Problem saving session after segmentation regions deleted

[christophe.leterrier@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-01-24)
Description
When I try to save a session after deleting some of the segmentation clusters (using "Close" in the Models panel to close a bunch of them by multiple selection), I get the following error and I can't save the session:

RuntimeError: Error while saving session data for 'tools' -> -> 'segment map' -> 'Roi001_C1b_N11_PFA_b4s-clath-b2s_3D_647_65K_63K_rot-90_TS3D gaussian.seg' -> : 'NoneType' object is not subscriptable

File "/Applications/ChimeraX_Daily.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.

Log:
UCSF ChimeraX version: 0.92 (2020-01-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/christo/Travail/Labo/Manuscrits/201610 Archan clathrin/Fig 5
> (PAINT#9)/Illu C1b_N11 #3/RoiXL.cxs"

Summary of feedback from opening /Users/christo/Travail/Labo/Manuscrits/201610
Archan clathrin/Fig 5 (PAINT#9)/Illu C1b_N11 #3/RoiXL.cxs  
---  
note | Showing Roi001_C1b_N11_PFA_b4s-clath-b2s_3D_647_65K_63K_rot-90_TS3D
gaussian.seg - 35 regions, 35 surfaces  
  
opened ChimeraX session  

> volume #3 region 653,0,0,769,290,299

> volume #4 region 570,0,0,844,290,299

> ui mousemode rightMode "delete markers"

> marker delete #5:1

> marker delete #5:4

> marker delete #5:5

> marker delete #5:2

> save session "/Users/christo/Travail/Labo/Manuscrits/201610 Archan
> clathrin/Fig 5 (PAINT#9)/Illu C1b_N11 #3/Roi005.cxs"

> hide #!4 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  

> hide sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  

> view orient

> view initial

Drag select of 332, 2406 of 10460 triangles  

> select #2

141 models selected  

> ~select #2

Nothing selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  

> view orient

> view initial

Drag select of  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  

> hide sel

Drag select of  

> hide sel

> view orient

> view initial

> show #!4 models

> select #4

3 models selected  

> volume sel showOutlineBox true

> select #3

2 models selected  

> volume sel showOutlineBox false

> select #3

2 models selected  

> ~select #3

Nothing selected  

> save session "/Users/christo/Travail/Labo/Manuscrits/201610 Archan
> clathrin/Fig 5 (PAINT#9)/Illu C1b_N11 #3/Roi005.cxs"

> marker #5 2.28,1.16,0 color yellow radius 0.01

> marker #5 3.376,1.16,0 color yellow radius 0.01

> marker #5 3.376,0.66,0 color yellow radius 0.01

> marker #5 2.28,0.66,0 color yellow radius 0.01

> view

> view

> save /Users/christo/Desktop/image1.png supersample 3

> hide #5 models

> save /Users/christo/Desktop/image2.png supersample 3

> save session "/Users/christo/Travail/Labo/Manuscrits/201610 Archan
> clathrin/Fig 5 (PAINT#9)/Illu C1b_N11 #3/Roi005.cxs"

> show #5 models

> view

> save /Users/christo/Desktop/image1.png supersample 3

> hide #5 models

> save /Users/christo/Desktop/image2.png supersample 3

> show #5 models

> save session "/Users/christo/Travail/Labo/Manuscrits/201610 Archan
> clathrin/Fig 5 (PAINT#9)/Illu C1b_N11 #3/Roi005.cxs"

> open "/Users/christo/Travail/Labo/Manuscrits/201610 Archan clathrin/Fig 5
> (PAINT#9)/Illu C1b_N11 #3/RoiXL.cxs"

