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#8203 closed defect (duplicate)

Save mouse undo info: models is None

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

Description

The following bug report has been submitted:
Platform:        Linux-5.15.0-53-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> MRVRGIWKNWPQWLIWSILGFWIGNMEGSWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTPLCVTLNCTNVKGNESDTSEVMKNCSFKATTELKDKKHKVHALFYKLDVVPLNGNSSSSGEYRLINCNTSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNNTRKSIRIGPGQTFYATGDIIGNIRQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDGGQSNETNDTETFRPGGGDMRDNWRSELYKYKVVEIKPLGVAPTECKRRVVERRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQSNLLRAPEAQQHMLQLTVWGIKQLQARVLAIERYLKDQQLLGMWGCSGKLICCTAVPWNSSWSNKSQNEIWGNMTWMQWDREINNYTNTIYRLLEDSQNQQEKNEKDLLALD,MRVRGIWKNWPQWLIWSILGFWIGNMEGSWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTPLCVTLNCTNVKGNESDTSEVMKNCSFKATTELKDKKHKVHALFYKLDVVPLNGNSSSSGEYRLINCNTSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNNTRKSIRIGPGQTFYATGDIIGNIRQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDGGQSNETNDTETFRPGGGDMRDNWRSELYKYKVVEIKPLGVAPTECKRRVVERRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQSNLLRAPEAQQHMLQLTVWGIKQLQARVLAIERYLKDQQLLGMWGCSGKLICCTAVPWNSSWSNKSQNEIWGNMTWMQWDREINNYTNTIYRLLEDSQNQQEKNEKDLLALD,MRVRGIWKNWPQWLIWSILGFWIGNMEGSWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTPLCVTLNCTNVKGNESDTSEVMKNCSFKATTELKDKKHKVHALFYKLDVVPLNGNSSSSGEYRLINCNTSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNNTRKSIRIGPGQTFYATGDIIGNIRQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDGGQSNETNDTETFRPGGGDMRDNWRSELYKYKVVEIKPLGVAPTECKRRVVERRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQSNLLRAPEAQQHMLQLTVWGIKQLQARVLAIERYLKDQQLLGMWGCSGKLICCTAVPWNSSWSNKSQNEIWGNMTWMQWDREINNYTNTIYRLLEDSQNQQEKNEKDLLALD

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /home/abontempo/Downloads/ChimeraX/AlphaFold/prediction_2  

Downloaded prediction file not found:
/home/abontempo/Downloads/ChimeraX/AlphaFold/prediction_2/best_model.pdb  

AlphaFold prediction finished  
Results in /home/abontempo/Downloads/ChimeraX/AlphaFold/prediction_3  

Downloaded prediction file not found:
/home/abontempo/Downloads/ChimeraX/AlphaFold/prediction_3/best_model.pdb  

> open /home/abontempo/Downloads/result_model_1_multimer_v2_pred_0.pkl

Unrecognized file suffix '.pkl'  

> open
> /home/abontempo/Downloads/result_model_1_multimer_v2_pred_0.7jEwubs9.pkl.part

Unrecognized file suffix '.part'  

> open /home/abontempo/Downloads/5633898.pdb

Chain information for 5633898.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> style sphere

Changed 30683 atom styles  

> style sphere

Changed 30683 atom styles  

> rename #1 "alphafold 1086.pdb"

> show atoms

> hide atoms

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> style sphere

Changed 30683 atom styles  

> style sphere

Changed 30683 atom styles  

> style sphere

Changed 30683 atom styles  

> show surfaces

> open /home/abontempo/Desktop/belnap1/Class3D/job038/run_it025_class017.mrc
> format mrc

Opened run_it025_class017.mrc as #2, grid size 160,160,160, pixel 1.36, shown
at level 0.0451, step 1, values float32  

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #2.1 models

> show #2.1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> hide #2.1 models

> show #!1 models

> close #2

> open "/home/abontempo/Desktop/belnap 1086 final model 1222.mrc"

Opened belnap 1086 final model 1222.mrc as #2, grid size 256,256,256, pixel
1.22, shown at level 0.00932, step 1, values float32  

> volume #2 level 0.008888

> volume #2 level 0.0107

> hide #!2 models

> show #!2 models

Drag select of 2 belnap 1086 final model 1222.mrc  

> ui mousemode right "rotate selected particles"

> mousemode rightMode "rotate selected particles"

