Opened 8 months ago

Closed 8 months ago

#17044 closed defect (fixed)

Restore surface: 'points' is None

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
I can't open the file that I created

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 7926 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this.  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\jonah\OneDrive\Desktop\Tesi triennale
> Mariam\Multiwfn_3.8_dev_bin_Win64\Multiwfn_3.8_dev_bin_Win64\hino1w.cxs"
> format session

Opened func1.cub as #2, grid size 182,107,91, pixel 0.0659, shown at level
-0.157,0.157, step 1, values float32  
Opened func2.cub as #3, grid size 182,107,91, pixel 0.0659, shown at level
0.5,100, step 1, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 238, in restore_snapshot  
c = cls(surf, palette = data['colormap'], range = None, transparency =
data.get('transparency'),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 149, in __init__  
self.set_colormap(palette, range)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 168, in set_colormap  
r = self.value_range() if _use_full_range(range, palette) else range  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 211, in value_range  
v = self.values(va)  
^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 286, in values  
d = distances_from_origin(vertices, self.origin)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 296, in distances_from_origin  
d = zeros(len(points), floatc)  
^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
Log from Sat Mar 8 00:16:00 2025 Startup Messages  
---  
warning | Your computer has Intel graphics driver 7926 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this.  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\ProgramData\ChimeraX\confa1.cxs format session

Opened func1.cub as #2, grid size 182,107,91, pixel 0.0659, shown at level
-0.174,0.174, step 1, values float32  
Opened func2.cub as #3, grid size 182,107,91, pixel 0.0659, shown at level
0.5,100, step 1, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 238, in restore_snapshot  
c = cls(surf, palette = data['colormap'], range = None, transparency =
data.get('transparency'),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 149, in __init__  
self.set_colormap(palette, range)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 168, in set_colormap  
r = self.value_range() if _use_full_range(range, palette) else range  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 211, in value_range  
v = self.values(va)  
^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 286, in values  
d = distances_from_origin(vertices, self.origin)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 296, in distances_from_origin  
d = zeros(len(points), floatc)  
^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
Log from Sat Mar 8 00:02:33 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\jonah\OneDrive\Desktop\Tesi triennale
> Mariam\Multiwfn_3.8_dev_bin_Win64\Multiwfn_3.8_dev_bin_Win64\confa1.cxs"
> format session

Opened func1.cub as #2, grid size 155,114,100, pixel 0.0599, shown at level
-0.174,0.174, step 1, values float32  
Opened func2.cub as #3, grid size 155,114,100, pixel 0.0599, shown at level
0.5,100, step 1, values float32  
Log from Fri Mar 7 23:43:47 2025 Startup Messages  
---  
warning | Your computer has Intel graphics driver 7926 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this.  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_a_1.xyz"

Unrecognized file suffix '.xyz'  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_a_1.pdb"

Summary of feedback from opening C:/Users/jonah/OneDrive/Desktop/Tesi
triennale
Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_a_1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Generated by Multiwfn, Totally 24 atoms  
  

> color byelement

> represent bs

Unknown command: represent bs  

> color byelement

> represent bs

Unknown command: represent bs  

> style ball

Changed 24 atom styles  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func1.cub"

Opened func1.cub as #2, grid size 152,118,99, pixel 0.0602, shown at level
-0.174,0.174, step 1, values float32  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func2.cub"

Opened func2.cub as #3, grid size 152,118,99, pixel 0.0602, shown at level
-100,100, step 1, values float32  

> ui tool show "Volume Viewer"

> ui tool show "Surface Color"

> ui tool show "Volume Viewer"

> color electrostatic #3.1#3.2 map #3 palette
> -0.025,#ff0000:0,#ffffff:0.025,#0000ff

> volume #3 level 0.5 level 100

> volume #2 level 0.5 level 0.1735

> toolshed show

> close #2

> close #3

> undo

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func1.cub"

Opened func1.cub as #2, grid size 152,118,99, pixel 0.0602, shown at level
-0.174,0.174, step 1, values float32  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func2.cub"

