Problem getting matrix origin while saving map in session

[linan_9095@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8.dev202403271703 (2024-03-27 17:03:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Failed to save the cxs file

Log:
UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/linan/Downloads/cryosparc_P20_J1475_class_00_00103_volume.mrc

Opened cryosparc_P20_J1475_class_00_00103_volume.mrc as #1, grid size
224,224,224, pixel 0.93, shown at level 0.0489, step 1, values float32  

> open C:/Users/linan/Downloads/cryosparc_P20_J1475_class_01_00103_volume.mrc

Opened cryosparc_P20_J1475_class_01_00103_volume.mrc as #2, grid size
224,224,224, pixel 0.93, shown at level 0.0632, step 1, values float32  

> open C:/Users/linan/Downloads/cryosparc_P20_J1475_class_02_00103_volume.mrc

Opened cryosparc_P20_J1475_class_02_00103_volume.mrc as #3, grid size
224,224,224, pixel 0.93, shown at level 0.0459, step 1, values float32  

> open C:/Users/linan/Downloads/cryosparc_P20_J1475_class_03_00103_volume.mrc

Opened cryosparc_P20_J1475_class_03_00103_volume.mrc as #4, grid size
224,224,224, pixel 0.93, shown at level 0.0611, step 1, values float32  

> open C:/Users/linan/Downloads/cryosparc_P20_J1475_class_04_00103_volume.mrc

Opened cryosparc_P20_J1475_class_04_00103_volume.mrc as #5, grid size
224,224,224, pixel 0.93, shown at level 0.0574, step 1, values float32  

> open C:/Users/linan/Downloads/cryosparc_P20_J1475_class_05_00103_volume.mrc

Opened cryosparc_P20_J1475_class_05_00103_volume.mrc as #6, grid size
224,224,224, pixel 0.93, shown at level 0.0002, step 1, values float32  

> set bgColor white

> lighting soft

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> show #!6 models

> hide #!5 models

> hide #!6 models

> show #!5 models

> ui tool show "Side View"

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!5 models

> volume flip #5

Opened cryosparc_P20_J1475_class_04_00103_volume.mrc z flip as #7, grid size
224,224,224, pixel 0.93, shown at step 1, values float32  

> windowsize height 600 width 600

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!4 models

> hide #!4 models

> show #!6 models

> hide #!6 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> show #!4 models

> hide #!4 models

> color #6 #ffb7afff models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!7 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> color #2 #ffffbbff models

> color #2 #ffb7afff models

> show #!2 models

> hide #!7 models

> hide #!2 models

> show #!3 models

> color #3 #ffb7afff models

> color #3 #bb22bbff models

> color #3 #b2b2b2ff models

> hide #!3 models

> show #!2 models

> color #2 #b2b2b2ff models

> show #!3 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> show #!4 models

> color #4 #b2b2b2ff models

> color #4 #ffffbbff models

> color #4 #ffb7afff models

> hide #!4 models

> show #!5 models

> show #!7 models

> hide #!5 models

> show #!6 models

> color #6 #bb22bbff models

> color #6 #b2b2b2ff models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> color #7 #ffb7afff models

> show #!4 models

> hide #!4 models

> hide #!7 models

> show #!4 models

> volume #4 level 0.0822

> hide #!4 models

> show #!7 models

> volume #7 level 0.08644

> volume #7 level 0.08229

> volume #7 level 0.07814

> hide #!7 models

> show #!4 models

> volume #4 level 0.08411

> volume #4 level 0.08028

> volume #4 level 0.07836

> hide #!4 models

> show #!7 models

> hide #!7 models

> show #!4 models

> ui tool show "Hide Dust"

> surface dust #4 size 3.58

> volume #4 level 0.07836

> hide #!4 models

> show #!7 models

> show #!4 models

> hide #!7 models

> volume #4 level 0.07645

> volume #4 level 0.07836

> save D:/GPR4/GPR4_map&model/GPR4_Gi/J1475/class03.tif width 600 height 600
> supersample 3 transparentBackground true

> hide #!6 models

> show #!6 models

> hide #!4 models

> hide #!6 models

> show #!4 models

> hide #!4 models

> show #!7 models

> surface dust #5 size 3.58

[Repeated 1 time(s)]

