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Opened 5 years ago
Closed 5 years ago
#3154 closed defect (can't reproduce)
Model panel problem
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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:
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/RIP-20200425.cxs format session
opened ChimeraX session
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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.
> close #1.1.1
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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.
> hide sel cartoons
> select clear
> select clear
> hide sel cartoons
> select clear
> select clear
> hide sel cartoons
> toolshed show "Side View"
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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.
> open /Users/chunyan/2020/gp8-asym/part/gp8-asym-300-400-part.mrc
Opened gp8-asym-300-400-part.mrc, grid size 400,400,400, pixel 1.05, shown at
level 5.08e-06, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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.
> toolshed show "Side View"
> select clear
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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.
> ui mousemode rightMode "rotate selected models"
> volume #37 level 0.006161
> volume #37 step 1
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> toolshed show "Side View"
> view
> ui mousemode rightMode "translate selected models"
> fitmap #37 inMap #11
Fit map gp8-asym-300-400-part.mrc in map gp8-basen-new.mrc using 147173 points
correlation = 0.3146, correlation about mean = 0.04917, overlap = 6.203
steps = 88, shift = 4.74, angle = 3.98 degrees
Position of gp8-asym-300-400-part.mrc (#37) relative to gp8-basen-new.mrc
(#11) coordinates:
Matrix rotation and translation
-0.99518848 -0.03072345 -0.09303738 447.14164523
-0.03952662 0.99475822 0.09430653 -5.99863737
0.08965227 0.09753022 -0.99118632 390.07986007
Axis 0.01762256 -0.99868594 -0.04812315
Axis point 214.57314960 0.00000000 205.44584815
Rotation angle (degrees) 174.75210610
Shift along axis -4.90133727
> volume #11 level 0.007051
> volume #37 level 0.0105
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #37 inMap #11
Fit map gp8-asym-300-400-part.mrc in map gp8-basen-new.mrc using 87142 points
correlation = 0.3814, correlation about mean = 0.03852, overlap = 5.845
steps = 76, shift = 6.03, angle = 4.94 degrees
Position of gp8-asym-300-400-part.mrc (#37) relative to gp8-basen-new.mrc
(#11) coordinates:
Matrix rotation and translation
-0.64228132 -0.76646896 -0.00008215 505.83912721
-0.76646609 0.64227862 0.00280807 235.63361319
-0.00209954 0.00186654 -0.99999604 436.65243484
Axis -0.42291805 0.90616702 0.00128927
Axis point 308.04005138 0.00000000 218.00322664
Rotation angle (degrees) 179.93622174
Shift along axis 0.15787310
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #37 inMap #11
Fit map gp8-asym-300-400-part.mrc in map gp8-basen-new.mrc using 87142 points
correlation = 0.3824, correlation about mean = 0.03981, overlap = 5.862
steps = 84, shift = 3.67, angle = 4.04 degrees
Position of gp8-asym-300-400-part.mrc (#37) relative to gp8-basen-new.mrc
(#11) coordinates:
Matrix rotation and translation
-0.17336858 -0.98485622 -0.00123484 453.42883693
-0.98485459 0.17336525 0.00242886 380.00466870
-0.00217800 0.00163722 -0.99999627 436.71861867
Axis -0.64289740 0.76595116 0.00132708
Axis point 386.27971754 0.00000000 217.93897713
Rotation angle (degrees) 179.96472402
Shift along axis 0.13635913
> open /Users/chunyan/2020/gp8-asym/gp8-asym-3.6.mrc
Opened gp8-asym-3.6.mrc, grid size 400,400,400, pixel 1.05, shown at level
0.015, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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.