Opened func2.cub as #3, grid size 152,118,99, pixel 0.0602, shown at level
-100,100, step 1, values float32  

> volume #3 level 0.5 level 100

> ui tool show "Side View"

> ui tool show Toolbar

> camera mode perspective

Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword  

> fielOfView 15.6389

Unknown command: fielOfView 15.6389  

> view

> lighting shadows true

> graphics silhouettes true

> lighting shadows false

> lighting model three-point

Missing or invalid "models" argument: invalid models specifier  

> save "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/confa1.cxs"

——— End of log from Fri Mar 7 23:43:47 2025 ———

opened ChimeraX session  

> ui tool show "Surface Color"

> color radial #3.1#3.2 palette #ff0000:#00aa00:#0000ff

> save C:/ProgramData/ChimeraX/confa1.cxs

——— End of log from Sat Mar 8 00:02:33 2025 ———

opened ChimeraX session  

> open C:\ProgramData\ChimeraX\confa1.cxs format session

Opened func1.cub as #2, grid size 182,107,91, pixel 0.0659, shown at level
-0.174,0.174, step 1, values float32  
Opened func2.cub as #3, grid size 182,107,91, pixel 0.0659, shown at level
0.5,100, step 1, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 238, in restore_snapshot  
c = cls(surf, palette = data['colormap'], range = None, transparency =
data.get('transparency'),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 149, in __init__  
self.set_colormap(palette, range)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 168, in set_colormap  
r = self.value_range() if _use_full_range(range, palette) else range  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 211, in value_range  
v = self.values(va)  
^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 286, in values  
d = distances_from_origin(vertices, self.origin)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 296, in distances_from_origin  
d = zeros(len(points), floatc)  
^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
Log from Sat Mar 8 00:02:33 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\jonah\OneDrive\Desktop\Tesi triennale
> Mariam\Multiwfn_3.8_dev_bin_Win64\Multiwfn_3.8_dev_bin_Win64\confa1.cxs"
> format session

Opened func1.cub as #2, grid size 155,114,100, pixel 0.0599, shown at level
-0.174,0.174, step 1, values float32  
Opened func2.cub as #3, grid size 155,114,100, pixel 0.0599, shown at level
0.5,100, step 1, values float32  
Log from Fri Mar 7 23:43:47 2025 Startup Messages  
---  
warning | Your computer has Intel graphics driver 7926 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this.  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_a_1.xyz"

Unrecognized file suffix '.xyz'  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_a_1.pdb"

Summary of feedback from opening C:/Users/jonah/OneDrive/Desktop/Tesi
triennale
Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_a_1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Generated by Multiwfn, Totally 24 atoms  
  

> color byelement

> represent bs

Unknown command: represent bs  

> color byelement

> represent bs

Unknown command: represent bs  

> style ball

Changed 24 atom styles  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func1.cub"

Opened func1.cub as #2, grid size 152,118,99, pixel 0.0602, shown at level
-0.174,0.174, step 1, values float32  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func2.cub"

Opened func2.cub as #3, grid size 152,118,99, pixel 0.0602, shown at level
-100,100, step 1, values float32  

> ui tool show "Volume Viewer"

> ui tool show "Surface Color"

> ui tool show "Volume Viewer"

> color electrostatic #3.1#3.2 map #3 palette
> -0.025,#ff0000:0,#ffffff:0.025,#0000ff

> volume #3 level 0.5 level 100

> volume #2 level 0.5 level 0.1735

> toolshed show

> close #2

> close #3

> undo

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func1.cub"

Opened func1.cub as #2, grid size 152,118,99, pixel 0.0602, shown at level
-0.174,0.174, step 1, values float32  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func2.cub"

Opened func2.cub as #3, grid size 152,118,99, pixel 0.0602, shown at level
-100,100, step 1, values float32  

> volume #3 level 0.5 level 100

> ui tool show "Side View"