> surface dust #7 size 3.58

> hide #!4 models

> volume #7 level 0.07607

[Repeated 2 time(s)]

> surface dust #7 size 3.58

> surface dust #7 size 4.58

[Repeated 1 time(s)]

> show #!4 models

> hide #!4 models

> volume #7 level 0.07607

> volume #7 level 0.06569

> volume #7 level 0.07814

> save D:/GPR4/GPR4_map&model/GPR4_Gi/J1475/class04.tif width 600 height 600
> supersample 3 transparentBackground true

> hide #!7 models

> show #!4 models

> hide #!4 models

> show #!2 models

> save D:/GPR4/GPR4_map&model/GPR4_Gi/J1475/class01.tif width 600 height 600
> supersample 3 transparentBackground true

> hide #!2 models

> show #!3 models

> save D:/GPR4/GPR4_map&model/GPR4_Gi/J1475/class02.tif width 600 height 600
> supersample 3 transparentBackground true

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!6 models

> volume #6 level 0.1372

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!1 models

> save D:/GPR4/GPR4_map&model/GPR4_Gi/J1475/class00.tif width 600 height 600
> supersample 3 transparentBackground true

> save D:/GPR4/GPR4_map&model/GPR4_Gi/J1475/J1475.cxs includeMaps true

Traceback (most recent call last):  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map\session.py", line 201, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map\session.py", line 322, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\flip.py", line 36, in matrix  
origin = self.flipped_origin(ijk_origin, ijk_size)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\flip.py", line 70, in flipped_origin  
origin[ai] = self.data.size[ai] - (ijk_origin[ai] + ijk_size[ai])  
~~~~~~~~^^^^  
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 (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000001C68ABFB7D0> ->
<chimerax.surface.dust.Redust object at 0x000001C699717F90> ->
<chimerax.map.volume.VolumeSurface object at 0x000001C690A12790> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001C690969550>
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->
<chimerax.map.session.GridDataState object at 0x000001C699715C50>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 917, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 641, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000001C68ABFB7D0> ->
<chimerax.surface.dust.Redust object at 0x000001C699717F90> ->
<chimerax.map.volume.VolumeSurface object at 0x000001C690A12790> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001C690969550>
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->
<chimerax.map.session.GridDataState object at 0x000001C699715C50>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000001C68ABFB7D0> ->
<chimerax.surface.dust.Redust object at 0x000001C699717F90> ->
<chimerax.map.volume.VolumeSurface object at 0x000001C690A12790> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001C690969550>
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->
<chimerax.map.session.GridDataState object at 0x000001C699715C50>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' -> : Error while saving
session data for '_surface_updaters' -> -> -> 'surface' ->
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->  
  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, 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 (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map\session.py", line 201, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map\session.py", line 322, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\flip.py", line 36, in matrix  
origin = self.flipped_origin(ijk_origin, ijk_size)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\flip.py", line 70, in flipped_origin  
origin[ai] = self.data.size[ai] - (ijk_origin[ai] + ijk_size[ai])  
~~~~~~~~^^^^  
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 (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000001C68ABFB7D0> ->
<chimerax.surface.dust.Redust object at 0x000001C699717F90> ->
<chimerax.map.volume.VolumeSurface object at 0x000001C690A12790> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001C690969550>
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->
<chimerax.map.session.GridDataState object at 0x000001C699715C50>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 917, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 641, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000001C68ABFB7D0> ->
<chimerax.surface.dust.Redust object at 0x000001C699717F90> ->
<chimerax.map.volume.VolumeSurface object at 0x000001C690A12790> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001C690969550>
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->
<chimerax.map.session.GridDataState object at 0x000001C699715C50>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000001C68ABFB7D0> ->
<chimerax.surface.dust.Redust object at 0x000001C699717F90> ->
<chimerax.map.volume.VolumeSurface object at 0x000001C690A12790> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001C690969550>
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->
<chimerax.map.session.GridDataState object at 0x000001C699715C50>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' -> : Error while saving
session data for '_surface_updaters' -> -> -> 'surface' ->
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->  
  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save D:/GPR4/GPR4_map&model/GPR4_Gi/J1475/J1475.cxs includeMaps true