Invalid "rightMode" argument: Should be one of 'bond rotation', 'clip', 'clip
rotate', 'contour level', 'crop volume', 'delete markers', 'distance',
'identify object', 'label', 'link markers', 'map eraser', 'mark center', 'mark
maximum', 'mark plane', 'mark point', 'mark surface', 'minimize', 'move
label', 'move markers', 'move picked models', 'move planes', 'next docked',
'none', 'pick blobs', 'pivot', 'play coordinates', 'play map series', 'resize
markers', 'rotate', 'rotate and select', 'rotate independent', 'rotate
selected atoms', 'rotate selected models', 'rotate slab', 'rotate z selected
models', 'select', 'select add', 'select subtract', 'select toggle', 'swapaa',
'swipe as scroll', 'tape measure', 'translate', 'translate selected atoms',
'translate selected models', 'translate xy selected models', 'tug',
'windowing', 'zone', or 'zoom'  

> select clear

> ui mousemode right "rotate selected particles"

> mousemode rightMode "rotate selected particles"

Invalid "rightMode" argument: Should be one of 'bond rotation', 'clip', 'clip
rotate', 'contour level', 'crop volume', 'delete markers', 'distance',
'identify object', 'label', 'link markers', 'map eraser', 'mark center', 'mark
maximum', 'mark plane', 'mark point', 'mark surface', 'minimize', 'move
label', 'move markers', 'move picked models', 'move planes', 'next docked',
'none', 'pick blobs', 'pivot', 'play coordinates', 'play map series', 'resize
markers', 'rotate', 'rotate and select', 'rotate independent', 'rotate
selected atoms', 'rotate selected models', 'rotate slab', 'rotate z selected
models', 'select', 'select add', 'select subtract', 'select toggle', 'swapaa',
'swipe as scroll', 'tape measure', 'translate', 'translate selected atoms',
'translate selected models', 'translate xy selected models', 'tug',
'windowing', 'zone', or 'zoom'  

> ui mousemode right translate

[Repeated 2 time(s)]

> artiax view xy

> artiax view xz

> select add #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.60161,-0.052225,-0.79708,382.12,-0.18981,0.97863,0.079139,18.457,0.77591,0.1989,-0.59866,121.62

> view matrix models
> #2,-0.30954,0.028646,-0.95045,351.76,-0.20163,0.97484,0.095047,18.136,0.92926,0.22106,-0.29598,44.448

> view matrix models
> #2,-0.31617,0.11787,-0.94135,337.71,-0.30408,0.92731,0.21824,20.046,0.89865,0.35524,-0.25735,22.237

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.31617,0.11787,-0.94135,213.21,-0.30408,0.92731,0.21824,-50.586,0.89865,0.35524,-0.25735,21.508

> view matrix models
> #2,-0.31617,0.11787,-0.94135,160.49,-0.30408,0.92731,0.21824,-35.283,0.89865,0.35524,-0.25735,7.0048

> view matrix models
> #2,-0.31617,0.11787,-0.94135,165.66,-0.30408,0.92731,0.21824,-29.262,0.89865,0.35524,-0.25735,-3.9996

> select subtract #2

Nothing selected  

> select add #2

2 models selected  

> view matrix models
> #2,-0.31617,0.11787,-0.94135,141.72,-0.30408,0.92731,0.21824,-38.173,0.89865,0.35524,-0.25735,-34.088

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.31851,0.13129,-0.93878,139.61,-0.27968,0.93326,0.22541,-43.939,0.90572,0.33435,-0.26053,-31.452

> view matrix models
> #2,-0.21997,0.13088,-0.96669,129.56,-0.16311,0.97207,0.16872,-57.81,0.96178,0.19479,-0.19248,-30.146

> view matrix models
> #2,-0.20717,0.14477,-0.96753,125.67,-0.11905,0.97791,0.17182,-65.828,0.97103,0.15078,-0.18535,-26.065

> view matrix models
> #2,-0.29054,-0.20048,-0.93563,185.14,-0.062159,0.97969,-0.19062,-13.826,0.95484,0.0027746,-0.2971,17.536

> view matrix models
> #2,-0.59789,0.13556,-0.79003,155.95,-0.063907,0.9744,0.21556,-80.915,0.79903,0.17937,-0.57392,60.628

> view matrix models
> #2,-0.18709,0.19591,-0.96261,114.09,-0.11547,0.96873,0.2196,-72.994,0.97553,0.15223,-0.15862,-31.447