> ui tool show Toolbar

> camera mode perspective

Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword  

> fielOfView 15.6389

Unknown command: fielOfView 15.6389  

> view

> lighting shadows true

> graphics silhouettes true

> lighting shadows false

> lighting model three-point

Missing or invalid "models" argument: invalid models specifier  

> save "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/confa1.cxs"

——— End of log from Fri Mar 7 23:43:47 2025 ———

opened ChimeraX session  

> ui tool show "Surface Color"

> color radial #3.1#3.2 palette #ff0000:#00aa00:#0000ff

> save C:/ProgramData/ChimeraX/confa1.cxs

——— End of log from Sat Mar 8 00:02:33 2025 ———

opened ChimeraX session  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_1w_004.pdb"

Summary of feedback from opening C:/Users/jonah/OneDrive/Desktop/Tesi
triennale
Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_1w_004.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Generated by Multiwfn, Totally 27 atoms  
  

> lighting model three-point

Missing or invalid "models" argument: invalid models specifier  

> color byelements

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color byelement

> represent bs

Unknown command: represent bs  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func1.cub"

Opened func1.cub as #2, grid size 182,107,91, pixel 0.0659, shown at level
-0.157,0.157, step 1, values float32  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func2.cub"

Opened func2.cub as #3, grid size 182,107,91, pixel 0.0659, shown at level
-100,100, step 1, values float32  

> style #1,3 ball

Changed 27 atom styles  

> ui tool show "Volume Viewer"

> ui tool show "Surface Color"

> color radial #3.1#3.2 palette #ff0000:#00aa00:#0000ff

[Repeated 1 time(s)]

> volume #3 level 0.5 level 100

> save "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino1w.cxs"

——— End of log from Sat Mar 8 00:16:00 2025 ———

opened ChimeraX session  

> open "C:\Users\jonah\OneDrive\Desktop\Tesi triennale
> Mariam\Multiwfn_3.8_dev_bin_Win64\Multiwfn_3.8_dev_bin_Win64\hino1w.cxs"
> format session

Opened func1.cub as #2, grid size 182,107,91, pixel 0.0659, shown at level
-0.157,0.157, step 1, values float32  
Opened func2.cub as #3, grid size 182,107,91, pixel 0.0659, shown at level
0.5,100, step 1, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 238, in restore_snapshot  
c = cls(surf, palette = data['colormap'], range = None, transparency =
data.get('transparency'),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 149, in __init__  
self.set_colormap(palette, range)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 168, in set_colormap  
r = self.value_range() if _use_full_range(range, palette) else range  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 211, in value_range  
v = self.values(va)  
^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 286, in values  
d = distances_from_origin(vertices, self.origin)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 296, in distances_from_origin  
d = zeros(len(points), floatc)  
^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
Log from Sat Mar 8 00:16:00 2025 Startup Messages  
---  
warning | Your computer has Intel graphics driver 7926 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this.  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\ProgramData\ChimeraX\confa1.cxs format session

Opened func1.cub as #2, grid size 182,107,91, pixel 0.0659, shown at level
-0.174,0.174, step 1, values float32  
Opened func2.cub as #3, grid size 182,107,91, pixel 0.0659, shown at level
0.5,100, step 1, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 238, in restore_snapshot  
c = cls(surf, palette = data['colormap'], range = None, transparency =
data.get('transparency'),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 149, in __init__  
self.set_colormap(palette, range)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 168, in set_colormap  
r = self.value_range() if _use_full_range(range, palette) else range  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 211, in value_range  
v = self.values(va)  
^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 286, in values  
d = distances_from_origin(vertices, self.origin)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 296, in distances_from_origin  
d = zeros(len(points), floatc)  
^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
Log from Sat Mar 8 00:02:33 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\jonah\OneDrive\Desktop\Tesi triennale
> Mariam\Multiwfn_3.8_dev_bin_Win64\Multiwfn_3.8_dev_bin_Win64\confa1.cxs"
> format session

