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Opened 6 years ago
Last modified 6 years ago
#3163 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-11-26)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.91 (2019-11-26)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/chunyan/2020/RIP-20200425.cxs format session
opened ChimeraX session
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> close #1.1.1
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> hide sel cartoons
> select clear
> select clear
> hide sel cartoons
> select clear
> select clear
> hide sel cartoons
> toolshed show "Side View"
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> open /Users/chunyan/2020/gp8-asym/part/gp8-asym-300-400-part.mrc
Opened gp8-asym-300-400-part.mrc, grid size 400,400,400, pixel 1.05, shown at
level 5.08e-06, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> toolshed show "Side View"
> select clear
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> ui mousemode rightMode "rotate selected models"
> volume #37 level 0.006161
> volume #37 step 1
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> toolshed show "Side View"
> view
> ui mousemode rightMode "translate selected models"
> fitmap #37 inMap #11
Fit map gp8-asym-300-400-part.mrc in map gp8-basen-new.mrc using 147173 points
correlation = 0.3146, correlation about mean = 0.04917, overlap = 6.203
steps = 88, shift = 4.74, angle = 3.98 degrees
Position of gp8-asym-300-400-part.mrc (#37) relative to gp8-basen-new.mrc
(#11) coordinates:
Matrix rotation and translation
-0.99518848 -0.03072345 -0.09303738 447.14164523
-0.03952662 0.99475822 0.09430653 -5.99863737
0.08965227 0.09753022 -0.99118632 390.07986007
Axis 0.01762256 -0.99868594 -0.04812315
Axis point 214.57314960 0.00000000 205.44584815
Rotation angle (degrees) 174.75210610
Shift along axis -4.90133727
> volume #11 level 0.007051
> volume #37 level 0.0105
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #37 inMap #11
Fit map gp8-asym-300-400-part.mrc in map gp8-basen-new.mrc using 87142 points
correlation = 0.3814, correlation about mean = 0.03852, overlap = 5.845
steps = 76, shift = 6.03, angle = 4.94 degrees
Position of gp8-asym-300-400-part.mrc (#37) relative to gp8-basen-new.mrc
(#11) coordinates:
Matrix rotation and translation
-0.64228132 -0.76646896 -0.00008215 505.83912721
-0.76646609 0.64227862 0.00280807 235.63361319
-0.00209954 0.00186654 -0.99999604 436.65243484
Axis -0.42291805 0.90616702 0.00128927
Axis point 308.04005138 0.00000000 218.00322664
Rotation angle (degrees) 179.93622174
Shift along axis 0.15787310
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #37 inMap #11
Fit map gp8-asym-300-400-part.mrc in map gp8-basen-new.mrc using 87142 points
correlation = 0.3824, correlation about mean = 0.03981, overlap = 5.862
steps = 84, shift = 3.67, angle = 4.04 degrees
Position of gp8-asym-300-400-part.mrc (#37) relative to gp8-basen-new.mrc
(#11) coordinates:
Matrix rotation and translation
-0.17336858 -0.98485622 -0.00123484 453.42883693
-0.98485459 0.17336525 0.00242886 380.00466870
-0.00217800 0.00163722 -0.99999627 436.71861867
Axis -0.64289740 0.76595116 0.00132708
Axis point 386.27971754 0.00000000 217.93897713
Rotation angle (degrees) 179.96472402
Shift along axis 0.13635913
> open /Users/chunyan/2020/gp8-asym/gp8-asym-3.6.mrc
Opened gp8-asym-3.6.mrc, grid size 400,400,400, pixel 1.05, shown at level
0.015, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> ui mousemode rightMode "rotate selected models"
> select #38
2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #38 inMap #11
Fit map gp8-asym-3.6.mrc in map gp8-basen-new.mrc using 79941 points
correlation = 0.4549, correlation about mean = 0.05236, overlap = 9.372
steps = 852, shift = 4.07, angle = 4.74 degrees
Position of gp8-asym-3.6.mrc (#38) relative to gp8-basen-new.mrc (#11)
coordinates:
Matrix rotation and translation
-0.39867075 0.91709398 -0.00050397 101.33307182
0.91709398 0.39867094 0.00034637 -66.40725091
0.00051857 -0.00032410 -0.99999981 423.68628677
Axis -0.54832810 -0.83626329 -0.00000686
Axis point 72.36032986 0.00000000 211.86193308
Rotation angle (degrees) 179.96497098
Shift along axis -0.03273208
> surface dust #38 size 40
> surface dust #38 size 10
> volume #38 level 0.01159
> volume #38 level 0.01055
> volume #38 step 1
> volume #38 level 0.0122
> volume #38 level 0.01413
> volume #38 level 0.0111
> volume #38 level 0.01495
> open /Users/chunyan/2020/gp8-asym/part/gp8-asym-300-400-part.mrc
Opened gp8-asym-300-400-part.mrc, grid size 400,400,400, pixel 1.05, shown at
level 5.08e-06, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> volume #40 level 0.008885
> volume #40 step 1
> select clear
> select #38
2 models selected
> select clear
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> volume #40 level 0.01302
> fitmap #40 inMap #38
Fit map gp8-asym-300-400-part.mrc in map gp8-asym-3.6.mrc using 63324 points
correlation = 0.4019, correlation about mean = 0.06306, overlap = 5.887
steps = 112, shift = 6.72, angle = 5.71 degrees
Position of gp8-asym-300-400-part.mrc (#40) relative to gp8-asym-3.6.mrc (#38)
coordinates:
Matrix rotation and translation
0.88041247 0.47419664 -0.00338290 -73.68794519
-0.47419223 0.88041895 0.00205422 124.15906451
0.00395247 -0.00020442 0.99999217 -18.10534238
Axis -0.00238147 -0.00773431 -0.99996725
Axis point 209.61876027 208.17205764 0.00000000
Rotation angle (degrees) 28.30792305
Shift along axis 17.31995101
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #40 inMap #38
Fit map gp8-asym-300-400-part.mrc in map gp8-asym-3.6.mrc using 63324 points
correlation = 0.4019, correlation about mean = 0.06306, overlap = 5.887
steps = 88, shift = 0.241, angle = 8.43 degrees
Position of gp8-asym-300-400-part.mrc (#40) relative to gp8-asym-3.6.mrc (#38)
coordinates:
Matrix rotation and translation
0.88043156 0.47416047 -0.00348300 -73.66670303
-0.47415557 0.88043841 0.00217082 124.12603993
0.00409588 -0.00025978 0.99999158 -18.12040541
Axis -0.00256298 -0.00799165 -0.99996478
Axis point 209.59576053 208.12228712 0.00000000
Rotation angle (degrees) 28.30562925
Shift along axis 17.31660117
> ui mousemode rightMode "rotate selected models"
> volume #40 level 0.01312
> volume #40 level 0.01374
> volume #40 level 0.01446
> volume #40 level 0.01529
> volume #40 level 0.0156
> volume #40 level 0.0157
> volume #40 level 0.01612
> volume #40 level 0.01674
> volume #40 level 0.01694
> volume #40 level 0.01705
> volume #40 level 0.01736
> volume #40 level 0.01767
> volume #40 level 0.01798
> volume #40 level 0.0188
> volume #40 level 0.01932
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> open /Users/chunyan/2020/gp8-asym/part/gp8-asym-300-400-part-genome.mrc
Opened gp8-asym-300-400-part-genome.mrc, grid size 400,400,400, pixel 1.05,
shown at level 1.61e-06, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> select #41
2 models selected
> ui mousemode rightMode "translate selected models"
> volume #38 color #ffffb2a7
> volume #38 color #ffffb28e
> volume #38 color #ffffb270
> ui mousemode rightMode "rotate selected models"
> fitmap #41 inMap #38
Fit map gp8-asym-300-400-part-genome.mrc in map gp8-asym-3.6.mrc using 1031
points
correlation = 0.9109, correlation about mean = 0.6062, overlap = 0.1874
steps = 1724, shift = 9.41, angle = 106 degrees
Position of gp8-asym-300-400-part-genome.mrc (#41) relative to
gp8-asym-3.6.mrc (#38) coordinates:
Matrix rotation and translation
0.90157171 0.43262356 0.00230586 -70.00335224
-0.43262105 0.90150712 0.01113286 109.45688413
0.00273759 -0.01103464 0.99993537 2.84766914
Axis -0.02561151 -0.00049881 -0.99967185
Axis point 205.50884166 208.63317298 0.00000000
Rotation angle (degrees) 25.64311888
Shift along axis -1.10844150
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> lighting soft
> lighting soft
> lighting flat
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> graphics silhouettes true
> lighting soft
> volume #41 color #8db2ff
> volume #41 color #8ddbff
