The following bug report has been submitted:
Platform: Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-03-14)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.93 (2020-03-14)
© 2016-2020 Regents of the University of California. All rights reserved.
> save session
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs includeMaps true
Log from Sun Aug 2 17:01:27 2020UCSF ChimeraX version: 0.93 (2020-03-14)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs format session
Log from Sun Aug 2 16:15:18 2020UCSF ChimeraX version: 0.93 (2020-03-14)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs format session
Log from Mon Jul 27 16:49:17 2020UCSF ChimeraX version: 0.93 (2020-03-14)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/hybrid.pdb
File not found:
/Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
compare/mapping-hybrid/hybrid.pdb
> open
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/hybrid.pdb
File not found:
/Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
compare/mapping-hybrid/hybrid.pdb
> open
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/hybrid-MB.pdb
Summary of feedback from opening
/Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
compare/mapping-hybrid/hybrid-MB.pdb
---
warnings | Duplicate atom serial number found: 30
Duplicate atom serial number found: 31
Duplicate atom serial number found: 32
Duplicate atom serial number found: 33
Duplicate atom serial number found: 34
1508 messages similar to the above omitted
Chain information for hybrid-MB.pdb #1
---
Chain | Description
A | No description available
> close session
> open
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/hybrid-MB.pdb
Summary of feedback from opening
/Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
compare/mapping-hybrid/for-figure/hybrid-MB.pdb
---
warnings | Duplicate atom serial number found: 30
Duplicate atom serial number found: 31
Duplicate atom serial number found: 32
Duplicate atom serial number found: 33
Duplicate atom serial number found: 34
1508 messages similar to the above omitted
Chain information for hybrid-MB.pdb #1
---
Chain | Description
A | No description available
> select : 332-532
1590 atoms, 1634 bonds, 1 model selected
> select ~sel
6233 atoms, 6365 bonds, 14 pseudobonds, 2 models selected
> hide ribbons
Expected ',' or a keyword
> hide sel ribbons
> set bgColor white
> set bgColor black
> set bgColor gray
> set bgColor white
> set bgColor black
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> view sel
> view
> view orient
> toolshed show "Side View"
> view orient
> view orient
Unknown command: select: 532
> select : 532
8 atoms, 7 bonds, 1 model selected
> color sel red
> ui mousemode rightMode "mark maximum"
> ui mousemode rightMode "delete markers"
> select : 444
9 atoms, 8 bonds, 1 model selected
> ui mousemode rightMode "move label"
> view orient
> 2dlabels text "RBD-N ter"
> ui mousemode rightMode "move label"
> ui mousemode rightMode "move label"
> 2dlabels #2.1 xpos 0.784 ypos 0.806
> view orient
> view orient
> ui mousemode rightMode "move label"
> 2dlabels #2.1 xpos 0.786 ypos 0.735
> view orient
> 2dlabels #2.1 xpos 0.750 ypos 0.160
> 2dlabels #2.1 xpos 0.753 ypos 0.146
> 2dlabels text "RBD-N ter" color red
> redo
> redo
> redo
> redo
> 2dlabels #2.2 xpos 0.617 ypos 0.069
> 2dlabels #2.1 xpos 0.753 ypos 0.146
> 2dlabels #2.2 xpos 0.608 ypos 0.088
> 2dlabels delete #2.1
> view orient
> 2dlabels #2.2 xpos 0.746 ypos 0.156
> view orient
> 2dlabels #2.2 xpos 0.747 ypos 0.106
> 2dlabels arrow start .5,.075 end .9,.2 color red
> view orient
> 2dlabels #2.2 xpos 0.861 ypos 0.309
> undo
> close session
> open
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/hybrid-MB.pdb
Summary of feedback from opening
/Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
compare/mapping-hybrid/for-figure/hybrid-MB.pdb
---
warnings | Duplicate atom serial number found: 30
Duplicate atom serial number found: 31
Duplicate atom serial number found: 32
Duplicate atom serial number found: 33
Duplicate atom serial number found: 34
1508 messages similar to the above omitted
Chain information for hybrid-MB.pdb #1
---
Chain | Description
A | No description available
> select up
Nothing selected
> select up
Nothing selected
> select : 332-532
1590 atoms, 1634 bonds, 1 model selected
> select ~sel
6233 atoms, 6365 bonds, 14 pseudobonds, 2 models selected
Expected ',' or a keyword
> hide sel cartoons
> view orient
> select :
> 417,446,449,453,455,456,473,475,476,484,486,487,489,490,493,496,498,500,501,502,505
181 atoms, 174 bonds, 1 model selected
> select :
> 417,446,449,453,455,456,473,475,476,484,486,487,489,490,493,496,498,500,501,502,505
181 atoms, 174 bonds, 1 model selected
> color sel cyan
> select :
> 334,335,337,339,340,341,343,344,345,346,354,356,358,359,360,361,440,441,444,509
155 atoms, 146 bonds, 1 model selected
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel orange
> select :
> 369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,385,386,389,390,392,427,428,429,430,515,516,517,519
232 atoms, 234 bonds, 1 model selected
> color sel hotpink
> select : 346,444,446,447,448,449,450,452,483,484,485,490,494
101 atoms, 96 bonds, 1 model selected
> color sel yellow
> select :
> 403,405,406,409,415,416,417,420,421,453,455,456,457,458,459,460,473,474,475,476,477,486,487,489,490,493,494,495,496,498,500,501,502,503,505
298 atoms, 293 bonds, 1 model selected
> color sel cornflowerblue
> select :
> 417,446,449,453,455,456,473,475,476,484,486,487,489,490,493,496,498,500,501,502,505
181 atoms, 174 bonds, 1 model selected
> color sel cyan
> view orient
> view orient
> view orient
> select clear
> save session
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-MB.cxs includeMaps true
> view orient
> select : 532
8 atoms, 7 bonds, 1 model selected
> color sel red
> select clear
> set bgColor white
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting flat
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting full
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> lighting simple
> lighting simple
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting full
> lighting full
> lighting soft
> lighting simple
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select : 444,508
21 atoms, 20 bonds, 1 model selected
> color sel blue
> select clear
> view orient
> graphics silhouettes false
> lighting simple
> lighting full
> lighting full
> lighting simple
> view
> graphics silhouettes true
> select : 444,508
21 atoms, 20 bonds, 1 model selected
> color sel green
> select clear
> save session
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-MB.cxs includeMaps true
> save /Users/munmunbhasin/Desktop/image1.png supersample 3
> view orient
> save /Users/munmunbhasin/Desktop/image1.png supersample 3
> select : 532
8 atoms, 7 bonds, 1 model selected
> label sel
> ui mousemode rightMode "move label"
> label size 30
> label size 40
Missing or invalid "atoms" argument: invalid atoms specifier
> label sel
> label sel size 40 color red
> label sel size 50 color red
> label sel size 100 color red
> label sel size 100 height 10 color red
> label sel size 100 height 5 color red
> label sel size 50 height 5 color red
> label sel size 40 height 5 color red
> label sel size 40 height 2 color red
> ui mousemode rightMode "move label"
> save /Users/munmunbhasin/Desktop/image1.png supersample 3
> 2dlabels text "RBM-N terminus" color green
> 2dlabels #2.1 xpos 0.359 ypos 0.879
> 2dlabels #2.1 xpos 0.355 ypos 0.882
Expected a keyword
> 2dlabels text "RBM-N terminus" color green size 40
> 2dlabels delete #2.2
> 2dlabels arrow color green
No 2D arrows in session
> undo
> undo
> redo
> 2dlabels #2.1 xpos 0.222 ypos 0.895
> 2dlabels #2.1 size 20
> 2dlabels #2.1 size 25
> 2dlabels #2.1 size 22
> 2dlabels #2.1 xpos 0.133 ypos 0.809
> 2dlabels #2.1 xpos 0.133 ypos 0.809
> 2dlabels #2.1 xpos 0.222 ypos 0.919
> 2dlabels #2.1 xpos 0.221 ypos 0.903
> 2dlabels text "RBM-C terminus" color green size 22
> 2dlabels #2.2 xpos 0.414 ypos 0.877
> 2dlabels #2.2 xpos 0.428 ypos 0.894
> 2dlabels #2.1 xpos 0.219 ypos 0.903
> 2dlabels #2.2 xpos 0.428 ypos 0.891
> 2dlabels #2.2 xpos 0.428 ypos 0.891
> 2dlabels #2.2 xpos 0.428 ypos 0.903
> save session
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs includeMaps true
> 2dlabels arrow start 0.2,0.9 end 0.4,0.9 color green
> 2dlabels #2.1 xpos 0.224 ypos 0.919
> 2dlabels #2.1 xpos 0.221 ypos 0.917
Expected 'all' or a label/arrow models specifier or a keyword
Expected 'all' or a label/arrow models specifier or a keyword
Expected 'all' or a label/arrow models specifier or a keyword
Expected 'all' or a label/arrow models specifier or a keyword
Expected 'all' or a label/arrow models specifier or a keyword
> 2dlabels delete #2.3
> 2dlabels delete #3.1
> 2dlabels #2.1 xpos 0.221 ypos 0.917
> 2dlabels #2.1 xpos 0.220 ypos 0.912
> 2dlabels #2.1 xpos 0.220 ypos 0.908
> save session
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs includeMaps true
> ui mousemode rightMode zoom
> ui mousemode rightMode select
> select clear
> select /A:372
5 atoms, 4 bonds, 1 model selected
> ui mousemode rightMode label
> label delete residues
> ui mousemode rightMode "move label"
> select : 532
8 atoms, 7 bonds, 1 model selected
> label sel size 40 height 2 color red
> save session
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs includeMaps true
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> 2dlabels arrow start 0.4,0.9 end 0.4,0.7 color green
> 2dlabels arrow start 0.4,0.9 end 0.4,0.7 color green weight 0.5
> 2dlabels delete #3.1
> 2dlabels delete #3.2
> 2dlabels arrow start 0.4,0.9 end 0.4,0.8 color green weight 0.2
> 2dlabels arrow start 0.2,0.9 end 0.2,0.8 color green weight 0.2
> 2dlabels arrow start 0.3,0.9 end 0.3,0.8 color green weight 0.2
> 2dlabels delete #3.2
> 2dlabels delete #3.1
> 2dlabels #2.1 xpos 0.190 ypos 0.906
> 2dlabels #2.2 xpos 0.379 ypos 0.899
> 2dlabels arrow start 0.4,0.9 end 0.4,0.8 color green weight 0.2
> 2dlabels #2.2 xpos 0.374 ypos 0.905
> 2dlabels delete #3.3
> 2dlabels delete #3.4
> 2dlabels delete #3.1
> 2dlabels arrow start 0.3,0.9 end 0.3,0.8 color green weight 0.2
> 2dlabels arrow start 0.4,0.9 end 0.4,0.7 color green weight 0.2
> 2dlabels delete #3.1
> 2dlabels arrow start 0.32,0.9 end 0.32,0.8 color green weight 0.2
> save session
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs includeMaps true
> save /Users/munmunbhasin/Desktop/image1.png supersample 3
> select clear
> save /Users/munmunbhasin/Desktop/image1.png supersample 3
> save session
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs includeMaps true
opened ChimeraX session
> select : 343
8 atoms, 7 bonds, 1 model selected
> color sel red
> label sel
> label sel size 40 height 2 color red
> undo
> redo
> select clear
> save /Users/munmunbhasin/Desktop/image1.png supersample 3
> save session
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs includeMaps true
opened ChimeraX session
> select : 527
7 atoms, 7 bonds, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> 2dlabels arrow start 0.32,0.9 end 0.32,0.8 color red weight 0.2
> 2dlabels delete #3.4
> 2dlabels delete #3.3
> select up
Nothing selected
> 2dlabels arrow start 0.5,0.9 end 0.32,0.8 color red weight 0.2
> 2dlabels arrow #3.3 start 1.5,1.9 end 1.32,1.8 color red weight 0.2
> 2dlabels arrow start 0.5,0.9 end 0.32,0.8 color red weight 0.2
> 2dlabels delete #3.4
> 2dlabels arrow #3.3 start 0.9,1.9 end 0.7,1.8 color red weight 0.2
> 2dlabels arrow #3.3 start 0.9,0.9 end 0.7,0.8 color red weight 0.2
> 2dlabels arrow #3.3 start 0.7,0.9 end 0.7,0.8 color red weight 0.2
> 2dlabels arrow #3.3 start 0.6,0.9 end 0.7,0.8 color red weight 0.2
> 2dlabels arrow #3.3 start 0.6,0.9 end 0.5,0.8 color red weight 0.2
> 2dlabels arrow #3.3 start 0.6,0.9 end 0.5,0.9 color red weight 0.2
> 2dlabels arrow #3.3 start 0.6,0.9 end 0.5,0.6 color red weight 0.2
> 2dlabels arrow #3.3 start 0.6,0.9 end 0.5,0.5 color red weight 0.2
> 2dlabels arrow #3.3 start 0.6,0.9 end 0.5,0.8 color red weight 0.2
> 2dlabels arrow #3.3 start 0.6,0.9 end 0.5,0.85 color red weight 0.2
> 2dlabels arrow #3.3 start 0.6,0.9 end 0.5,0.75 color red weight 0.2
> 2dlabels arrow #3.3 start 0.572,0.888
> 2dlabels arrow #3.3 end 0.500,0.724
> 2dlabels arrow #3.3 start 0.568,0.887
> 2dlabels #2.1 xpos 0.173 ypos 0.912
> 2dlabels arrow #3.2 start 0.295,0.902
> 2dlabels arrow #3.2 end 0.311,0.806
> 2dlabels #2.2 xpos 0.352 ypos 0.909
> 2dlabels arrow #3.1 end 0.401,0.696
> 2dlabels arrow #3.1 start 0.392,0.897
> 2dlabels arrow #3.3 start 0.543,0.888
> 2dlabels arrow #3.3 start 0.542,0.885
> 2dlabels arrow #3.3 start 0.542,0.892
> 2dlabels arrow start 0.5,0.9 end 0.32,0.8 color red weight 0.2
> 2dlabels arrow #3.4 start 0.849,0.688
> 2dlabels arrow #3.4 end 0.628,0.705
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
> 2dlabels arrow #3.4 end 0.847,0.675
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
Can't find font for arrow
> 2dlabels arrow #3.4 start 0.847,0.771
> 2dlabels arrow #3.4 end 0.866,0.604
> 2dlabels arrow #3.4 start 0.866,0.695
> 2dlabels arrow #3.4 end 0.867,0.603
> 2dlabels arrow #3.4 end 0.862,0.602
> 2dlabels arrow #3.4 start 0.866,0.687
> 2dlabels arrow #3.1 end 0.399,0.666
> 2dlabels arrow #3.2 end 0.307,0.807
> 2dlabels arrow #3.3 end 0.497,0.702
> 2dlabels arrow #3.3 start 0.533,0.861
> 2dlabels arrow #3.4 end 0.855,0.525
> 2dlabels arrow #3.4 start 0.859,0.615
> save session
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs includeMaps true
> save /Users/munmunbhasin/Desktop/image1.png supersample 3
> save session
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs includeMaps true
Summary of feedback from opening
/Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs
---
notes |
> open
> /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes-
> compare/mapping-hybrid/for-figure/epitopes-labels-MB.cxs format session
opened ChimeraX session
opened ChimeraX session
> close session
Traceback (most recent call last):
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 939, in <lambda>
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 655, in file_close_cb
run(session, 'close session')
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/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
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/close.py", line 60, in close_session
session.reset()
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 469, in reset
sm.reset_state(container, self)
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 528, in reset_state
self.close([m for m in self.list() if not m.SESSION_ENDURING])
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 705, in close
mremoved = self.remove(models)
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 688, in remove
del self._models[model_id]
KeyError: (1, 2)
KeyError: (1, 2)
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 688, in remove
del self._models[model_id]
See log for complete Python traceback.
> close session
Traceback (most recent call last):
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 939, in <lambda>
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 655, in file_close_cb
run(session, 'close session')
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/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
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/close.py", line 60, in close_session
session.reset()
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 469, in reset
sm.reset_state(container, self)
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 528, in reset_state
self.close([m for m in self.list() if not m.SESSION_ENDURING])
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 705, in close
mremoved = self.remove(models)
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 684, in remove
m.removed_from_session(session)
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 133, in removed_from_session
self._graphics_updater.remove_structure(self)
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2659, in remove_structure
self._structures.remove(s)
KeyError: <chimerax.atomic.structure.AtomicStructure object at 0x12253a790>
KeyError:
File
"/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/896BEB6C-7347-4BD0-897F-D2D8EC2F079B/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2659, in remove_structure
self._structures.remove(s)
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
You are using a very old version of ChimeraX 0.93. Current version is 1.1. This bug closing a session is probably fixed in 1.1.