Summary of feedback from opening /Users/christo/Travail/Labo/Manuscrits/201610
Archan clathrin/Fig 5 (PAINT#9)/Illu C1b_N11 #3/RoiXL.cxs  
---  
note | Showing Roi001_C1b_N11_PFA_b4s-clath-b2s_3D_647_65K_63K_rot-90_TS3D
gaussian.seg - 35 regions, 35 surfaces  
  
opened ChimeraX session  

> marker delete #5:1

> marker delete #5:3

> marker delete #5:4

> marker delete #5:5

> view orient

> view initial

> save session "/Users/christo/Travail/Labo/Manuscrits/201610 Archan
> clathrin/Fig 5 (PAINT#9)/Illu C1b_N11 #3/RoiXL_nomarkers.cxs"

> volume #3 region 435,0,0,551,290,299

> volume #4 region 360,0,0,626,290,299

> select #4

3 models selected  

> volume sel showOutlineBox true

> hide #!4 models

> show #!1 models

> hide #!1 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  

> hide sel

Drag select of  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  

> hide sel

> show #!4 models

> select #3

2 models selected  

> volume sel showOutlineBox false

> select #3

2 models selected  

> ~select #3

Nothing selected  

> marker #5 1.44,1.16,0 color yellow radius 0.01

> marker #5 2.504,1.16,0 color yellow radius 0.01

> marker #5 2.504,0.66,0 color yellow radius 0.01

> marker #5 1.44,0.66,0 color yellow radius 0.01

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  

> view orient

> view initial

> select #2

141 models selected  

> ~select #2

Nothing selected  
Drag select of  

> view

> save session "/Users/christo/Travail/Labo/Manuscrits/201610 Archan
> clathrin/Fig 5 (PAINT#9)/Illu C1b_N11 #3/Roi004.cxs"

> save /Users/christo/Desktop/image3.png supersample 3

> hide #5 models

> save /Users/christo/Desktop/image4.png supersample 3

> show #5 models

> open "/Users/christo/Travail/Labo/Manuscrits/201610 Archan clathrin/Fig 5
> (PAINT#9)/Illu C1b_N11 #3/RoiXL_nomarkers.cxs"

Summary of feedback from opening /Users/christo/Travail/Labo/Manuscrits/201610
Archan clathrin/Fig 5 (PAINT#9)/Illu C1b_N11 #3/RoiXL_nomarkers.cxs  
---  
note | Showing Roi001_C1b_N11_PFA_b4s-clath-b2s_3D_647_65K_63K_rot-90_TS3D
gaussian.seg - 35 regions, 35 surfaces  
  
opened ChimeraX session  

> volume #3 region 142,0,0,260,290,299

> volume #4 region 67,0,0,335,290,299

> hide #!4 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  

> hide sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  
Drag select of  

> hide sel

> view orient

> view initial

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up  
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 192, in mouse_drag_select  
select_pick(session, pick, mode)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 211, in select_pick  
session.logger.info('Drag select of %s' % _pick_description(pick))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 229, in _pick_description  
count, name = d.split(maxsplit = 1)  
  
See log for complete Python traceback.  
  

> hide sel

Drag select of  

> show #!4 models

> select #4

3 models selected  

> volume sel showOutlineBox true

> select #3

2 models selected  

> volume sel showOutlineBox false

> select #3

2 models selected  

> ~select #3

Nothing selected  

> view orient

> view initial

Unknown command: `  

> close #2.1-141

> close #2.143-144

> close #2.146-149

> close #2.151-157

> close #2.159-168

> close #2.170

> close #2.172-175

> marker #5 0.268,1.16,0 color yellow radius 0.01

> marker #5 1.34,1.16,0 color yellow radius 0.01

> marker #5 1.34,0.66,0 color yellow radius 0.01

> marker #5 0.268,0.66,0 color yellow radius 0.01

> view

> save session "/Users/christo/Travail/Labo/Manuscrits/201610 Archan
> clathrin/Fig 5 (PAINT#9)/Illu C1b_N11 #3/Roi002.cxs"

