Context Navigation

← Previous Ticket
Next Ticket →

#3950 closed defect

After closing some models from restored session, session save fails — at Version 1

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 (1)

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

Note: See TracTickets for help on using tickets.

Download in other formats: