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
> save image /Users/chunyan/2020/20200506-Figure5-5.tif pixelSize 0.1
> supersample 4 transparentBackground true
> open /Users/chunyan/2020/gp8-asym/gp8-asym-manmade.mrc
Opened gp8-asym-manmade.mrc, grid size 400,400,400, pixel 1.05, shown at level
0.00252, 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 #19 level 0.008312
> select #19
2 models selected
> volume #19 level 0.007183
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 color #cccc99b5
> volume #19 color #cccccdb5
> volume #19 color #cccc04b5
> volume #19 color #ccccccb5
> volume #19 color #ccccccb3
> volume #19 color #cccccca7
> volume #19 color #cccccc99
> volume #19 color #cccccc9f
> volume #19 color #cccccca8
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #19 inMap #15
Fit map gp8-asym-manmade.mrc in map tail-3.4-with-gp17N.mrc using 38029 points
correlation = 0.929, correlation about mean = 0.7605, overlap = 10.91
steps = 156, shift = 12.1, angle = 14 degrees
Position of gp8-asym-manmade.mrc (#19) relative to tail-3.4-with-gp17N.mrc
(#15) coordinates:
Matrix rotation and translation
0.49996048 0.86604715 0.00136383 -77.17345654
-0.86604776 0.49995795 0.00182694 286.54466673
0.00090036 -0.00209454 0.99999740 0.27412174
Axis -0.00226400 0.00026757 -0.99999740
Axis point 209.55464710 210.10301175 0.00000000
Rotation angle (degrees) 60.00278451
Shift along axis -0.02272822
> volume #19 step 1
> surface dust #19 size 40
> select clear
> 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
> volume #19 color #cccccca7
> volume #19 color #cccccca2
> volume #19 color #cccccc94
> volume #19 color #cccccc93
> volume #19 color #cccccc92
> volume #19 color #cccccc91
> volume #19 color #cccccc8d
> volume #19 color #cccccc8c
> volume #19 color #cccccc8b
> volume #19 color #cccccc88
> volume #19 color #cccccc86
> volume #19 color #cccccc85
> volume #19 color #cccccc84
> volume #19 color #cccccc83
> volume #19 color #cccccc80
> volume #19 color #cccccc76
> volume #19 color #cccccc74
> volume #19 color #cccccc71
> volume #19 color #cccccc6d
> volume #19 color #cccccc6b
> volume #19 color #cccccc68
> volume #19 color #cccccc67
> volume #19 color #cccccc64
> volume #19 color #cccccc61
> volume #19 color #cccccc5f
> volume #19 color #cccccc5d
> volume #19 color #cccccc5c
> volume #19 color #cccccc5a
> volume #19 color #cccccc59
> volume #19 color #cccccc57
> volume #19 color #cccccc56
> volume #19 color #cccccc55
> volume #19 color #cccccc54
> volume #19 color #cccccc53
> volume #19 color #cccccc52
> volume #19 color #cccccc51
> volume #19 color #cccccc50
> volume #19 color #cccccc4e
[had to reduce the Description length]
> volume #10 color #a2a6d280
> volume #10 color #a2a6a780
> volume #10 color #b4a6a780
> volume #10 color #b4b4a780
> volume #10 color #b4b4b480
> volume #23 color #d2d2b48f
> volume #23 color #d2d2b40c
> volume #23 color #d2d2b480
> volume #23 color #d3d2b480
> volume #23 color #e9d2b480
> volume #23 color #ffd2b480
> volume #23 color #ffd3b480
> volume #23 color #ffd6b480
> volume #23 color #fff9b480
> volume #23 color #ffffb480
> volume #23 color #ffffb580
> volume #23 color #ffffc480
> volume #23 color #ffffff80
> volume #11 color #d3d2d266
> volume #11 color #fed2d266
> volume #11 color #fee6d266
> volume #11 color #feffd266
> volume #11 color #fefff266
> volume #11 color #feffff66
> volume #11 color #feffff80
> volume #10 color #c3b4b480
> volume #10 color #dbb4b480
> volume #10 color #ffb4b480
