![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 years ago
Closed 5 years ago
#3291 closed defect (duplicate)
Model panel, list index out of range, restoring session
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-11-26)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warning | 'clip' is a prefix of an existing command 'clipper'
UCSF ChimeraX version: 0.91 (2019-11-26)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/chunyan/2020/gp8-asym/gp8-asym-20200521.cxs
opened ChimeraX session
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> view p6
> view p3
> open /Users/chunyan/2020/gp8-asym/gp8-asym-20200521.cxs
opened ChimeraX session
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
> toolshed show "Side View"
> view orient
> transparency #7 30
> transparency #7 0
Expected a keyword
> surface dust #7 size 30
> hide sel cartoons
> select clear
> select clear
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> show sel atoms
> select clear
> open /Users/chunyan/2020/gp8-asym/gp8-asym-3.8-masked.mrc
Opened gp8-asym-3.8-masked.mrc, grid size 400,400,400, pixel 1.05, shown at
level 0.00372, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> volume #25 level 0.007402
> select #25
2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> volume #10 color #ffff0080
> volume #10 color #ff000080
> volume #10 color #fff30080
> volume #10 color #fff40080
> volume #10 color #fff50080
> volume #10 color #fff80080
> volume #10 color #fffe0080
> volume #10 color #ffff0080
> volume #10 color #ffb20080
> volume #10 color #ff970080
> volume #10 color #ff970280
> volume #10 color #ff970680
> volume #10 color #ff970682
> volume #10 color #ff970686
> volume #10 color #ff97069f
> volume #10 color #ff9706ba
> volume #10 color #ff9706d7
> volume #10 color #ff9706f2
> volume #10 color #ff9706
> volume #10 color #ff9705
> volume #10 color #ff9701
> volume #10 color #ff9700
> volume #10 color #ff9600
> volume #10 color #ff9400
> volume #10 color #ff8700
> volume #10 color #ff8000
> volume #10 color #ff7600
> volume #10 color #ff7400
> volume #10 color #ff6e00
> volume #10 color #ff6a00
> volume #10 color #ff6900
> volume #10 color #ff6c00
> volume #10 color #ff6d00
> volume #10 color #ff7100
> volume #10 color #ff7800
> volume #10 color #ff7c00
> volume #10 color #ff7f00
> volume #10 color #ff8200
> volume #10 color #ff8500
> volume #10 color #ff8600
> volume #10 color #ff8800
> volume #10 color #ff8900
> volume #10 color #ff8b00
> volume #10 color #ff8f00
> volume #10 color #ff9100
> volume #10 color #ff9200
> volume #10 color #ff9300
> volume #10 color #ff9400
> volume #10 color #ff9300
> volume #10 color #ff9200
> volume #10 color #ff8f00
> volume #10 color #ff8e00
> volume #10 color #ff8d00
> volume #10 color darkorange
> volume #10 color #ff8b00
> volume #10 color #ff8800
> volume #10 color #ff8600
> volume #10 color #ff8500
> volume #10 color #ff8400
> volume #10 color #ff8300
> volume #10 color #ff8200
> volume #10 color #ff8100
> volume #10 color #ff8000
> volume #10 color #ff8a00
> volume #10 color #ff8e00
> volume #10 color #ff9400
> volume #10 color #ff9600
> volume #10 color #ff9700
> lighting soft
> fitmap #25 inMap #11
Fit map gp8-asym-3.8-masked.mrc in map gp8-basen-new.mrc using 44005 points
correlation = 0.9045, correlation about mean = 0.7313, overlap = 7.239
steps = 172, shift = 16, angle = 7.26 degrees
Position of gp8-asym-3.8-masked.mrc (#25) relative to gp8-basen-new.mrc (#11)
coordinates:
Matrix rotation and translation
0.11304689 0.99358827 -0.00165499 -21.85520186
0.99358559 -0.11304151 0.00304704 24.49850256
0.00284042 -0.00198884 -0.99999399 420.92730551
Axis -0.74600412 -0.66594121 -0.00039710
Axis point 0.00000000 22.48019073 210.44189297
Rotation angle (degrees) 179.80661289
Shift along axis -0.17764405
> select clear
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> lighting flat
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Expected a keyword
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> volume #15 level 0.01338
> surface dust #15 size 40
> lighting soft
> volume #15 level 0.0109
> lighting flat
Expected a keyword
> select #37
49008 atoms, 49740 bonds, 1 model selected
> ui mousemode rightMode "rotate selected models"
> fitmap #37 inMap #15
Fit molecule gp8-new-assembled.pdb (#37) to map tail-3.4-with-gp17N.mrc (#15)
using 49008 atoms
average map value = 0.01759, steps = 100
shifted from previous position = 0.232
rotated from previous position = 6.63 degrees
atoms outside contour = 17140, contour level = 0.010899
Position of gp8-new-assembled.pdb (#37) relative to tail-3.4-with-gp17N.mrc
(#15) coordinates:
Matrix rotation and translation
0.86311350 -0.50500130 0.00296534 134.14689635
0.50500449 0.86311664 -0.00039374 -77.14260288
-0.00236060 0.00183735 0.99999553 -1.31341551
Axis 0.00220894 0.00527309 0.99998366
Axis point 209.36258472 208.89278919 0.00000000
Rotation angle (degrees) 30.33209188
Shift along axis -1.42385073
> select #25
3 models selected
> ui mousemode rightMode "rotate selected models"
> fitmap #25 inMap #15
Fit map gp8-asym-3.8-masked.mrc in map tail-3.4-with-gp17N.mrc using 44005
points
correlation = 0.8297, correlation about mean = 0.6237, overlap = 8.214
steps = 100, shift = 2.11, angle = 9.76 degrees
Position of gp8-asym-3.8-masked.mrc (#25) relative to tail-3.4-with-gp17N.mrc
(#15) coordinates:
Matrix rotation and translation
0.86336823 -0.50453896 0.00597993 133.38722274
0.50455144 0.86338137 -0.00069311 -76.87992840
-0.00481326 0.00361559 0.99998189 1.33029931
Axis 0.00426961 0.01069526 0.99993369
Axis point 208.67695926 207.85455238 0.00000000
Rotation angle (degrees) 30.30338631
Shift along axis 1.07747130
> fitmap #25 inMap #11
Fit map gp8-asym-3.8-masked.mrc in map gp8-basen-new.mrc using 44005 points
correlation = 0.9046, correlation about mean = 0.7316, overlap = 7.235
steps = 48, shift = 0.133, angle = 0.349 degrees
Position of gp8-asym-3.8-masked.mrc (#25) relative to gp8-basen-new.mrc (#11)
coordinates:
Matrix rotation and translation
0.80401021 -0.59460524 0.00349140 165.24766420
-0.59460904 -0.80401498 0.00006338 503.50291688
0.00276945 -0.00212698 -0.99999390 420.98042313
Axis -0.94973950 0.31303701 -0.00164835
Axis point 0.00000000 279.11230770 210.19397549
Rotation angle (degrees) 179.93393018
Shift along axis -0.02111110
> volume #25 color #b2ffb2
> volume #25 color #f7ffb2
> volume #25 color #f8ffb2
> volume #25 color #f9ffb2
> volume #25 color #fbffb2
> volume #25 color #ffffb2
> volume #25 color #ffffb1
> volume #25 color #ffffab
> volume #25 color #ffff77
> volume #25 color #ffff3c
> volume #25 color #ffff09
> volume #25 color yellow
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> volume #25 step 1
> volume #25 level 0.008697
> surface dust #25 size 40
> lighting soft
> select clear
> surface dust #10 size 40
> volume #23 color #19ff00fc
> volume #23 color #19ff00
> surface dust #23 size 40
> volume #25 level 0.01016
> volume #25 level 0.008783
> volume #25 level 0.00792
> volume #25 level 0.006712
> surface dust #25 size 40
> surface dust #25 size 80
> volume #25 level 0.006
> volume #25 level 0.007
> volume #25 level 0.008
> select #44
49008 atoms, 49740 bonds, 1 model selected
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> volume #25 level 0.008518
> select #34
1640 atoms, 1838 bonds, 1 model selected
> hide sel atoms
> hide sel cartoons
> surface dust #9 size 80
> volume #25 level 0.009554
> surface dust #25 size 40
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> show sel cartoons
> volume #25 level 0.007137
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> volume #42.1 level 0.007857
> volume #42.1 step 1
> fitmap #42.1 inMap #15
Fit map gp8-asym-300-400-part-genome-lp.mrc in map tail-3.4-with-gp17N.mrc
using 7295 points
correlation = 0.9747, correlation about mean = 0.7871, overlap = 1.653
steps = 836, shift = 0.458, angle = 64.6 degrees
Position of gp8-asym-300-400-part-genome-lp.mrc (#42.1) relative to
tail-3.4-with-gp17N.mrc (#15) coordinates:
Matrix rotation and translation
0.99945406 0.03299615 -0.00169109 -6.53474252
-0.03299466 0.99945513 0.00089887 6.88940865
0.00171983 -0.00084258 0.99999818 -0.22980511
Axis -0.02634495 -0.05160095 -0.99832023
Axis point 205.54971269 201.40985746 0.00000000
Rotation angle (degrees) 1.89402317
Shift along axis 0.04607652
> fitmap #41 inMap #15
Fit map gp8-asym-300-400-part-genome.mrc in map tail-3.4-with-gp17N.mrc using
8254 points
correlation = 0.9786, correlation about mean = 0.8194, overlap = 1.879
steps = 820, shift = 0.413, angle = 62.8 degrees
Position of gp8-asym-300-400-part-genome.mrc (#41) relative to tail-3.4-with-
gp17N.mrc (#15) coordinates:
Matrix rotation and translation
0.99970264 0.02435993 -0.00111280 -4.86107680
-0.02435906 0.99970297 0.00078689 5.04147379
0.00113164 -0.00075955 0.99999908 -0.11220201
Axis -0.03169230 -0.04599728 -0.99843871
Axis point 204.56630756 202.00484631 0.00000000
Rotation angle (degrees) 1.39801766
Shift along axis 0.03419147
> volume #42.1 color #3dc5dbfd
> volume #42.1 color #3dc5dbfe
> volume #42.1 color #3dc5db
> volume #25 level 0.006717
> volume #25 level 0.006
> volume #25 level 0.007
> volume #25 level 0.0075
> volume #25 level 0.008
> volume #25 level 0.009
> select clear
> select #44
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> volume #25 level 0.001
> volume #25 level 0.0001
> volume #25 level 0.001
Unknown command: 9
> volume #25 level 0.007
> volume #25 level 0.008
> volume #25 level 0.009
> surface dust #25 size 40
> surface dust #25 size 80
> surface dust #25 size 100
> volume #25 level 0.0099
> volume #25 level 0.0097
> surface dust #25 size 50
> surface dust #9 size 50
> surface dust #9 size 30
> lighting flat
> save session /Users/chunyan/2020/gp8-asym/gp8-asym-20200521-with-movie.cxs
> lighting soft
> lighting flat
> roll y
> stop
> view name p1
> lighting soft
> movie record
> roll y
> stop
> view p1
> movie record
Already recording a movie
> movie reset
> view p1
> movie record
> roll y
> stop
> movie encode /Users/chunyan/Desktop/Figure15-M1.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-M1.mp4
> view name p2
> movie record
> roll y
> stop
> view p2
> movie record
Already recording a movie
> movie reset
> movie record
> roll y
> lighting flat
> movie reset
> stop
> roll y
> stop
> lighting soft
> roll y
> roll y
> stop
> view name p1
> movie record
> roll y
> stop
> movie encode /Users/chunyan/Desktop/Figure15-M1.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-M1.mp4
> view name p2
> movie record
> roll y
> stop
> movie encode /Users/chunyan/Desktop/Figure15-M2.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-M2.mp4
> movie record
> view p2 2
> view p2
> movie record
Already recording a movie
> movie reset
> movie record
> roll y
> stop
> movie encode /Users/chunyan/Desktop/Figure15-M2.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-M2.mp4
> view name p3
> movie record
> view p3 3
> stop
> movie encode /Users/chunyan/Desktop/Figure15-M3.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-M3.mp4
> movie record
> view p3 3
> stop
> movie encode /Users/chunyan/Desktop/Figure15-M3.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-M3.mp4
> volume #25 color #c8ff00
> volume #25 color #c8c800
> volume #25 color #c8c8c8
> volume #25 color #c8c8c84c
> select #44
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> delete #44
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> color #37 yellow
> color #37:371-383 orange
> volume #25 color #c818c84c
> volume #25 color #c8cdc84c
> volume #25 color #c8cd004c
> volume #25 color #c8cf004c
> volume #25 color #c8d6004c
> volume #25 color #c8de004c
> volume #25 color #c8e7004c
> volume #25 color #c8ed004c
> volume #25 color #c8fc004c
> volume #25 color #c8ff004c
> volume #25 color #c9ff004c
> volume #25 color #ceff004c
> volume #25 color #e0ff004c
> volume #25 color #ffff004c
> volume #25 color #ff8e004c
> volume #25 color #fff7004c
> volume #25 color #fff6004c
> volume #25 color #fff6ed4c
> volume #25 color #fff6ee4c
> volume #25 color #c8f6ee4c
> volume #25 color #c8c8ee4c
> volume #25 color #c8c8c84c
> color #37:371-383 #FF8E00
> view p3
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> view p3
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> volume #25 color #c8c8004c
> volume #25 color #c8e3004c
> volume #25 color #c8ed004c
> volume #25 color #c8ff004c
> volume #25 color #c9ff004c
> volume #25 color #d0ff004c
> volume #25 color #e0ff004c
> volume #25 color #ffff004c
> volume #25 color #ffff004d
> volume #25 color #ffff0053
> volume #25 color #ffff00e8
> volume #25 color yellow
> volume #25 level 0.0099
> surface dust #25 size 30
> surface dust #25 size 100
> volume #25 level 0.0001
> volume #25 level 0.001
> volume #25 level 0.0001
> volume #25 level 0.00099
> volume #25 level 0.0099
> volume #25 level 0.01
> volume #25 level 0.012
> volume #25 level 0.011
> volume #25 level 0.01
> volume #25 level 0.02
> volume #25 level 0.01
> volume #25 level 0.01059
> view p3
> view name p4
> view p3
> view p4 50
> view p3
> movie record
> view p4 60
> view p3
> movie reset
> volume #25 level 0.01101
> surface dust #25 size 30
> surface dust #25 size 10
> surface dust #25 size 20
> surface dust #25 size 30
> surface dust #25 size 25
> view p4
> view p3
> movie record
> view p4 60
> stop
> movie encode /Users/chunyan/Desktop/Figure15-N1.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-N1.mp4
> volume #25 color #ffffc8
> volume #25 color #ffc8c8
> volume #25 color #c8c8c8
> volume #25 color #c8c8c84c
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> select clear
> view p4
> view p4
> view p4
> movie record
> roll y
> stop
> movie encode /Users/chunyan/Desktop/Figure15-N2.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-N2.mp4
> view name p5
> volume #25 level 0.005968
> volume #25 level 0.006472
> volume #42.1 color #ddc5db
> volume #42.1 color #dcc5db
> volume #42.1 color #dce3db
> volume #42.1 color #dce3c8
> volume #42.1 color #dcc8c8
> volume #42.1 color #c8c8c8
> volume #42.1 color #c8c8c8b3
> volume #42.1 color #c8c8c884
> volume #42.1 color #c8c8c864
> volume #42.1 color #c8c8c82a
> volume #42.1 color #c8c8c84c
> view name p6
> view p5
> volume #25 level 0.0105
> volume #42.1 level 0.008697
> surface dust #42.1
> surface dust #42.1 size 40
> view p5
> view p6 30
> volume #42.1 level 0.007
> volume #42.1 level 0.008501
> volume #25 level 0.006556
> view p5
> volume #25 level 0.007396
> select #37
49008 atoms, 49740 bonds, 1 model selected
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> lighting soft
> movie record
> view p6 2
> view p5
> view p6
> view p5
> movie reset
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> select clear
> view name p6
> view p5
> view p5
> volume #25 level 0.01008
> volume #25 level 0.00958
> view p5
> view p6
> view p5
> movie record
> view p6 60
> stop
> movie encode /Users/chunyan/Desktop/Figure15-N3.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-N3.mp4
> view p4
> movie record
> roll y
> stop
> movie encode /Users/chunyan/Desktop/Figure15-N2.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-N2.mp4
> view name p5
> view name p6
> view p5
> view p6 5
> view p5
> view p5
> view p6
> view p5
> view p6
> view p5
> movie record
> roll y
> stop
> movie reset
> view p5
> view p6
> view p5
> movie record
> view p6 50
> stop
> movie encode /Users/chunyan/Desktop/Figure15-N3.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-N3.mp4
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> color #37:300-400 #C8C8C8
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> volume #43 color #b2fbb380
> volume #43 color #b2fab380
> volume #43 color #b2f6b380
> volume #43 color #b2d8b380
> volume #43 color #b2d5b380
> volume #43 color #b2d4b380
> volume #43 color #c8d4b380
> volume #43 color #c8d3b380
> volume #43 color #c8c8b380
> volume #43 color #c8c8c880
> volume #43 color #c8c80080
> volume #43 color #fec80080
> volume #43 color #ffc80080
> volume #43 color #ff830080
> volume #43 color #ff820080
> volume #43 color #ff8200f5
> volume #43 color #ff8200f6
> volume #43 color #ff8200fb
> volume #43 color #ff8200
> volume #43 color #ff2800
> volume #43 color #ffa300
> volume #43 color #ff9000
> color #37:371-383 #FF9700
> select clear
> movie record
> view p6 3
> stop
> movie encode /Users/chunyan/Desktop/Figure15-N4.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-N4.mp4
> movie record
> view p6 3
> stop
> movie encode /Users/chunyan/Desktop/Figure15-N5.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-N5.mp4
> movie record
> view p6 3
> stop
> movie encode /Users/chunyan/Desktop/Figure15-N6.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-N6.mp4
> volume #42.1 color #c8c8c8d6
> volume #42.1 color #c8c8c8
> volume #42.1 color #3dc5db
> select clear
> view p6
> movie record
> view p6 3
> stop
> movie encode /Users/chunyan/Desktop/Figure15-N6.mp4
Movie saved to /Users/chunyan/Desktop/Figure15-N6.mp4
> color #37:371 #C8C8C8
> color #37:359-370 yellow
> select clear
> color #37:358 magenta
> color #37:358 #C8C8C8
> color #37:368 magenta
> color #37:368 yellow
> view p6
> view name p7
> view p6
> view p7 40
> view name p7
> view p6
> view p7 40
> view p7
> view p6
> view p7 30
> view name p7
> view p6
> view p7 30
> view name p8
> view p6
> view p7
> view p6
> view p7 40
> view p8 40
> view p7
> view p7
> view name p8
> view p6
> view p7 30
> view p8 30
> view name p8
> view p6
> view p7
> view p6
> view p7 30
> view p8 30
> view p6
> view p7 30
> view p8 30
> view p6
> view p8 60
> volume #42.1 level 0.0112
> volume #42.1 level 0.01234
> volume #42.1 level 0.01426
> volume #42.1 level 0.01378
> volume #42.1 level 0.01348
> view p7
> view name p8
> view p6
> view p7 40
> view p8 40
> view p7
> view name p8
> view p6
> view p7 30
> view p8 30
> view p7
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> view name p8
> view p6
> view p8 30
> view p6
> view p6
> movie record
> view p6 3
> volume #42.1 level 0.0136
> movie record
Already recording a movie
> movie reset
> movie record
> view p6 3
> movie reset
> movie record
> view p6 3
> stop
> movie encode /Users/chunyan/Desktop/Figure1-O1.mp4
Movie saved to /Users/chunyan/Desktop/Figure1-O1.mp4
> movie record
> view p6 3
> stop
> movie encode /Users/chunyan/Desktop/Figure1-O2.mp4
Movie saved to /Users/chunyan/Desktop/Figure1-O2.mp4
> view p8
> view p7
> view p6
> movie record
> view p8 100
> stop
> movie encode /Users/chunyan/Desktop/Figure1-O3.mp4
Movie saved to /Users/chunyan/Desktop/Figure1-O3.mp4
> view p5
> view p6
> view p5
> view p4
> view p4
> view p5 400
> stop
> view p4
> view p5 40
> view p4
> volume #25 color #c8c8004c
> volume #25 color #c8f7004c
> volume #25 color #c8fa004c
> volume #25 color #c8ff004c
> volume #25 color #c9ff004c
> volume #25 color #d3ff004c
> volume #25 color #e6ff004c
> volume #25 color #ffff004c
> volume #25 color #ffff004b
> volume #25 color #ffff0040
> volume #25 color #ffff0000
> volume #25 color #ffff000b
> volume #25 color #ffff0035
> volume #25 color #ffff00bf
> volume #25 color #ffff00de
> volume #25 color #ffff00fd
> volume #25 color yellow
> volume #25 color #ffc800
> volume #25 color #c8c800
> volume #25 color #c8c8c8
> volume #25 color #c8c8c84c
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> select clear
> movie record
> view p5 50
> stop
> movie encode /Users/chunyan/Desktop/Figure1-P1.mp4
Movie saved to /Users/chunyan/Desktop/Figure1-P1.mp4
> view p6 30
> view p5
> movie record
> view p6 50
> stop
> movie encode /Users/chunyan/Desktop/Figure1-P2.mp4
Movie saved to /Users/chunyan/Desktop/Figure1-P2.mp4
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> volume #25 level 0.009076
> movie record
> view p6 2
> stop
> movie encode /Users/chunyan/Desktop/Figure1-P3.mp4
Movie saved to /Users/chunyan/Desktop/Figure1-P3.mp4
> movie record
> view p6 2
> stop
> movie encode /Users/chunyan/Desktop/Figure1-P4.mp4
Movie saved to /Users/chunyan/Desktop/Figure1-P4.mp4
> movie record
> view p8 60
> stop
> movie encode /Users/chunyan/Desktop/Figure1-P5.mp4
Movie saved to /Users/chunyan/Desktop/Figure1-P5.mp4
> view p7
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel cartoons
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1640 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1640 atom styles
> style sel stick
Changed 1640 atom styles
> hide sel atoms
> show sel atoms
> volume #42.1 level 0.005019
> hide sel cartoons
> hide sel atoms
> volume #42.1 level 0.00694
> open /Users/chunyan/2020/gp8-asym/part/gp8-asym-300-400-part-genome-lp1.mrc
Opened gp8-asym-300-400-part-genome-lp1.mrc, grid size 400,400,400, pixel
1.05, shown at level 1.32e-06, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> volume #27 level 0.002829
> select clear
> select #27
2 models selected
> ui mousemode rightMode "rotate selected models"
> lighting flat
> ui mousemode rightMode "translate selected models"
> volume #27 step 1
> volume #27 level 0.004242
> fitmap #27 inMap #42.1
Fit map gp8-asym-300-400-part-genome-lp1.mrc in map gp8-asym-300-400-part-
genome-lp.mrc using 9231 points
correlation = 0.9903, correlation about mean = 0.9502, overlap = 1.193
steps = 368, shift = 7.67, angle = 23.7 degrees
Position of gp8-asym-300-400-part-genome-lp1.mrc (#27) relative to
gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates:
Matrix rotation and translation
0.99789601 0.06480577 -0.00194233 -12.82157289
-0.06480126 0.99789554 0.00230197 13.65166742
0.00208742 -0.00217126 0.99999547 -0.10851142
Axis -0.03447658 -0.03105856 -0.99892279
Axis point 204.09218651 204.40497683 0.00000000
Rotation angle (degrees) 3.71958413
Shift along axis 0.12643737
> volume #27 color #3dc5db
> select clear
> lighting soft
> select clear
> volume #27 level 0.004091
> view p5
> view p6
> volume #27 level 0.004293
> select #37
49008 atoms, 49740 bonds, 1 model selected
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel cartoons
> fitmap #34 inMap #27
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
genome-lp1.mrc (#27) using 1640 atoms
average map value = 0.004237, steps = 64
shifted from previous position = 0.994
rotated from previous position = 1.19 degrees
atoms outside contour = 1015, contour level = 0.0042928
Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
gp8-asym-300-400-part-genome-lp1.mrc (#27) coordinates:
Matrix rotation and translation
0.38365140 0.92282724 -0.03466275 -58.44612736
-0.91835984 0.38520257 0.09074238 306.69512865
0.09709172 -0.00298056 0.99527098 -24.97746181
Axis -0.05070839 -0.07128518 -0.99616619
Axis point 201.94937982 197.88533734 0.00000000
Rotation angle (degrees) 67.53850471
Shift along axis 5.98259393
> select #34
1640 atoms, 1838 bonds, 1 model selected
> hide sel cartoons
> view p6
> movie record
> view p6 2
> stop
> movie encode /Users/chunyan/Desktop/Figure1-Q1.mp4
Movie saved to /Users/chunyan/Desktop/Figure1-Q1.mp4
> movie record
> view p6 2
> stop
> movie encode /Users/chunyan/Desktop/Figure1-Q1.mp4
Movie saved to /Users/chunyan/Desktop/Figure1-Q1.mp4
> movie record
> view p6 2
> stop
> movie encode /Users/chunyan/Desktop/Figure1-Q2.mp4
Movie saved to /Users/chunyan/Desktop/Figure1-Q2.mp4
> movie record
> view p8 80
> stop
> movie encode /Users/chunyan/Desktop/Figure1-Q3.mp4
Movie saved to /Users/chunyan/Desktop/Figure1-Q3.mp4
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/31E1A339-4F85-4972-9B5C-D8940F23CD60/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Change History (2)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → General Controls |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Model panel, list index out of range, restoring session |
comment:2 by , 5 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
Exact duplicate of #3279 (same user/session)