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.18709,0.19591,-0.96261,109.43,-0.11547,0.96873,0.2196,-98.418,0.97553,0.15223,-0.15862,-34.182

> ui mousemode right zoom

> select subtract #2

Nothing selected  

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.18709,0.19591,-0.96261,112.45,-0.11547,0.96873,0.2196,-91.15,0.97553,0.15223,-0.15862,-39.367

> view matrix models
> #2,-0.18709,0.19591,-0.96261,111.79,-0.11547,0.96873,0.2196,-90.548,0.97553,0.15223,-0.15862,-37.759

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.35101,0.068487,-0.93386,150.88,-0.08711,0.99061,0.10539,-78.956,0.93231,0.11834,-0.34175,4.5924

> show surfaces

> select subtract #2

Nothing selected  

> select add #1

30683 atoms, 31016 bonds, 1956 residues, 1 model selected  

> show sel surfaces

[Repeated 3 time(s)]

> show sel cartoons

[Repeated 1 time(s)]

> color sel byhetero

> color sel bychain

> color sel bypolymer

> color sel bychain

> rainbow sel

[Repeated 1 time(s)]

> mlp sel

Map values for surface "alphafold 1086.pdb_A SES surface": minimum -27.32,
mean -4.064, maximum 25.33  
Map values for surface "alphafold 1086.pdb_B SES surface": minimum -27.72,
mean -4.04, maximum 25.24  
Map values for surface "alphafold 1086.pdb_C SES surface": minimum -26.97,
mean -4.062, maximum 25.24  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for alphafold 1086.pdb_A SES surface #1.1: minimum, -18.87,
mean 0.98, maximum 23.11  
Coulombic values for alphafold 1086.pdb_B SES surface #1.2: minimum, -14.21,
mean 0.98, maximum 18.07  
Coulombic values for alphafold 1086.pdb_C SES surface #1.3: minimum, -13.54,
mean 0.99, maximum 20.20  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel

Coulombic values for alphafold 1086.pdb_A SES surface #1.1: minimum, -18.87,
mean 0.98, maximum 23.11  
Coulombic values for alphafold 1086.pdb_B SES surface #1.2: minimum, -14.21,
mean 0.98, maximum 18.07  
Coulombic values for alphafold 1086.pdb_C SES surface #1.3: minimum, -13.54,
mean 0.99, maximum 20.20  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!2 models

> show #!2 models

> select subtract #1

3 models selected  

> select clear

> lighting soft

> lighting full

> lighting simple

> lighting full

> lighting simple

> select add #1

30683 atoms, 31016 bonds, 1956 residues, 1 model selected  

> volume style surface

> volume style mesh

[Repeated 1 time(s)]

> volume style surface

> select subtract #1

3 models selected  

> select add #1

30683 atoms, 31016 bonds, 1956 residues, 1 model selected  

> volume style surface

[Repeated 1 time(s)]

> volume style mesh

> volume style surface

> surface dust #2 size 12.2

> volume style surface

> volume style mesh

> volume style surface

> view matrix models
> #1,0.99169,-0.12425,-0.033214,-0.22633,0.11182,0.96054,-0.25467,1.1719,0.063547,0.24885,0.96646,0.96309

> undo

> select subtract #1

3 models selected  

> select add #2

2 models selected  

> view matrix models
> #2,-0.31992,0.17719,-0.93073,129.22,-0.085505,0.97295,0.21462,-94.849,0.94358,0.14824,-0.29612,-9.2843

> select subtract #2

Nothing selected  

> set bgColor white

> set bgColor #ffffff00

> lighting full

> color byhetero

> color bychain

> volume #2 level 0.009493

> volume #2 level 0.01226

> volume #2 level 0.01088

> color #2 #33d17a models transparency 0

> save /home/abontempo/Desktop/image13.png supersample 3

> select add #2

2 models selected  

> view matrix models
> #2,-0.56955,0.0029758,-0.82195,174.82,-0.022125,0.99958,0.01895,-75.565,0.82166,0.028979,-0.56924,72.904

> view matrix models
> #2,-0.4932,-0.187,-0.84958,196.77,-0.061385,0.98167,-0.18044,-33.506,0.86775,-0.03684,-0.49564,63.609

> view matrix models
> #2,-0.67193,0.2305,-0.70383,135.9,0.029281,0.95786,0.28574,-121.73,0.74004,0.17139,-0.65036,77.197

> view matrix models
> #2,-0.57417,-0.0073355,-0.8187,176.53,-0.022407,0.99973,0.0067571,-73.499,0.81843,0.022224,-0.57418,75.242