> ui mousemode rightMode "rotate selected models"
> select #38
2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #38 inMap #11
Fit map gp8-asym-3.6.mrc in map gp8-basen-new.mrc using 79941 points
correlation = 0.4549, correlation about mean = 0.05236, overlap = 9.372
steps = 852, shift = 4.07, angle = 4.74 degrees
Position of gp8-asym-3.6.mrc (#38) relative to gp8-basen-new.mrc (#11)
coordinates:
Matrix rotation and translation
-0.39867075 0.91709398 -0.00050397 101.33307182
0.91709398 0.39867094 0.00034637 -66.40725091
0.00051857 -0.00032410 -0.99999981 423.68628677
Axis -0.54832810 -0.83626329 -0.00000686
Axis point 72.36032986 0.00000000 211.86193308
Rotation angle (degrees) 179.96497098
Shift along axis -0.03273208
> surface dust #38 size 40
> surface dust #38 size 10
> volume #38 level 0.01159
> volume #38 level 0.01055
> volume #38 step 1
> volume #38 level 0.0122
> volume #38 level 0.01413
> volume #38 level 0.0111
> volume #38 level 0.01495
> open /Users/chunyan/2020/gp8-asym/part/gp8-asym-300-400-part.mrc
Opened gp8-asym-300-400-part.mrc, grid size 400,400,400, pixel 1.05, shown at
level 5.08e-06, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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 #40 level 0.008885
> volume #40 step 1
> select clear
> select #38
2 models selected
> select clear
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> volume #40 level 0.01302
> fitmap #40 inMap #38
Fit map gp8-asym-300-400-part.mrc in map gp8-asym-3.6.mrc using 63324 points
correlation = 0.4019, correlation about mean = 0.06306, overlap = 5.887
steps = 112, shift = 6.72, angle = 5.71 degrees
Position of gp8-asym-300-400-part.mrc (#40) relative to gp8-asym-3.6.mrc (#38)
coordinates:
Matrix rotation and translation
0.88041247 0.47419664 -0.00338290 -73.68794519
-0.47419223 0.88041895 0.00205422 124.15906451
0.00395247 -0.00020442 0.99999217 -18.10534238
Axis -0.00238147 -0.00773431 -0.99996725
Axis point 209.61876027 208.17205764 0.00000000
Rotation angle (degrees) 28.30792305
Shift along axis 17.31995101
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #40 inMap #38
Fit map gp8-asym-300-400-part.mrc in map gp8-asym-3.6.mrc using 63324 points
correlation = 0.4019, correlation about mean = 0.06306, overlap = 5.887
steps = 88, shift = 0.241, angle = 8.43 degrees
Position of gp8-asym-300-400-part.mrc (#40) relative to gp8-asym-3.6.mrc (#38)
coordinates:
Matrix rotation and translation
0.88043156 0.47416047 -0.00348300 -73.66670303
-0.47415557 0.88043841 0.00217082 124.12603993
0.00409588 -0.00025978 0.99999158 -18.12040541
Axis -0.00256298 -0.00799165 -0.99996478
Axis point 209.59576053 208.12228712 0.00000000
Rotation angle (degrees) 28.30562925
Shift along axis 17.31660117
> ui mousemode rightMode "rotate selected models"
> volume #40 level 0.01312
> volume #40 level 0.01374
> volume #40 level 0.01446
> volume #40 level 0.01529
> volume #40 level 0.0156
> volume #40 level 0.0157
> volume #40 level 0.01612
> volume #40 level 0.01674
> volume #40 level 0.01694
> volume #40 level 0.01705
> volume #40 level 0.01736
> volume #40 level 0.01767
> volume #40 level 0.01798
> volume #40 level 0.0188
> volume #40 level 0.01932
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> open /Users/chunyan/2020/gp8-asym/part/gp8-asym-300-400-part-genome.mrc
Opened gp8-asym-300-400-part-genome.mrc, grid size 400,400,400, pixel 1.05,
shown at level 1.61e-06, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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 #41
2 models selected
> ui mousemode rightMode "translate selected models"
> volume #38 color #ffffb2a7
> volume #38 color #ffffb28e
> volume #38 color #ffffb270