> volume #41 color #8dddff
> volume #41 color #8ddddc
> volume #41 color #8dddf8
> volume #41 color #8dedf8
> volume #41 color #8deef8
> lighting soft
> volume #41 color #67eef8
> volume #41 color #67d4f8
> volume #41 color #67d5f8
> volume #41 color #67e7f8
> volume #41 color #67e7dc
> volume #41 color #67f5dc
> volume #41 color #67f6dc
> volume #41 color #67f6fb
> volume #41 color #83f6fb
> volume #41 color #82f6fb
> volume #41 color #7ef6fb
> volume #41 color #65f6fb
> volume #41 color #5ef6fb
> volume #41 color #5df6fb
> volume #41 color #5bf6fb
> volume #41 color #59f6fb
> volume #41 color #58f6fb
> volume #41 color #57f6fb
> volume #41 color #54f6fb
> volume #41 color #51f6fb
> volume #41 color #50f6fb
> volume #41 color #4ff6fb
> volume #41 color #4ef6fb
> volume #41 color #4df6fb
> volume #41 color #4cf6fb
> volume #41 color #4cf5fb
> volume #41 color #4cf2fb
> volume #41 color #4ce9fb
> volume #41 color #4ce7fb
> volume #41 color #4ce5fb
> volume #41 color #4ce3fb
> volume #41 color #4ce2fb
> volume #41 color #4ce3fb
> volume #41 color #4ce4fb
> volume #41 color #4ce6fb
> volume #41 color #4ce7fb
> volume #41 color #4ce9fb
> volume #41 color #4cebfb
> volume #41 color #4ceefb
> volume #41 color #4ceffb
> volume #41 color #4cf1fb
> volume #41 color #4cf3fb
> volume #41 color #4cf3f9
> volume #41 color #4cf3e8
> volume #41 color #4cf3de
> volume #41 color #4cf3df
> volume #41 color #4cf3e2
> volume #41 color #4cf3fd
> volume #41 color #4cf3ff
> volume #41 color #66f3ff
> volume #41 color #38f3ff
> volume #41 color #2af3ff
> volume #41 color #2affff
> volume #41 color #2afeff
> volume #41 color #2af0ff
> volume #41 color #2ac3ff
> volume #41 color #2ac1ff
> volume #41 color #2ad4ff
> volume #41 color #2adbff
> volume #41 color #2ae3ff
> volume #41 color #2aedff
> volume #41 color #2af1ff
> volume #41 color #2af5ff
> volume #41 color #2af8ff
> volume #41 color #2af9ff
> volume #41 color #2afbff
> volume #41 color #2afdff
> volume #41 color #2afeff
> volume #41 color #2affff
> volume #41 color #4dffff
> volume #41 color #4dffd9
> volume #41 color #4dffa5
> volume #41 color #4dffe9
> volume #41 step 1
> volume #41 level 0.008186
> surface dust #41 size 40
> volume #41 level 0.009233
> select #37
3 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> open /Users/chunyan/2020/gp8-asym/gp8-new-assembled.pdb
Chain information for gp8-new-assembled.pdb #37
---
Chain | Description
A B C D E F G H I J K L | No description available
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> lighting flat
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> hide sel atoms
> show sel cartoons
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> fitmap #37 inMap #11
Fit molecule gp8-new-assembled.pdb (#37) to map gp8-basen-new.mrc (#11) using
49008 atoms
average map value = 0.01383, steps = 112
shifted from previous position = 3.73
rotated from previous position = 8.12 degrees
atoms outside contour = 13411, contour level = 0.0070512
Position of gp8-new-assembled.pdb (#37) relative to gp8-basen-new.mrc (#11)
coordinates:
Matrix rotation and translation
0.91705730 0.39875537 0.00023372 -66.37710555
0.39875525 -0.91705728 0.00043699 318.68975009
0.00038859 -0.00030754 -0.99999987 423.66876613
Axis -0.97904472 -0.20364529 -0.00016016
Axis point 0.00000000 166.28936439 211.80886941
Rotation angle (degrees) 179.97821425
Shift along axis 0.01863426
> preset cartoons/nucleotides cylinders/stubs
Changed 212848 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
> select clear
> select clear
> hide sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> color #37 yellow
> select clear
> color #37 white
> color #37 yellow
> lighting soft
> select clear
> lighting full
> lighting simple
> lighting soft
> select clear
> lighting full
> select clear
> select clear
> volume #41 color #4de9e9
> volume #41 color #4ddde9
> volume #41 color #4dddd3
> color #37 grey
> color #37 white
> volume #41 color #d7ddd3
> volume #41 color #e9ddd3
> volume #41 color #e8ddd3