Traceback (most recent call last):  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map\session.py", line 201, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map\session.py", line 322, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\flip.py", line 36, in matrix  
origin = self.flipped_origin(ijk_origin, ijk_size)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\flip.py", line 70, in flipped_origin  
origin[ai] = self.data.size[ai] - (ijk_origin[ai] + ijk_size[ai])  
~~~~~~~~^^^^  
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 (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000001C68ABFB7D0> ->
<chimerax.surface.dust.Redust object at 0x000001C699717F90> ->
<chimerax.map.volume.VolumeSurface object at 0x000001C690A12790> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001C690969550>
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->
<chimerax.map.session.GridDataState object at 0x000001C699771E90>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 917, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 641, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000001C68ABFB7D0> ->
<chimerax.surface.dust.Redust object at 0x000001C699717F90> ->
<chimerax.map.volume.VolumeSurface object at 0x000001C690A12790> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001C690969550>
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->
<chimerax.map.session.GridDataState object at 0x000001C699771E90>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000001C68ABFB7D0> ->
<chimerax.surface.dust.Redust object at 0x000001C699717F90> ->
<chimerax.map.volume.VolumeSurface object at 0x000001C690A12790> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001C690969550>
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->
<chimerax.map.session.GridDataState object at 0x000001C699771E90>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' -> : Error while saving
session data for '_surface_updaters' -> -> -> 'surface' ->
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->  
  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, 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 (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map\session.py", line 201, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map\session.py", line 322, in state_from_grid_data  
bytes = dt.matrix().tobytes()  
^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\flip.py", line 36, in matrix  
origin = self.flipped_origin(ijk_origin, ijk_size)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\map_filter\flip.py", line 70, in flipped_origin  
origin[ai] = self.data.size[ai] - (ijk_origin[ai] + ijk_size[ai])  
~~~~~~~~^^^^  
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 (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000001C68ABFB7D0> ->
<chimerax.surface.dust.Redust object at 0x000001C699717F90> ->
<chimerax.map.volume.VolumeSurface object at 0x000001C690A12790> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001C690969550>
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->
<chimerax.map.session.GridDataState object at 0x000001C699771E90>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 917, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 641, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000001C68ABFB7D0> ->
<chimerax.surface.dust.Redust object at 0x000001C699717F90> ->
<chimerax.map.volume.VolumeSurface object at 0x000001C690A12790> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001C690969550>
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->
<chimerax.map.session.GridDataState object at 0x000001C699771E90>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x000001C68ABFB7D0> ->
<chimerax.surface.dust.Redust object at 0x000001C699717F90> ->
<chimerax.map.volume.VolumeSurface object at 0x000001C690A12790> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001C690969550>
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->
<chimerax.map.session.GridDataState object at 0x000001C699771E90>  
  
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' -> : Error while saving
session data for '_surface_updaters' -> -> -> 'surface' ->
'cryosparc_P20_J1475_class_04_00103_volume.mrc z flip' ->  
  
File "C:\Program Files (x86)\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 531.88
OpenGL renderer: NVIDIA GeForce RTX 3050 4GB Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: windows

Manufacturer: LENOVO
Model: 21HW
OS: Microsoft Windows 11 家庭中文版 (Build 22631)
Memory: 34,071,240,704
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i7-13700H
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.5.1
    build: 1.1.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202403271703
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.37.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.3.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.50.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.0
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    setuptools: 69.2.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.0
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.9.2
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1

[Eric Pettersen]

Reported by Chen

[Tom Goddard]

The error saving the session is because you used "volume flip #5" which produced new map #7 and then somehow map #5 was closed. The flipped map uses the data from the original map so closing the original map makes it not possible to retrieve the values of the flipped map. This is bad. I guess closing map #5 should also close the flipped map #7.

The reason it works this way is that it allow you to flip a very large map without copying it all into memory, because it just uses the original map to get the values.

[Tom Goddard]

Actually that analysis was not right. Map #5 was not closed, but saving the flipped map failed because of an error in the code. I'll look at how to fix that. You would be able to save the session if you deleted the flipped map.

[Tom Goddard]

Fixed.

Saving a flipped volume in a session was broken by a code change on Jan 22, 2024 that was trying to fix a different volume flip bug #14392.

Also if you close the original unflipped volume the session save also works now.