> ui mousemode rightMode "rotate selected models"
> fitmap #41 inMap #38
Fit map gp8-asym-300-400-part-genome.mrc in map gp8-asym-3.6.mrc using 1031
points
correlation = 0.9109, correlation about mean = 0.6062, overlap = 0.1874
steps = 1724, shift = 9.41, angle = 106 degrees
Position of gp8-asym-300-400-part-genome.mrc (#41) relative to
gp8-asym-3.6.mrc (#38) coordinates:
Matrix rotation and translation
0.90157171 0.43262356 0.00230586 -70.00335224
-0.43262105 0.90150712 0.01113286 109.45688413
0.00273759 -0.01103464 0.99993537 2.84766914
Axis -0.02561151 -0.00049881 -0.99967185
Axis point 205.50884166 208.63317298 0.00000000
Rotation angle (degrees) 25.64311888
Shift along axis -1.10844150
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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 soft
> lighting soft
> lighting flat
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> graphics silhouettes true
> lighting soft
> volume #41 color #8db2ff
> volume #41 color #8ddbff
> volume #41 color #8dddff
> volume #41 color #8ddddc
> volume #41 color #8dddf8
> volume #41 color #8dedf8
> volume #41 color #8deef8
> lighting soft
> volume #41 color #67eef8
> volume #41 color #67d4f8
> volume #41 color #67d5f8
> volume #41 color #67e7f8
> volume #41 color #67e7dc
> volume #41 color #67f5dc
> volume #41 color #67f6dc
> volume #41 color #67f6fb
> volume #41 color #83f6fb
> volume #41 color #82f6fb
> volume #41 color #7ef6fb
> volume #41 color #65f6fb
> volume #41 color #5ef6fb
> volume #41 color #5df6fb
> volume #41 color #5bf6fb
> volume #41 color #59f6fb
> volume #41 color #58f6fb
> volume #41 color #57f6fb
> volume #41 color #54f6fb
> volume #41 color #51f6fb
> volume #41 color #50f6fb
> volume #41 color #4ff6fb
> volume #41 color #4ef6fb
> volume #41 color #4df6fb
> volume #41 color #4cf6fb
> volume #41 color #4cf5fb
> volume #41 color #4cf2fb
> volume #41 color #4ce9fb
> volume #41 color #4ce7fb
> volume #41 color #4ce5fb
> volume #41 color #4ce3fb
> volume #41 color #4ce2fb
> volume #41 color #4ce3fb
> volume #41 color #4ce4fb
> volume #41 color #4ce6fb
> volume #41 color #4ce7fb
> volume #41 color #4ce9fb
> volume #41 color #4cebfb
> volume #41 color #4ceefb
> volume #41 color #4ceffb
> volume #41 color #4cf1fb
> volume #41 color #4cf3fb
> volume #41 color #4cf3f9
> volume #41 color #4cf3e8
> volume #41 color #4cf3de
> volume #41 color #4cf3df
> volume #41 color #4cf3e2
> volume #41 color #4cf3fd
> volume #41 color #4cf3ff
> volume #41 color #66f3ff
> volume #41 color #38f3ff
> volume #41 color #2af3ff
> volume #41 color #2affff
> volume #41 color #2afeff
> volume #41 color #2af0ff
> volume #41 color #2ac3ff
> volume #41 color #2ac1ff
> volume #41 color #2ad4ff
> volume #41 color #2adbff
> volume #41 color #2ae3ff
> volume #41 color #2aedff
> volume #41 color #2af1ff
> volume #41 color #2af5ff
> volume #41 color #2af8ff
> volume #41 color #2af9ff
> volume #41 color #2afbff
> volume #41 color #2afdff
> volume #41 color #2afeff
> volume #41 color #2affff
> volume #41 color #4dffff
> volume #41 color #4dffd9
> volume #41 color #4dffa5
> volume #41 color #4dffe9
> volume #41 step 1
> volume #41 level 0.008186
> surface dust #41 size 40
> volume #41 level 0.009233
> select #37
3 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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.
> open /Users/chunyan/2020/gp8-asym/gp8-new-assembled.pdb
Chain information for gp8-new-assembled.pdb #37
---
Chain | Description
A B C D E F G H I J K L | No description available
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> hide sel atoms
> show sel cartoons
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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.