> color #37 #E8DDD3
> volume #41 color #e8edd3
> volume #41 color #e8ede9
> volume #41 color #e8e6e9
> volume #41 color #e6e6e9
> volume #41 color #e6e6e6
> color #37 #E6E6E6
> volume #41 color #4dddd3
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #37:356-370 orange
> color #37:356-370 yellow
> color #37:371-383 orange
> select clear
> lighting soft
> save image /Users/chunyan/2020/20200506-Figure5-1.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> hide #32,37#17.1,3#!25,27#!17.2 atoms
> lighting flat
> open /Users/chunyan/2020/gp8-asym/gp8-asym-3.8-masked.mrc
Opened gp8-asym-3.8-masked.mrc, grid size 400,400,400, pixel 1.05, shown at
level 0.00568, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> volume #38 level 0.004615
> view
> volume #38 level 0.009247
> volume #38 step 1
> volume #38 level 0.01051
> surface dust #38 size 40
> select #38
3 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #38 inMap #11
Fit map gp8-asym-3.8-masked.mrc in map gp8-basen-new.mrc using 228882 points
correlation = 0.892, correlation about mean = 0.5465, overlap = 49.79
steps = 84, shift = 6.28, angle = 1.79 degrees
Position of gp8-asym-3.8-masked.mrc (#38) relative to gp8-basen-new.mrc (#11)
coordinates:
Matrix rotation and translation
0.99360065 -0.11290714 0.00311886 24.44739584
-0.11291247 -0.99360367 0.00158787 441.84326323
0.00291963 -0.00192986 -0.99999388 420.92524376
Axis -0.99839888 0.05654552 -0.00151198
Axis point 0.00000000 221.79961732 210.24919929
Rotation angle (degrees) 179.89906278
Shift along axis -0.06042623
> volume #38 level 0.007355
> volume #38 level 0.008301
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> open /Users/chunyan/2020/gp8-asym/gp8-asym-3.6.mrc
Opened gp8-asym-3.6.mrc, grid size 400,400,400, pixel 1.05, shown at level
0.015, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> view
> select #15
3 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #15 inMap #23
Fit map gp8-asym-3.6.mrc in map gp12-new.mrc using 79941 points
correlation = 0.6579, correlation about mean = 0.4284, overlap = 15.44
steps = 224, shift = 11.2, angle = 4.14 degrees
Position of gp8-asym-3.6.mrc (#15) relative to gp12-new.mrc (#23) coordinates:
Matrix rotation and translation
0.99387077 -0.11052813 0.00209438 -186.00463191
-0.11052853 -0.99387294 0.00007073 231.85649298
0.00207373 -0.00030179 -0.99999779 212.39384721
Axis -0.99846668 0.05534602 -0.00105397
Axis point 0.00000000 110.78296404 106.28477897
Rotation angle (degrees) 179.98931187
Shift along axis 198.32790434
> volume #15 level 0.01072
> volume #15 step 1
> volume #15 level 0.01347
> volume #15 level 0.01222
> surface dust #15 size 50
> vop gaussian #15 sdev 3.15
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> volume #19 level 0.0043
> volume #19 level 0.006483
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> volume #15 step 2
> volume #15 level 0.01127
> select #15
3 models selected
> select #41
3 models selected
> select #41
3 models selected
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> open /Users/chunyan/2020/fiber/tail-3.4-with-gp17N.mrc
Opened tail-3.4-with-gp17N.mrc, grid size 400,400,400, pixel 1.05, shown at
level 0.0152, step 2, values float32
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> select #15
3 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #15 inMap #23
Fit map tail-3.4-with-gp17N.mrc in map gp12-new.mrc using 79956 points
correlation = 0.6496, correlation about mean = 0.4146, overlap = 16.66
steps = 208, shift = 6.62, angle = 7.47 degrees
Position of tail-3.4-with-gp17N.mrc (#15) relative to gp12-new.mrc (#23)
coordinates:
Matrix rotation and translation
-0.99448678 0.10485847 0.00083210 186.66062254
0.10485896 0.99448691 0.00057114 -231.04483958
-0.00076762 0.00065525 -0.99999946 211.20724641
Axis 0.05250248 0.99862075 0.00030918
Axis point 99.44626669 0.00000000 105.59963605
Rotation angle (degrees) 179.95410797
Shift along axis -220.86072236
> volume #15 level 0.01133
> fitmap #41 inMap #15