> view matrix models
> #2,-0.54026,-0.084583,-0.83724,186.25,-0.03087,0.99626,-0.080728,-57.025,0.84093,-0.017768,-0.54085,72.329

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.65373,0.18692,-0.73328,144.72,0.092868,0.98151,0.1674,-114.99,0.75101,0.041335,-0.659,96.698

> view matrix models
> #2,-0.24917,0.1844,-0.95074,120.86,0.13317,0.9789,0.15496,-118.56,0.95926,-0.087994,-0.26847,19.506

> view matrix models
> #2,-0.45561,0.10698,-0.88373,152.33,0.15156,0.98758,0.041411,-103.59,0.87718,-0.11507,-0.46617,69.098

> view matrix models
> #2,-0.36512,0.14104,-0.92022,139.71,0.14647,0.98485,0.092824,-111.03,0.91937,-0.1009,-0.38024,46.202

> save /home/abontempo/Desktop/image14.png supersample 3

>

Incomplete command: remotecontrol  

>

Incomplete command: remotecontrol  

>

Incomplete command: remotecontrol  

> select add #1

30683 atoms, 31016 bonds, 1956 residues, 3 models selected  

> select subtract #2

30683 atoms, 31016 bonds, 1956 residues, 4 models selected  
No atomic structure models chosen  

> select subtract #1

3 models selected  

> select add #1

30683 atoms, 31016 bonds, 1956 residues, 1 model selected  
No atomic structure models chosen  

> view matrix models
> #1,0.83118,0.28699,0.47622,-2.0374,-0.25498,0.95787,-0.13221,-2.3574,-0.4941,-0.011537,0.86933,-4.6743

> view matrix models
> #1,0.7858,0.5285,0.32126,-1.7053,-0.50925,0.84765,-0.14883,-5.1043,-0.35098,-0.046647,0.93522,-3.4137

> view matrix models
> #1,0.70993,0.67429,0.20332,-1.6895,-0.65631,0.73812,-0.1563,-6.7867,-0.25546,-0.022481,0.96656,-2.5263

> undo

[Repeated 3 time(s)]Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 639, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_up  
self._undo_save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
TypeError: 'NoneType' object is not iterable  
  
TypeError: 'NoneType' object is not iterable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 531, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_up  
self._undo_save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
TypeError: 'NoneType' object is not iterable  
  
TypeError: 'NoneType' object is not iterable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 639, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_up  
self._undo_save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
TypeError: 'NoneType' object is not iterable  
  
TypeError: 'NoneType' object is not iterable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 531, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_up  
self._undo_save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
TypeError: 'NoneType' object is not iterable  
  
TypeError: 'NoneType' object is not iterable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 639, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_up  
self._undo_save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
TypeError: 'NoneType' object is not iterable  
  
TypeError: 'NoneType' object is not iterable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 531, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_up  
self._undo_save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
TypeError: 'NoneType' object is not iterable  
  
TypeError: 'NoneType' object is not iterable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 639, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_up  
self._undo_save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
TypeError: 'NoneType' object is not iterable  
  
TypeError: 'NoneType' object is not iterable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 531, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_up  
self._undo_save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
TypeError: 'NoneType' object is not iterable  
  
TypeError: 'NoneType' object is not iterable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 639, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_up  
self._undo_save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
TypeError: 'NoneType' object is not iterable  
  
TypeError: 'NoneType' object is not iterable  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 482, in _undo_save  
new_model_positions = [m.position for m in models]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 22.0.5
OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CFL GT2)
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: Dell Inc.
Model: OptiPlex 7070
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz
Cache Size: 9216 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           7.5Gi       5.0Gi       126Mi       1.0Gi       2.4Gi       1.2Gi
	Swap:          2.0Gi       1.9Gi       110Mi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation CoffeeLake-S GT2 [UHD Graphics 630] [8086:3e92]	
	DeviceName: Onboard - Video	
	Subsystem: Dell CometLake-S GT2 [UHD Graphics 630] [1028:092e]

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    pandas: 1.4.4
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    starfile: 0.4.11
    suds-community: 1.0.0
    superqt: 0.3.5
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    typing-extensions: 4.3.0
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component:	Unassigned → Undo/Redo
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Save mouse undo info: models is None

comment:2 by Eric Pettersen, 3 years ago

Resolution:	→ duplicate
Status:	assigned → closed

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