> fitmap #37 inMap #11
Fit molecule gp8-new-assembled.pdb (#37) to map gp8-basen-new.mrc (#11) using
49008 atoms
average map value = 0.01383, steps = 112
shifted from previous position = 3.73
rotated from previous position = 8.12 degrees
atoms outside contour = 13411, contour level = 0.0070512
Position of gp8-new-assembled.pdb (#37) relative to gp8-basen-new.mrc (#11)
coordinates:
Matrix rotation and translation
0.91705730 0.39875537 0.00023372 -66.37710555
0.39875525 -0.91705728 0.00043699 318.68975009
0.00038859 -0.00030754 -0.99999987 423.66876613
Axis -0.97904472 -0.20364529 -0.00016016
Axis point 0.00000000 166.28936439 211.80886941
Rotation angle (degrees) 179.97821425
Shift along axis 0.01863426
> preset cartoons/nucleotides cylinders/stubs
Changed 212848 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
> select clear
> select clear
> hide sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> color #37 yellow
> select clear
> color #37 white
> color #37 yellow
> lighting soft
> select clear
> lighting full
> lighting simple
> lighting soft
> select clear
> lighting full
> select clear
> select clear
> volume #41 color #4de9e9
> volume #41 color #4ddde9
> volume #41 color #4dddd3
> color #37 grey
> color #37 white
> volume #41 color #d7ddd3
> volume #41 color #e9ddd3
> volume #41 color #e8ddd3
> color #37 #E8DDD3
> volume #41 color #e8edd3
> volume #41 color #e8ede9
> volume #41 color #e8e6e9
> volume #41 color #e6e6e9
> volume #41 color #e6e6e6
> color #37 #E6E6E6
> volume #41 color #4dddd3
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #37:356-370 orange
> color #37:356-370 yellow
> color #37:371-383 orange
> select clear
> lighting soft
> save image /Users/chunyan/2020/20200506-Figure5-1.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37:300-400
9360 atoms, 9480 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
> hide #32,37#17.1,3#!25,27#!17.2 atoms
> lighting flat
> 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 0.00568, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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 #38 level 0.004615
> view
> volume #38 level 0.009247
> volume #38 step 1
> volume #38 level 0.01051
> surface dust #38 size 40
> select #38
3 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #38 inMap #11
Fit map gp8-asym-3.8-masked.mrc in map gp8-basen-new.mrc using 228882 points
correlation = 0.892, correlation about mean = 0.5465, overlap = 49.79
steps = 84, shift = 6.28, angle = 1.79 degrees
Position of gp8-asym-3.8-masked.mrc (#38) relative to gp8-basen-new.mrc (#11)
coordinates:
Matrix rotation and translation
0.99360065 -0.11290714 0.00311886 24.44739584
-0.11291247 -0.99360367 0.00158787 441.84326323
0.00291963 -0.00192986 -0.99999388 420.92524376
Axis -0.99839888 0.05654552 -0.00151198
Axis point 0.00000000 221.79961732 210.24919929
Rotation angle (degrees) 179.89906278
Shift along axis -0.06042623
> volume #38 level 0.007355
> volume #38 level 0.008301
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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.
> open /Users/chunyan/2020/gp8-asym/gp8-asym-3.6.mrc
Opened gp8-asym-3.6.mrc, grid size 400,400,400, pixel 1.05, shown at level
0.015, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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
> select #15
3 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #15 inMap #23
Fit map gp8-asym-3.6.mrc in map gp12-new.mrc using 79941 points
correlation = 0.6579, correlation about mean = 0.4284, overlap = 15.44
steps = 224, shift = 11.2, angle = 4.14 degrees
Position of gp8-asym-3.6.mrc (#15) relative to gp12-new.mrc (#23) coordinates:
Matrix rotation and translation
0.99387077 -0.11052813 0.00209438 -186.00463191
-0.11052853 -0.99387294 0.00007073 231.85649298
0.00207373 -0.00030179 -0.99999779 212.39384721
Axis -0.99846668 0.05534602 -0.00105397
Axis point 0.00000000 110.78296404 106.28477897
Rotation angle (degrees) 179.98931187
Shift along axis 198.32790434
> volume #15 level 0.01072
> volume #15 step 1
> volume #15 level 0.01347
> volume #15 level 0.01222
> surface dust #15 size 50
> vop gaussian #15 sdev 3.15
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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 #19 level 0.0043
> volume #19 level 0.006483
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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 #15 step 2
> volume #15 level 0.01127
> select #15
3 models selected
> select #41
3 models selected
> select #41
3 models selected
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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.