> volume #10 color #ffc5b480
> volume #10 color #ffd0b480
> volume #10 color #ffffb480
> volume #10 color #ffffb680
> volume #10 color #ffffc380
> volume #10 color #ffffff80
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-B1.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save image /Users/chunyan/2020/20200507-Figure5-B1.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save image /Users/chunyan/2020/20200507-Figure5-B1.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save image /Users/chunyan/2020/20200507-Figure5-B2.tif pixelSize 0.1
> supersample 4 transparentBackground true
> volume #42.1 color #4dddd3a9
> volume #42.1 color #d8ddd3a9
> volume #42.1 color #d8ddd3a8
> volume #42.1 color #d3ddd3a8
> volume #42.1 color #d3d3d3a8
> volume #42.1 color #d3d3d3a4
> volume #42.1 color #d3d3d3a1
> volume #42.1 color #d3d3d39d
> volume #42.1 color #d3d3d39c
> volume #42.1 color #d3d3d39b
> volume #42.1 color #d3d3d399
> volume #42.1 color #d3d3d397
> volume #42.1 color #d3d3d396
> volume #42.1 color #d3d3d395
> volume #42.1 color #d3d3d394
> volume #42.1 color #d3d3d393
> volume #42.1 color #d3d3d392
> save image /Users/chunyan/2020/20200507-Figure5-B3.tif pixelSize 0.1
> supersample 4 transparentBackground true
> volume #23 color #ffffa880
> volume #23 color #19ffa880
> volume #23 color #19aba880
> volume #23 color #19f1a880
> volume #23 color #19f2a880
> volume #23 color #19f8a880
> volume #23 color #19fda880
> volume #23 color #19fea880
> volume #23 color #19ffa880
> volume #23 color #19ff9080
> volume #23 color #19ff7180
> volume #23 color #19ff3a80
> volume #23 color #19ff2080
> volume #23 color #19ff0e80
> volume #23 color #19ff0080
> select #42.1
3 models selected
> hide #32,34#17.1,3#42.2#!25,27,37#!17.2 cartoons
> hide #32,34#17.1,3#42.2#!25,27,37#!17.2 atoms
Must specify one map, got 0
> fitmap #41 inMap #42.1
Fit map gp8-asym-300-400-part-genome.mrc in map gp8-asym-300-400-part-genome-
lp.mrc using 5944 points
correlation = 0.9974, correlation about mean = 0.9757, overlap = 1.313
steps = 700, shift = 0.425, angle = 62.8 degrees
Position of gp8-asym-300-400-part-genome.mrc (#41) relative to
gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates:
Matrix rotation and translation
0.99920712 -0.03979034 0.00136575 8.27097455
0.03979205 0.99920720 -0.00125261 -7.97369474
-0.00131482 0.00130597 0.99999828 0.08962952
Axis 0.03211525 0.03364651 0.99891768
Axis point 204.51636536 203.71848140 0.00000000
Rotation angle (degrees) 2.28294183
Shift along axis 0.08686989
> select #37
49008 atoms, 49740 bonds, 1 model selected
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> volume #42.1 color #3dc5db92
> volume #42.1 color #3dc5dbd0
> volume #42.1 color #3dc5dbf2
> volume #42.1 color #3dc5db
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-B4.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> hide sel atoms
> hide sel cartoons
> hide sel atoms
> hide sel cartoons
> hide sel cartoons
> volume #41 level 0.008402
> volume #42.1 color #3dc5dbb2
> volume #42.1 color #c5c5dbb2
> volume #42.1 color #c5c5c5b2
> volume #42.1 color #c5c5c5b0
> volume #42.1 color #c5c5c594
> volume #42.1 color #c5c5c584
> volume #42.1 color #c5c5c56a
> volume #42.1 color #c5c5c550
> volume #42.1 color #c5c5c54a
> volume #42.1 color #c5c5c547
> volume #42.1 color #c5c5c543
> volume #42.1 color #c5c5c542
> volume #42.1 color #c5c5c53e
> volume #42.1 color #c5c5c535
> volume #42.1 color #c5c5c52e
> volume #42.1 color #c5c5c529