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/regions.py", line 1353, in take_snapshot  
data['_surface_color'] = sp.color  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.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 'tools' ->
<chimerax.core.tools.Tools object at 0x11c1bbfd0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x129879f90> 'segment map' -> <chimerax.segger.regions.Segmentation object at
0x12ce4eb90> 'Roi001_C1b_N11_PFA_b4s-clath-b2s_3D_647_65K_63K_rot-90_TS3D
gaussian.seg' -> <chimerax.segger.regions.Region object at 0x125ad0590>:
'NoneType' object is not subscriptable  
  
RuntimeError: Error while saving session data for 'tools' -> -> 'segment map'
-> 'Roi001_C1b_N11_PFA_b4s-clath-b2s_3D_647_65K_63K_rot-90_TS3D gaussian.seg'
-> : 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/regions.py", line 1353, in take_snapshot  
data['_surface_color'] = sp.color  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 455, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1632, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/__init__.py", line 36, in run_provider  
tool.run_provider(session, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 223, in run_provider  
what(session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 205, in _file_save  
session.ui.main_window.file_save_cb(session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 643, in file_save_cb  
self.save_dialog.display(self, session)  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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 'tools' ->
<chimerax.core.tools.Tools object at 0x11c1bbfd0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x129879f90> 'segment map' -> <chimerax.segger.regions.Segmentation object at
0x12ce4eb90> 'Roi001_C1b_N11_PFA_b4s-clath-b2s_3D_647_65K_63K_rot-90_TS3D
gaussian.seg' -> <chimerax.segger.regions.Region object at 0x125ad0590>:
'NoneType' object is not subscriptable  
  

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/regions.py", line 1353, in take_snapshot  
data['_surface_color'] = sp.color  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 455, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1632, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/__init__.py", line 36, in run_provider  
tool.run_provider(session, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 223, in run_provider  
what(session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 205, in _file_save  
session.ui.main_window.file_save_cb(session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 643, in file_save_cb  
self.save_dialog.display(self, session)  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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 'tools' ->
<chimerax.core.tools.Tools object at 0x11c1bbfd0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x129879f90> 'segment map' -> <chimerax.segger.regions.Segmentation object at
0x12ce4eb90> 'Roi001_C1b_N11_PFA_b4s-clath-b2s_3D_647_65K_63K_rot-90_TS3D
gaussian.seg' -> <chimerax.segger.regions.Region object at 0x125ad0590>:
'NoneType' object is not subscriptable  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 122, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 462, in run_provider  
"run_provider() failed in bundle %s:\n%s" % (self.name, str(e)))  
chimerax.core.toolshed.ToolshedError: run_provider() failed in bundle
ChimeraX-Toolbar:  
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x11c1bbfd0> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x129879f90> 'segment map' -> <chimerax.segger.regions.Segmentation object at
0x12ce4eb90> 'Roi001_C1b_N11_PFA_b4s-clath-b2s_3D_647_65K_63K_rot-90_TS3D
gaussian.seg' -> <chimerax.segger.regions.Region object at 0x125ad0590>:
'NoneType' object is not subscriptable  
  
chimerax.core.toolshed.ToolshedError: run_provider() failed in bundle
ChimeraX-Toolbar:  
Error while saving session data for 'tools' -> -> 'segment map' ->
'Roi001_C1b_N11_PFA_b4s-clath-b2s_3D_647_65K_63K_rot-90_TS3D gaussian.seg' ->
: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 462, in run_provider  
"run_provider() failed in bundle %s:\n%s" % (self.name, str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.14
OpenGL renderer: Intel(R) Iris(TM) Graphics 550
OpenGL vendor: Intel Inc.

[Tom Goddard]

ChimeraX Segger is not deleting segmentation regions when their surfaces are closed with Model Panel. The deleted surface then causes session save to fail. Segger will need to listen for when surfaces are deleted and then delete the regions. I can probably fix this tomorrow.

[Tom Goddard]

Using the Segger menu Regions / Delete Selected Regions works correctly.

[Tom Goddard]

Fixed.

Made Segger realize when region surfaces are closed. This does not delete the region, just the surface depiction.
I also fixed a separate problem where Segger region surface models were duplicated after restoring a session.

The ChimeraX version of Segger is still rather buggy.