Fit map gp8-asym-300-400-part-genome.mrc in map tail-3.4-with-gp17N.mrc using
8254 points
correlation = 0.7688, correlation about mean = 0.2404, overlap = 1.166
steps = 100, shift = 11.3, angle = 9.96 degrees
Position of gp8-asym-300-400-part-genome.mrc (#41) relative to tail-3.4-with-
gp17N.mrc (#15) coordinates:
Matrix rotation and translation
-0.78903091 0.61236853 0.04934596 239.03052130
-0.60026716 -0.78555002 0.15030145 474.77736048
0.13080360 0.08897172 0.98740796 -55.50981035
Axis -0.05039771 -0.06693782 -0.99648352
Axis point 201.86595223 198.46702863 0.00000000
Rotation angle (degrees) 142.52194824
Shift along axis 11.48745990
> volume #15 step 1
> vop gaussian #15 sdev 3.15
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> volume #19 level 0.006344
Traceback (most recent call last):
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
IndexError: list index out of range
Error processing trigger "new frame":
IndexError: list index out of range
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
See log for complete Python traceback.
> volume #15 level 0.01133
> volume #15 level 0.01391
> view
> lighting soft
> save session /Users/chunyan/2020/gp8-asym/gp8-asym-20200507.cxs
> lighting soft
> lighting full
> lighting soft
> lighting simple
> volume #41 level 0.0106
> volume #41 level 0.01125
> save image /Users/chunyan/2020/20200506-Figure5-2.tif pixelSize 0.1
> supersample 4 transparentBackground true
> color #37:371-383 #FD8008
> volume #41 color #4dedd3
> volume #41 color #4defd3
> volume #41 color #4df0d3
> volume #41 color #4df3d3
> volume #41 color #4df2d3
> volume #41 color #4df0d3
> volume #41 color #4dedd3
> volume #41 color #4de9d3
> volume #41 color #4de8d3
> volume #41 color #4de6d3
> volume #41 color #4de5d3
> volume #41 color #4de3d3
> volume #41 color #4ce3d3
> volume #41 color #4ae3d3
> volume #41 color #49e3d3
> volume #41 color #48e3d3
> volume #41 color #47e3d3
> volume #41 color #46e3d3
> volume #41 color #44e3d3
> volume #41 color #43e3d3
> volume #41 color #42e3d3
> volume #41 color #41e3d3
> volume #41 color #40e3d3
> volume #41 color #3fe3d3
> volume #41 color #3ee3d3
> volume #41 color #3de3d3
> volume #41 color #3de2d3
> volume #41 color #3ddad3
> volume #41 color #3dcfd3
> volume #41 color #3dccd3
> volume #41 color #3dcad3
> volume #41 color #3dc9d3
> volume #41 color #3dc8d3
> volume #41 color #3dc7d3
> volume #41 color #3dc6d3
> volume #41 color #3dc5d3
> volume #41 color #3dc4d3
> volume #41 color #3dc1d3
> volume #41 color #3dc2d3
> volume #41 color #3dc5d3
> lighting simple
> lighting full
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting soft
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> lighting full
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> select clear
> save image /Users/chunyan/2020/20200506-Figure5-1.tif pixelSize 0.1
> supersample 4 transparentBackground true
> view name p1
> hide #32,37#17.1,3#!25,27#!17.2 cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> save image /Users/chunyan/2020/20200506-Figure5-2.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save image /Users/chunyan/2020/20200506-Figure5-3.tif pixelSize 0.1
> supersample 4 transparentBackground true
> volume #41 level 0.01054
> volume #41 level 0.01119
> volume #41 level 0.009827
> save image /Users/chunyan/2020/20200506-Figure5-4.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37.1
Nothing selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> select #37/E-F
8168 atoms, 8290 bonds, 1 model selected
> select #37/E-F-G-
8168 atoms, 8290 bonds, 1 model selected
> select #37/E-F-G-H
8168 atoms, 8290 bonds, 1 model selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/D
4084 atoms, 4145 bonds, 1 model selected
> select #37/F
4084 atoms, 4145 bonds, 1 model selected
> select #37/A
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> hide sel cartoons
> select #37/B
4084 atoms, 4145 bonds, 1 model selected
> select #37/C
4084 atoms, 4145 bonds, 1 model selected
> select #37/D