> volume #42.1 color #c5c5c527
> volume #42.1 color #c5c5c525
> volume #42.1 color #c5c5c526
> volume #42.1 color #c5c5c52d
> volume #42.1 color #c5c5c532
> volume #42.1 color #c5c5c536
> volume #42.1 color #c5c5c539
> volume #42.1 color #c5c5c53e
> volume #42.1 color #c5c5c542
> volume #42.1 color #c5c5c546
> volume #42.1 color #c5c5c548
> volume #42.1 color #c5c5c54c
> volume #42.1 color #c5c5c54f
> volume #42.1 color #c5c5c553
> volume #42.1 color #c5c5c555
> volume #42.1 color #c5c5c55b
> volume #42.1 color #c5c5c561
> volume #42.1 color #c5c5c564
> volume #42.1 color #c5c5c569
> volume #42.1 color #c5c5c56f
> volume #42.1 color #c5c5c575
> volume #42.1 color #c5c5c57c
> volume #42.1 color #c5c5c587
> volume #42.1 color #c5c5c590
> volume #42.1 color #c5c5c598
> volume #42.1 color #c5c5c59f
> volume #42.1 color #c5c5c5a2
> volume #42.1 color #c5c5c5a4
> volume #42.1 color #c5c5c5a5
> save image /Users/chunyan/2020/20200507-Figure5-B5.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save image /Users/chunyan/2020/20200507-Figure5-B6.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> show sel atoms
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-B7.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #34
1640 atoms, 1838 bonds, 1 model selected
> select clear
> select #42.1/1-11
Nothing selected
> select #42.2/1-11
Nothing selected
> hide #32,34#17.1,3#42.2#!25,27,37#!17.2 cartoons
> show #32,34#17.1,3#42.2#!25,27,37#!17.2 cartoons
> show #32,34#17.1,3#42.2#!25,27,37#!17.2 cartoons
> select #27
6313 atoms, 6474 bonds, 1 model selected
> hide sel cartoons
> select #32
63576 atoms, 55608 bonds, 1 model selected
> hide sel cartoons
> select #25
3610 atoms, 3660 bonds, 1 model selected
> hide sel cartoons
> select #17
60992 atoms, 61568 bonds, 64 pseudobonds, 5 models selected
> hide sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> select #34
1640 atoms, 1838 bonds, 1 model selected
> hide sel cartoons
> hide sel atoms
> lighting flat
> select :34
971 atoms, 785 bonds, 51 models 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
> select #42.2
1640 atoms, 1838 bonds, 1 model selected
> select #42.2:1-11
227 atoms, 253 bonds, 1 model selected
> volume #42.1 color #3dc5dba5
> color #42.2:1-11 yellow
> color #42.2:12-23 magenta
> color #42.2:24-35 blue
> color #42.2:36-38 red
> color #42.2/A:1-11 yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #42.2/A:12-23 magenta
> color #42.2/A:24-35 blue
> color #42.2/A:36-38 red
> color #42.2/B:36-38 red
> color #42.2/B:1-11 yellow
> save session /Users/chunyan/2020/gp8-asym/gp8-asym-20200507.cxs
> select #42.2/A:1-11
Nothing selected
> select #42.2/A:1-11
Nothing selected
> select #42.2
1640 atoms, 1838 bonds, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #42.2/A
820 atoms, 922 bonds, 1 model selected
> hide sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel cartoons
> hide sel cartoons
> select #42.2/B
820 atoms, 916 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select #42.2/B:1-11
227 atoms, 253 bonds, 1 model selected
> color #42.2/B:1-11 purple
> color #42.2/B:1-11 magenta
> color #42.2/B:12-23 green
> color #42.2/B:24-35 red
> color #42.2/B:36-38 blue
> color #42.2/B:36-39 blue
> color #42.2/B:36-40 blue
> open /Users/chunyan/2020/gp8-asym/part/Ideal-B-form-DNA-coot-38.pdb
Chain information for Ideal-B-form-DNA-coot-38.pdb #44
---
Chain | Description
A | No description available
B | 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.