> open /Users/chunyan/2020/fiber/tail-3.4-with-gp17N.mrc
Opened tail-3.4-with-gp17N.mrc, grid size 400,400,400, pixel 1.05, shown at
level 0.0152, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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 #15
3 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #15 inMap #23
Fit map tail-3.4-with-gp17N.mrc in map gp12-new.mrc using 79956 points
correlation = 0.6496, correlation about mean = 0.4146, overlap = 16.66
steps = 208, shift = 6.62, angle = 7.47 degrees
Position of tail-3.4-with-gp17N.mrc (#15) relative to gp12-new.mrc (#23)
coordinates:
Matrix rotation and translation
-0.99448678 0.10485847 0.00083210 186.66062254
0.10485896 0.99448691 0.00057114 -231.04483958
-0.00076762 0.00065525 -0.99999946 211.20724641
Axis 0.05250248 0.99862075 0.00030918
Axis point 99.44626669 0.00000000 105.59963605
Rotation angle (degrees) 179.95410797
Shift along axis -220.86072236
> volume #15 level 0.01133
> 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 = 0.7688, correlation about mean = 0.2404, overlap = 1.166
steps = 100, shift = 11.3, angle = 9.96 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
-0.78903091 0.61236853 0.04934596 239.03052130
-0.60026716 -0.78555002 0.15030145 474.77736048
0.13080360 0.08897172 0.98740796 -55.50981035
Axis -0.05039771 -0.06693782 -0.99648352
Axis point 201.86595223 198.46702863 0.00000000
Rotation angle (degrees) 142.52194824
Shift along axis 11.48745990
> volume #15 step 1
> vop gaussian #15 sdev 3.15
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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 #19 level 0.006344
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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/347285D8-B6DF-4FF1-9194-48E15CC67DD2/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 #15 level 0.01133
> volume #15 level 0.01391
> view
> lighting soft
> save session /Users/chunyan/2020/gp8-asym/gp8-asym-20200507.cxs
> lighting soft
> lighting full
> lighting soft
> lighting simple
> volume #41 level 0.0106
> volume #41 level 0.01125
> save image /Users/chunyan/2020/20200506-Figure5-2.tif pixelSize 0.1
> supersample 4 transparentBackground true
> color #37:371-383 #FD8008
> volume #41 color #4dedd3
> volume #41 color #4defd3
> volume #41 color #4df0d3
> volume #41 color #4df3d3
> volume #41 color #4df2d3
> volume #41 color #4df0d3
> volume #41 color #4dedd3
> volume #41 color #4de9d3
> volume #41 color #4de8d3
> volume #41 color #4de6d3
> volume #41 color #4de5d3
> volume #41 color #4de3d3
> volume #41 color #4ce3d3
> volume #41 color #4ae3d3
> volume #41 color #49e3d3
> volume #41 color #48e3d3
> volume #41 color #47e3d3
> volume #41 color #46e3d3
> volume #41 color #44e3d3
> volume #41 color #43e3d3
> volume #41 color #42e3d3
> volume #41 color #41e3d3
> volume #41 color #40e3d3
> volume #41 color #3fe3d3
> volume #41 color #3ee3d3
> volume #41 color #3de3d3
> volume #41 color #3de2d3
> volume #41 color #3ddad3
> volume #41 color #3dcfd3
> volume #41 color #3dccd3
> volume #41 color #3dcad3
> volume #41 color #3dc9d3
> volume #41 color #3dc8d3
> volume #41 color #3dc7d3
> volume #41 color #3dc6d3
> volume #41 color #3dc5d3
> volume #41 color #3dc4d3
> volume #41 color #3dc1d3
> volume #41 color #3dc2d3
> volume #41 color #3dc5d3
> lighting simple
> lighting full
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting soft
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> lighting full
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> select clear
> save image /Users/chunyan/2020/20200506-Figure5-1.tif pixelSize 0.1
> supersample 4 transparentBackground true
> view name p1
> hide #32,37#17.1,3#!25,27#!17.2 cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> save image /Users/chunyan/2020/20200506-Figure5-2.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save image /Users/chunyan/2020/20200506-Figure5-3.tif pixelSize 0.1
> supersample 4 transparentBackground true
> volume #41 level 0.01054
> volume #41 level 0.01119
> volume #41 level 0.009827