Opened func1.cub as #2, grid size 155,114,100, pixel 0.0599, shown at level
-0.174,0.174, step 1, values float32  
Opened func2.cub as #3, grid size 155,114,100, pixel 0.0599, shown at level
0.5,100, step 1, values float32  
Log from Fri Mar 7 23:43:47 2025 Startup Messages  
---  
warning | Your computer has Intel graphics driver 7926 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this.  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_a_1.xyz"

Unrecognized file suffix '.xyz'  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_a_1.pdb"

Summary of feedback from opening C:/Users/jonah/OneDrive/Desktop/Tesi
triennale
Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_a_1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Generated by Multiwfn, Totally 24 atoms  
  

> color byelement

> represent bs

Unknown command: represent bs  

> color byelement

> represent bs

Unknown command: represent bs  

> style ball

Changed 24 atom styles  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func1.cub"

Opened func1.cub as #2, grid size 152,118,99, pixel 0.0602, shown at level
-0.174,0.174, step 1, values float32  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func2.cub"

Opened func2.cub as #3, grid size 152,118,99, pixel 0.0602, shown at level
-100,100, step 1, values float32  

> ui tool show "Volume Viewer"

> ui tool show "Surface Color"

> ui tool show "Volume Viewer"

> color electrostatic #3.1#3.2 map #3 palette
> -0.025,#ff0000:0,#ffffff:0.025,#0000ff

> volume #3 level 0.5 level 100

> volume #2 level 0.5 level 0.1735

> toolshed show

> close #2

> close #3

> undo

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func1.cub"

Opened func1.cub as #2, grid size 152,118,99, pixel 0.0602, shown at level
-0.174,0.174, step 1, values float32  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func2.cub"

Opened func2.cub as #3, grid size 152,118,99, pixel 0.0602, shown at level
-100,100, step 1, values float32  

> volume #3 level 0.5 level 100

> ui tool show "Side View"

> ui tool show Toolbar

> camera mode perspective

Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword  

> fielOfView 15.6389

Unknown command: fielOfView 15.6389  

> view

> lighting shadows true

> graphics silhouettes true

> lighting shadows false

> lighting model three-point

Missing or invalid "models" argument: invalid models specifier  

> save "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/confa1.cxs"

——— End of log from Fri Mar 7 23:43:47 2025 ———

opened ChimeraX session  

> ui tool show "Surface Color"

> color radial #3.1#3.2 palette #ff0000:#00aa00:#0000ff

> save C:/ProgramData/ChimeraX/confa1.cxs

——— End of log from Sat Mar 8 00:02:33 2025 ———

opened ChimeraX session  

> open C:\ProgramData\ChimeraX\confa1.cxs format session

Opened func1.cub as #2, grid size 182,107,91, pixel 0.0659, shown at level
-0.174,0.174, step 1, values float32  
Opened func2.cub as #3, grid size 182,107,91, pixel 0.0659, shown at level
0.5,100, step 1, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 238, in restore_snapshot  
c = cls(surf, palette = data['colormap'], range = None, transparency =
data.get('transparency'),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 149, in __init__  
self.set_colormap(palette, range)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 168, in set_colormap  
r = self.value_range() if _use_full_range(range, palette) else range  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 211, in value_range  
v = self.values(va)  
^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 286, in values  
d = distances_from_origin(vertices, self.origin)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 296, in distances_from_origin  
d = zeros(len(points), floatc)  
^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
Log from Sat Mar 8 00:02:33 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\jonah\OneDrive\Desktop\Tesi triennale
> Mariam\Multiwfn_3.8_dev_bin_Win64\Multiwfn_3.8_dev_bin_Win64\confa1.cxs"
> format session

Opened func1.cub as #2, grid size 155,114,100, pixel 0.0599, shown at level
-0.174,0.174, step 1, values float32  
Opened func2.cub as #3, grid size 155,114,100, pixel 0.0599, shown at level
0.5,100, step 1, values float32  
Log from Fri Mar 7 23:43:47 2025 Startup Messages  
---  
warning | Your computer has Intel graphics driver 7926 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this.  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_a_1.xyz"

Unrecognized file suffix '.xyz'  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_a_1.pdb"