> view
> lighting flat
> matchmaker #44 to #42.2
No chains in reference structure Ideal-B-form-DNA-coot-0.pdb #42.2 compatible
with BLOSUM-62 similarity matrix
> matchmaker #44/a to #42.2/A
No chains in reference structure Ideal-B-form-DNA-coot-0.pdb #42.2 compatible
with BLOSUM-62 similarity matrix
> matchmaker #44/A to #42.2/A
No chains in reference structure Ideal-B-form-DNA-coot-0.pdb #42.2 compatible
with BLOSUM-62 similarity matrix
> select #44/B:1
19 atoms, 20 bonds, 1 model selected
> select #44/B:1
19 atoms, 20 bonds, 1 model selected
> select clear
> select clear
> select #44
1558 atoms, 1746 bonds, 1 model selected
> ui mousemode rightMode "translate selected models"
> split #44
Chain information for Ideal-B-form-DNA-coot-38.pdb A #44.1
---
Chain | Description
A | No description available
Chain information for Ideal-B-form-DNA-coot-38.pdb B #44.2
---
Chain | Description
B | No description available
Split Ideal-B-form-DNA-coot-38.pdb (#44) into 2 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.
> split #42.2
Chain information for Ideal-B-form-DNA-coot-0.pdb A #42.2.1
---
Chain | Description
A | No description available
Chain information for Ideal-B-form-DNA-coot-0.pdb B #42.2.2
---
Chain | Description
B | No description available
Split Ideal-B-form-DNA-coot-0.pdb (#42.2) into 2 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.
> matchmaker #44.1 to #42.2.1
No chains in reference structure Ideal-B-form-DNA-coot-0.pdb A #42.2.1
compatible with BLOSUM-62 similarity matrix
> select clear
> select #44.1
778 atoms, 872 bonds, 1 model selected
> delete #44.1
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.
> delete #44.2
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 #42.2.2
820 atoms, 916 bonds, 1 model selected
> show sel cartoons
> show sel cartoons
> select #42.2.1
820 atoms, 922 bonds, 1 model selected
> show sel cartoons
> select clear
> open /Users/chunyan/2020/gp8-asym/part/Ideal-B-form-DNA-coot-38.pdb
Chain information for Ideal-B-form-DNA-coot-38.pdb #46
---
Chain | Description
A | No description available
B | 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.
> matchmaker #46 to #42.2.1
No chains in reference structure Ideal-B-form-DNA-coot-0.pdb A #42.2.1
compatible with BLOSUM-62 similarity matrix
> matchmaker #46 to #42.2.1/B
No 'to' model specified
> matchmaker #46 to #42.2.1
No chains in reference structure Ideal-B-form-DNA-coot-0.pdb A #42.2.1
compatible with BLOSUM-62 similarity matrix
> select #46
1558 atoms, 1746 bonds, 1 model selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> select #42.2.1
820 atoms, 922 bonds, 1 model selected
> hide sel cartoons
> select #42.2.2
820 atoms, 916 bonds, 1 model selected
> hide sel cartoons
> fitmap #46 inMap #42.1
Fit molecule Ideal-B-form-DNA-coot-38.pdb (#46) to map gp8-asym-300-400-part-
genome-lp.mrc (#42.1) using 1558 atoms
average map value = 0.00458, steps = 224
shifted from previous position = 4.93
rotated from previous position = 8.31 degrees
atoms outside contour = 743, contour level = 0.00071868
Position of Ideal-B-form-DNA-coot-38.pdb (#46) relative to
gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates:
Matrix rotation and translation
0.21232023 0.97358360 -0.08399459 -23.59629446
0.97426410 -0.21755692 -0.05897846 61.27687421
-0.07569406 -0.06931059 -0.99471928 404.52729508
Axis -0.77856006 -0.62547170 0.05127748
Axis point 0.00000000 40.97854990 201.35498727
Rotation angle (degrees) 179.61981614
Shift along axis 0.78732203
> select #46
1558 atoms, 1746 bonds, 1 model selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "rotate selected models"
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select #46
1558 atoms, 1746 bonds, 1 model selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #46 inMap #42.1
Fit molecule Ideal-B-form-DNA-coot-38.pdb (#46) to map gp8-asym-300-400-part-
genome-lp.mrc (#42.1) using 1558 atoms
average map value = 0.004631, steps = 104
shifted from previous position = 3.27
rotated from previous position = 5.78 degrees
atoms outside contour = 639, contour level = 0.00071868
Position of Ideal-B-form-DNA-coot-38.pdb (#46) relative to
gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates:
Matrix rotation and translation
0.95148408 0.29318268 -0.09339142 -34.35564208
0.29177278 -0.95605644 -0.02871816 357.68617677
-0.09770713 0.00007580 -0.99521521 400.69987852
Axis 0.98779591 0.14805350 -0.04836744
Axis point 0.00000000 179.93965765 200.82850242
Rotation angle (degrees) 179.16489267
Shift along axis -0.36049938
> select #46/A:1-11
223 atoms, 248 bonds, 1 model selected
> color #46/A:1-11 magenta
> color #46/A:12-23 green
> color #46/A:24-35 red
> color #46/A:36-38 blue
> color #46/B:27-38 blue
> color #46/B:27-38 magenta
> color #46/B:15-26 green
> color #46/B:13-14 red
> color #46/B:3-14 red
> color #46/B:1-2 blue
> select clear
> volume #42.1 color #c7c5dba5
> volume #42.1 color #c7c5cba5
> volume #42.1 color #c7c5cbd2
> volume #42.1 color #c7c5cb71
> volume #42.1 color #c7c5ca71
> lighting soft
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> select #37:Arg368
Nothing selected
> select #34:Arg368
Nothing selected
> select #37:368
132 atoms, 120 bonds, 1 model selected
> volume #42.1 color #78c5ca71
> volume #42.1 color #66c5ca71
> volume #42.1 color #48c5ca71
> volume #42.1 color #48c51971
> volume #42.1 color #48c50871
> volume #42.1 color #48c50771
> volume #42.1 color #48c50071
> volume #42.1 color #36c50071
> volume #42.1 color #30c50071
> volume #42.1 color #00c50071
> volume #42.1 color #00d50071
> volume #42.1 color #00db0071
> volume #42.1 color #00ff0071
> volume #42.1 color #00ff00f5
> volume #42.1 color #00ff00f8
> volume #42.1 color lime
> color #37: 368 #00FF00
> select clear
> color #37: 368 magenta
> volume #42.1 color #00de00
> volume #42.1 color #00dd00
> volume #42.1 color #00b300
> volume #42.1 color #00b3df
> volume #42.1 color #00b3f3
> volume #42.1 color #00b3f4
> volume #42.1 color #00b3f8
> volume #42.1 color #00b3fa
> volume #42.1 color #00b3fb
> color #37: 368 #00B3FA
> lighting simple
> lighting full
> lighting soft
> lighting full
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 full
> lighting soft
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting full
> lighting soft
> volume #42.1 color #b3b3fb
> volume #42.1 color #b3b3b8
> volume #42.1 color #b3b3b8ac
> volume #42.1 color #b3b3b884
> volume #42.1 color #b3b3b865
> volume #42.1 color #b3b39865
> volume #42.1 color #b3b3c465
> volume #42.1 color #c3b3c465
> volume #42.1 color #a7b3c465
> volume #42.1 color #d0b3c465
> volume #42.1 color #a4b3c465
> volume #42.1 color #a4a5c465
> select #46/B:27-38
248 atoms, 278 bonds, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #46/A:1-11
223 atoms, 248 bonds, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> select #37:368
132 atoms, 120 bonds, 1 model selected
> color #37:368 yellow
> select clear
> color #46/B:13-14 blue
> color #46/B:13-14 red
> color #46/B:3-14 blue
> volume #42.1 color #a4ecc465
> volume #42.1 color #a4ecc565
> volume #42.1 color #a4ecdb65
> volume #42.1 color #a4ecff65
> volume #42.1 color #d2ecff65
> volume #42.1 color #9cecff65
> volume #42.1 color #71ecff65
> volume #42.1 color #71ecffda
> volume #42.1 color #71ecffdb
> volume #42.1 color #71ecffeb
> volume #42.1 color #71ecff
> volume #42.1 color #4eecff
> volume #42.1 color #3eecff
> volume #42.1 color #21ecff
> volume #42.1 color #23ecff
> volume #42.1 color #2fecff
> volume #42.1 color #3becff
> volume #42.1 color #3fecff
> volume #42.1 color #44ecff
> volume #42.1 color #4decff
> volume #42.1 color #52ecff
> volume #42.1 color #55ecff
> volume #42.1 color #57ecff
> volume #42.1 color #5aecff
> volume #42.1 color #5decff
> volume #42.1 color #5fecff
> volume #42.1 color #60ecff
> volume #42.1 color #61ecff
> volume #42.1 color #70ecff
> volume #42.1 color #71ecff
> volume #42.1 color #70ffff
> color #46/B:3-14 #70FFFF
> color #46/A:24-35 #70FFFF
> color #46/A:36-38 grey
> color #46/B:1-2 grey
> select #46
1558 atoms, 1746 bonds, 1 model selected
> show sel cartoons
> select clear
> volume #42.1 color #70beff
> volume #42.1 color #709bff
> volume #42.1 color #b49bff
> volume #42.1 color #b4c4ff
> volume #42.1 color #69c4ff
> volume #42.1 color #69c45e
> volume #42.1 color #69e95e
> volume #42.1 color #69fb5e
> volume #42.1 color #56fb5e
> volume #42.1 color #36fb5e
> volume #42.1 color #23fb5e
> volume #42.1 color #08fb5e
> volume #42.1 color #3ffb5e
> volume #42.1 color #3ffb5f
> volume #42.1 color #3fffff
> volume #42.1 color #3fff3c
> volume #42.1 color #3fff0a
> volume #42.1 color #3fff08
> volume #42.1 color #3fff00
> color #46/B:15-26 #3FFF00
> color #46/A:12-23 #3FFF00
> select clear
> view name p6
> save image /Users/chunyan/2020/20200507-Figure5-C!.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save image /Users/chunyan/2020/20200507-Figure5-C1.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> 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.
> save image /Users/chunyan/2020/20200507-Figure5-C2.tif pixelSize 0.1
> supersample 4 transparentBackground true
> 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
> select #37:368
132 atoms, 120 bonds, 1 model selected
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #37:368 magenta
> select clear
> view name p3
> save image /Users/chunyan/2020/20200507-Figure5-C3.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #46/A:1-11
223 atoms, 248 bonds, 1 model selected
> hide sel cartoons
> select #46/A:27-38
248 atoms, 278 bonds, 1 model selected
> select #46/B:27-38
248 atoms, 278 bonds, 1 model selected
> hide sel cartoons
> select #37:368
132 atoms, 120 bonds, 1 model selected
> color #37:368 yellow
> select clear
> select #46
1558 atoms, 1746 bonds, 1 model selected
> ui mousemode rightMode "rotate selected models"
> select clear
> view name p3
> save image /Users/chunyan/2020/20200507-Figure5-C4.tif pixelSize 0.1
> supersample 4 transparentBackground true
> volume #42.1 color #3fffaa
> volume #42.1 color #3fa8aa
> volume #42.1 color #a2a8aa
> volume #42.1 color #a2a8aa4a
> volume #42.1 color #a2a8aa67
> view name p3
> save image /Users/chunyan/2020/20200507-Figure5-C4.tif pixelSize 0.1
> supersample 4 transparentBackground true
> volume #41 level 0.009768
> volume #42.1 color #a2a8aa94
> volume #42.1 color #a2a8aab6
> volume #41 color #c5c5db
> volume #41 color #c5c5c1
> volume #41 color #c5c5c189
> volume #41 color #c5c5c15f
> volume #41 color #c5c5c198
> volume #41 color #c5c5c1a6
> volume #41 color #c5c5c1a7
> volume #41 color #c5c5c1b3
> volume #41 color #c5c5c0b3
> select #37
49008 atoms, 49740 bonds, 1 model selected
> select #46
1558 atoms, 1746 bonds, 1 model selected
> hide sel cartoons
> hide sel atoms
> volume #41 color #c5f1c0b3
> volume #41 color #67f1c0b3
> volume #41 color #3df1c0b3
> volume #41 color #3df1dab3
> volume #41 color #3df1daf4
> volume #41 color #3df1daf6
> volume #41 color #3df1da
> volume #41 color #3df1c0
> volume #41 color #3df1bf
> volume #41 color #3df1ad
> volume #41 color #3df1e7
> volume #41 color #3df1ba
> volume #41 color #3dc9ba
> volume #41 color #3ddcba
> volume #41 color #3ddcd5
> volume #41 color #3ddcc0
> volume #41 color #3ddcac
> volume #41 color #3dc7ac
> volume #41 color #66c7ac
> volume #41 color #72c7ac
> volume #41 color #72c6ac
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting soft
> lighting full
> lighting full
> lighting soft
> lighting full
> save image /Users/chunyan/2020/20200507-Figure5-C4.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select clear
> volume #11 level 0.0059
> save image /Users/chunyan/2020/20200507-Figure5-C5.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> 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.
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-C6.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #46
1558 atoms, 1746 bonds, 1 model selected
> show sel cartoons
> show sel atoms
> select clear
> select clear
Expected an objects specifier or a keyword
> select #46/A:1-11
223 atoms, 248 bonds, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #46/B:27-38
248 atoms, 278 bonds, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-C7.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #46
1558 atoms, 1746 bonds, 1 model selected
> show sel cartoons
> volume #42.1 color #a2caaab6
> volume #42.1 color #a2caddb6
> volume #42.1 color #e2caddb6
> volume #42.1 color #e2edddb6
> volume #42.1 color #e2ededb6
> volume #42.1 color #e2ededa4
> volume #42.1 color #e2ededa3
> volume #42.1 color #e2eded97
> volume #42.1 color #e2eded93
> volume #42.1 color #e2eded90
> volume #42.1 color #e2eded8b
> volume #42.1 color #e2eded87
> volume #42.1 color #e2eded85
> volume #42.1 color #e2eded82
> volume #42.1 color #e2eded81
> volume #42.1 color #e2eded7e
> volume #42.1 color #e2eded79
> volume #42.1 color #e2eded76
> volume #42.1 color #e2eded74
> volume #42.1 color #e2eded72
> volume #42.1 color #e2eded6d
> volume #42.1 color #e2eded6b
> volume #42.1 color #e2eded69
> volume #42.1 color #e2eded68
> volume #42.1 color #e2eded67
> volume #42.1 color #e2eded6c
> volume #42.1 color #e2eded6d
> volume #42.1 color #e2eded69
> volume #42.1 color #e2edec69
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-C8.tif pixelSize 0.1
> supersample 4 transparentBackground true
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 #23 color #19ae0080
> volume #23 color #b4ae0080
> volume #23 color #b4aeb080
> volume #23 color #b4aeb093
> volume #23 color #b4aeb0be
> volume #23 color #b4aeb0e6
> volume #23 color #b4aeb0
> volume #23 color #b4aeb0f3
> volume #23 color #b4aeb0f0
> volume #23 color #b4aeb041
> volume #23 color #b4aeb02e
> volume #23 color #b4aeb016
> volume #23 color #b4aeb00b
> volume #23 color #b4aeb002
> volume #23 color #b4aeb000
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.