> save image /Users/chunyan/2020/20200506-Figure5-4.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37.1
Nothing selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> select #37/E-F
8168 atoms, 8290 bonds, 1 model selected
> select #37/E-F-G-
8168 atoms, 8290 bonds, 1 model selected
> select #37/E-F-G-H
8168 atoms, 8290 bonds, 1 model selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/D
4084 atoms, 4145 bonds, 1 model selected
> select #37/F
4084 atoms, 4145 bonds, 1 model selected
> select #37/A
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> hide sel cartoons
> select #37/B
4084 atoms, 4145 bonds, 1 model selected
> select #37/C
4084 atoms, 4145 bonds, 1 model selected
> select #37/D
4084 atoms, 4145 bonds, 1 model selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> select #37/G
4084 atoms, 4145 bonds, 1 model selected
> select #37/H
4084 atoms, 4145 bonds, 1 model selected
> select #37/I
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/J
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/K
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/L
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/M
Nothing selected
> select #37/N
Nothing selected
> select #37/F
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/G
4084 atoms, 4145 bonds, 1 model selected
> select #37/H
4084 atoms, 4145 bonds, 1 model selected
> select #37/I
4084 atoms, 4145 bonds, 1 model selected
> select #37/K
4084 atoms, 4145 bonds, 1 model selected
> select #37/A
4084 atoms, 4145 bonds, 1 model selected
> select #37/B
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> select #37/A
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/B
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> hide sel cartoons
> select #37/C
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #37/D
4084 atoms, 4145 bonds, 1 model selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> select #37/F
4084 atoms, 4145 bonds, 1 model selected
> select #37/G
4084 atoms, 4145 bonds, 1 model selected
> select #37/H
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #37/G:300-400
780 atoms, 790 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select #37/G
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> show sel cartoons
> hide sel cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> select #37/A
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/B
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/C
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/D
4084 atoms, 4145 bonds, 1 model selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> select #37/F
4084 atoms, 4145 bonds, 1 model selected
> select #37/G
4084 atoms, 4145 bonds, 1 model selected
> select #37/H
4084 atoms, 4145 bonds, 1 model selected
> select #37/I
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> hide sel cartoons
> select #37/J
4084 atoms, 4145 bonds, 1 model selected
> select #37/K
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/L
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/L
4084 atoms, 4145 bonds, 1 model selected
> select #37/M
Nothing selected
> select #37/N
Nothing selected
> select #37/O
Nothing selected
> select #37/A
4084 atoms, 4145 bonds, 1 model selected
> select #37/B
4084 atoms, 4145 bonds, 1 model selected
> select #37/C
4084 atoms, 4145 bonds, 1 model selected
> select #37/D
4084 atoms, 4145 bonds, 1 model selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> select #37/F:383
8 atoms, 7 bonds, 1 model selected
> select #37/F
4084 atoms, 4145 bonds, 1 model selected
> select #37/J:352
8 atoms, 7 bonds, 1 model selected
> select #37/J
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
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 problem |
comment:2 by , 5 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
Note:
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Seen this once before. I *believe* it indicates that a level in the hierarchy doesn't have a corresponding model. I could be wrong. It would have been nice if the user attached the session.