacing 2.7

> surface gridSpacing 2.75

> surface gridSpacing 2.89

> surface gridSpacing 2.85

> surface gridSpacing 2.8

> surface gridSpacing 2.7

> select clear

> save C:\Users\claud\Desktop\image20.png supersample 3

> view 2

> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"

——— End of log from Fri Nov 13 02:10:38 2020 ———

opened ChimeraX session  

> close #3-5,11,13,15-16

> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure4_ArfB.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 577, in take_snapshot  
data = {attr:getattr(self, attr) for attr in init_attrs}  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 577, in <dictcomp>  
data = {attr:getattr(self, attr) for attr in init_attrs}  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000017A05370DC0> ->
<chimerax.std_commands.view.NamedView object at 0x0000017A05370F70> ->
<chimerax.surface.cap.ClipCap object at 0x0000017A14267490> 'cap near' ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x0000017A7D287310>
'5mdv.pdb_z SES surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 839, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000017A05370DC0> ->
<chimerax.std_commands.view.NamedView object at 0x0000017A05370F70> ->
<chimerax.surface.cap.ClipCap object at 0x0000017A14267490> 'cap near' ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x0000017A7D287310>
'5mdv.pdb_z SES surface': Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000017A05370DC0> ->
<chimerax.std_commands.view.NamedView object at 0x0000017A05370F70> ->
<chimerax.surface.cap.ClipCap object at 0x0000017A14267490> 'cap near' ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x0000017A7D287310>
'5mdv.pdb_z SES surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap near' -> '5mdv.pdb_z
SES surface': Error while saving session data for 'named views' -> -> -> 'cap
near' -> '5mdv.pdb_z SES surface'  
  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 577, in take_snapshot  
data = {attr:getattr(self, attr) for attr in init_attrs}  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 577, in <dictcomp>  
data = {attr:getattr(self, attr) for attr in init_attrs}  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 565, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000017A05370DC0> ->
<chimerax.std_commands.view.NamedView object at 0x0000017A05370F70> ->
<chimerax.surface.cap.ClipCap object at 0x0000017A14267490> 'cap near' ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x0000017A7D287310>
'5mdv.pdb_z SES surface'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\ui\gui.py", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 78, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 839, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000017A05370DC0> ->
<chimerax.std_commands.view.NamedView object at 0x0000017A05370F70> ->
<chimerax.surface.cap.ClipCap object at 0x0000017A14267490> 'cap near' ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x0000017A7D287310>
'5mdv.pdb_z SES surface': Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000017A05370DC0> ->
<chimerax.std_commands.view.NamedView object at 0x0000017A05370F70> ->
<chimerax.surface.cap.ClipCap object at 0x0000017A14267490> 'cap near' ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x0000017A7D287310>
'5mdv.pdb_z SES surface'  
  
ValueError: error processing: 'named views' -> -> -> 'cap near' -> '5mdv.pdb_z
SES surface': Error while saving session data for 'named views' -> -> -> 'cap
near' -> '5mdv.pdb_z SES surface'  
  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 26.20.100.7870
OpenGL renderer: Intel(R) Iris(R) Plus Graphics
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 81Q8
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 16,926,306,304
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-1065G7 CPU @ 1.30GHz
OSLanguage: de-DE
Locale: ('de_DE', 'cp1252')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.11.8
    cftime: 1.2.1
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.9.3
    ChimeraX-AtomicLibrary: 1.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202011140750
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.1
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.3.1
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.2.2
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3.1
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.6.3
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.5.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    netifaces: 0.10.9
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.8
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.1
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.1
    python-dateutil: 2.8.1
    pytz: 2020.4
    pywin32: 228
    pyzmq: 20.0.0
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.0
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.35.1
    WMI: 1.5.1

Change History (3)

comment:1 by Eric Pettersen, 5 years ago

Component:	Unassigned → Sessions
Description:	modified (diff)
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → After closing some models from restored session, session save fails

Seems to be because of a surface cap in a NamedView

comment:2 by Tom Goddard, 5 years ago

This appears to be the same bug #3920 that I fixed last Monday Nov 9. You are using the Nov 14 ChimeraX (good!) so I am surprised to see the bug again.

Could you possibly send me (goddard@…) a link to the session file that gives this error (Google drive, or Dropbox, or email it directly to me if small enough)..

C:\Users\claud\Documents\Reviews\FrontiersReview-Translation regulation\Figures\CimeraSessions\ChmX_Figure4_ArfB.cxs

That would make it easy to debug. So far I have not been able to reproduce this error.

The problem is that clipping is enabled and a cap on a clipped molecular surface somehow still exists even though you deleted the molecular surface. The cap apparently was not closed, which is the bug. The previously fixed bug was exactly this case and I found why the cap was not closed. But somehow you have a different situation.

comment:3 by Tom Goddard, 5 years ago

Resolution:	→ duplicate
Status:	assigned → closed

I think I figured out the bug. The problem is that that the session was saved with the Nov 4, 2020 ChimeraX that had the bug where clip caps did not get closed. So what happened is that old session had named views with clipping. Before it was saved the clipping was turned off and the clip cap surface on 5mdv chain z did not get properly closed. Then the saved session contained that half-closed cap. When you restore the session in the Nov 14, 2020 ChimeraX is has that half-closed cap (not shown in Model Panel). When you close some models the zombie clip cap still points to one of the closed models and that causes the save error.

The way to fix this is to delete or update the named view that still knows about the zombie clip cap. Unfortunately I don't know with named view it is and I see from the log you have at least 7 named views. It is one that has 5mdv chain z clipped if that helps you figure out which one. If it is view 2 you can update it with

view 2
view name 2

which just shows the view and replaces it. Or you could delete it if it is not needed

view delete 2

After that you should be able to save the session with the closed models.

Sorry for the trouble. Bugs that put mistakes into session files are especially bad and we try to avoid that.

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