> volume #23 color #b435b000
> volume #23 color #1335b000
> volume #23 color #1335d100
> volume #23 color #13e6d100
> volume #23 color #13e61800
> volume #23 color #13e60900
> volume #23 color #13e60000
> volume #23 color #13e600ce
> volume #23 color #13e600cf
> volume #23 color #13e600d1
> volume #23 color #13e600e1
> volume #23 color #13e600e9
> volume #23 color #13e600f2
> volume #23 color #13e600fe
> volume #23 color #13e600
> volume #23 color #13e500
> save image /Users/chunyan/2020/20200507-Figure5-C9.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save image /Users/chunyan/2020/20200507-Figure5-C10.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> save image /Users/chunyan/2020/20200507-Figure5-C11.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save image /Users/chunyan/2020/20200507-Figure5-C12.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel surfaces
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 surfaces
> show sel cartoons
> lighting flat
> select clear
> select #37/J:371
5 atoms, 4 bonds, 1 model selected
> select #37/J:357
8 atoms, 7 bonds, 1 model selected
> lighting soft
> select #37
49008 atoms, 49740 bonds, 10 models selected
> hide sel surfaces
> hide sel cartoons
> select #37 :300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> lighting flat
> select #37/H:355
5 atoms, 4 bonds, 1 model selected
> select #37/H:356
11 atoms, 11 bonds, 1 model selected
> select #37/H:355
5 atoms, 4 bonds, 1 model selected
> select #37/H:356
11 atoms, 11 bonds, 1 model selected
> select #37/H:356
11 atoms, 11 bonds, 1 model selected
> select #37/H:370
7 atoms, 6 bonds, 1 model selected
> select #37/H:383
8 atoms, 7 bonds, 1 model selected
> save session /Users/chunyan/2020/gp8-asym/gp8-asym-20200507.cxs
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/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
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/atomic/molobject.py", line 631, in take_snapshot
data = {'structure': self.structure,
File "cymol.pyx", line 1380, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
During handling of the above exception, another exception occurred:
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/session.py", line 796, in save
session.save(output, version=version, include_maps=include_maps)
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/session.py", line 556, in save
mgr.discovery(self._state_containers)
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/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
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/session.py", line 279, in process
raise RuntimeError(msg)
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x3bfd81490> ->
<chimerax.atomic.molobject.Residue object at 0x4088e1af0>: Residue already
deleted
RuntimeError: Error while saving session data for 'nucleotides' -> -> :
Residue already deleted
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/session.py", line 279, in process
raise RuntimeError(msg)
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/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
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/atomic/molobject.py", line 631, in take_snapshot
data = {'structure': self.structure,
File "cymol.pyx", line 1380, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
During handling of the above exception, another exception occurred:
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/ui/gui.py", line 911, in <lambda>
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))
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/ui/gui.py", line 641, in file_save_cb
self.save_dialog.display(self, session)
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/ui/save_dialog.py", line 139, in display
fmt.save(session, filename)
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/session.py", line 1100, in save
run(session, cmd)
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/commands/run.py", line 31, in run
results = command.run(text, log=log)
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/commands/cli.py", line 2837, in run
result = ci.function(session, **kw_args)
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/session.py", line 992, in save_session
save(session, filename, **kw)
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/commands/save.py", line 61, in save
fmt.export(session, filename, fmt.nicknames[0], **kw)
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/io.py", line 220, in export
result = self.export_func(session, path, **kw)
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/session.py", line 796, in save
session.save(output, version=version, include_maps=include_maps)
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/session.py", line 556, in save
mgr.discovery(self._state_containers)
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/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
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/session.py", line 279, in process
raise RuntimeError(msg)
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x3bfd81490> ->
<chimerax.atomic.molobject.Residue object at 0x4088e1af0>: Residue already
deleted
RuntimeError: Error while saving session data for 'nucleotides' -> -> :
Residue already deleted
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/session.py", line 279, in process
raise RuntimeError(msg)
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.
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