Summary of feedback from opening C:/Users/jonah/OneDrive/Desktop/Tesi
triennale
Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_a_1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Generated by Multiwfn, Totally 24 atoms  
  

> color byelement

> represent bs

Unknown command: represent bs  

> color byelement

> represent bs

Unknown command: represent bs  

> style ball

Changed 24 atom styles  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func1.cub"

Opened func1.cub as #2, grid size 152,118,99, pixel 0.0602, shown at level
-0.174,0.174, step 1, values float32  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func2.cub"

Opened func2.cub as #3, grid size 152,118,99, pixel 0.0602, shown at level
-100,100, step 1, values float32  

> ui tool show "Volume Viewer"

> ui tool show "Surface Color"

> ui tool show "Volume Viewer"

> color electrostatic #3.1#3.2 map #3 palette
> -0.025,#ff0000:0,#ffffff:0.025,#0000ff

> volume #3 level 0.5 level 100

> volume #2 level 0.5 level 0.1735

> toolshed show

> close #2

> close #3

> undo

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func1.cub"

Opened func1.cub as #2, grid size 152,118,99, pixel 0.0602, shown at level
-0.174,0.174, step 1, values float32  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func2.cub"

Opened func2.cub as #3, grid size 152,118,99, pixel 0.0602, shown at level
-100,100, step 1, values float32  

> volume #3 level 0.5 level 100

> ui tool show "Side View"

> ui tool show Toolbar

> camera mode perspective

Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword  

> fielOfView 15.6389

Unknown command: fielOfView 15.6389  

> view

> lighting shadows true

> graphics silhouettes true

> lighting shadows false

> lighting model three-point

Missing or invalid "models" argument: invalid models specifier  

> save "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/confa1.cxs"

——— End of log from Fri Mar 7 23:43:47 2025 ———

opened ChimeraX session  

> ui tool show "Surface Color"

> color radial #3.1#3.2 palette #ff0000:#00aa00:#0000ff

> save C:/ProgramData/ChimeraX/confa1.cxs

——— End of log from Sat Mar 8 00:02:33 2025 ———

opened ChimeraX session  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_1w_004.pdb"

Summary of feedback from opening C:/Users/jonah/OneDrive/Desktop/Tesi
triennale
Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino_1w_004.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Generated by Multiwfn, Totally 27 atoms  
  

> lighting model three-point

Missing or invalid "models" argument: invalid models specifier  

> color byelements

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color byelement

> represent bs

Unknown command: represent bs  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func1.cub"

Opened func1.cub as #2, grid size 182,107,91, pixel 0.0659, shown at level
-0.157,0.157, step 1, values float32  

> open "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/func2.cub"

Opened func2.cub as #3, grid size 182,107,91, pixel 0.0659, shown at level
-100,100, step 1, values float32  

> style #1,3 ball

Changed 27 atom styles  

> ui tool show "Volume Viewer"

> ui tool show "Surface Color"

> color radial #3.1#3.2 palette #ff0000:#00aa00:#0000ff

[Repeated 1 time(s)]

> volume #3 level 0.5 level 100

> save "C:/Users/jonah/OneDrive/Desktop/Tesi triennale
> Mariam/Multiwfn_3.8_dev_bin_Win64/Multiwfn_3.8_dev_bin_Win64/hino1w.cxs"

——— End of log from Sat Mar 8 00:16:00 2025 ———

opened ChimeraX session  




OpenGL version: 3.3.0 - Build 26.20.100.7926
OpenGL renderer: Intel(R) Iris(R) Plus Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: it_IT.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: HP
Model: HP Laptop 15s-fq1xxx
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 16,852,414,464
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-1065G7 CPU @ 1.30GHz
OSLanguage: it-IT

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    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: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 8 months ago

Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Restore surface: 'points' is None

comment:2 by Tom Goddard, 8 months ago

Resolution: → fixed
Status: assigned → closed

Fixed.

User applied radial coloring to an empty surface (e.g. a volume with threshold set above the highest intensity value) then saved the session. Session restore gave an error in that case. Fixed the code to handle restore where the surface is empty.

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