4084 atoms, 4145 bonds, 1 model selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> select #37/G
4084 atoms, 4145 bonds, 1 model selected
> select #37/H
4084 atoms, 4145 bonds, 1 model selected
> select #37/I
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/J
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/K
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/L
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/M
Nothing selected
> select #37/N
Nothing selected
> select #37/F
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/G
4084 atoms, 4145 bonds, 1 model selected
> select #37/H
4084 atoms, 4145 bonds, 1 model selected
> select #37/I
4084 atoms, 4145 bonds, 1 model selected
> select #37/K
4084 atoms, 4145 bonds, 1 model selected
> select #37/A
4084 atoms, 4145 bonds, 1 model selected
> select #37/B
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> select #37/A
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/B
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> hide sel cartoons
> select #37/C
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #37/D
4084 atoms, 4145 bonds, 1 model selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> select #37/F
4084 atoms, 4145 bonds, 1 model selected
> select #37/G
4084 atoms, 4145 bonds, 1 model selected
> select #37/H
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #37/G:300-400
780 atoms, 790 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select #37/G
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> show sel cartoons
> hide sel cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> select #37/A
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/B
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/C
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/D
4084 atoms, 4145 bonds, 1 model selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> select #37/F
4084 atoms, 4145 bonds, 1 model selected
> select #37/G
4084 atoms, 4145 bonds, 1 model selected
> select #37/H
4084 atoms, 4145 bonds, 1 model selected
> select #37/I
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> hide sel cartoons
> select #37/J
4084 atoms, 4145 bonds, 1 model selected
> select #37/K
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/L
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/L
4084 atoms, 4145 bonds, 1 model selected
> select #37/M
Nothing selected
> select #37/N
Nothing selected
> select #37/O
Nothing selected
> select #37/A
4084 atoms, 4145 bonds, 1 model selected
> select #37/B
4084 atoms, 4145 bonds, 1 model selected
> select #37/C
4084 atoms, 4145 bonds, 1 model selected
> select #37/D
4084 atoms, 4145 bonds, 1 model selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> select #37/F:383
8 atoms, 7 bonds, 1 model selected
> select #37/F
4084 atoms, 4145 bonds, 1 model selected
> select #37/J:352
8 atoms, 7 bonds, 1 model selected
> select #37/J
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> 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
> volume #19 color #cccccc45
> volume #19 color #cccccc43
> volume #19 color #cccccc3f
> volume #19 color #cccccc3e
> volume #19 color #cccccc3d
> volume #19 color #cccccc3b
> volume #19 color #cccccc38
> volume #19 color #cccccc36
> volume #19 color #cccccc35
> volume #19 color #cccccc33
> volume #19 color #cccccc32
> volume #19 color #cccccc30
> volume #19 color #cccccc2f
> volume #19 color #cccccc2e
> select clear
> lighting soft
> lighting soft
> lighting full
> select clear
> lighting shadows false
> lighting full
> lighting soft
> lighting soft
> lighting full
> select clear
> volume #19 color #cccccc2f
> volume #19 color #cccccc36
> volume #19 color #cccccc53
> volume #19 color #cccccc5a
> volume #19 color #cccccc5b
> volume #19 color #cccccc62
> volume #19 color #cccccc65
> volume #19 color #cccccc68
> volume #19 color #cccccc6d
> volume #19 color #cccccc6e
> volume #19 color #cccccc6f
> volume #19 color #cccccc72
> volume #19 color #cccccc73
> volume #19 color #cccccc77
> volume #19 color #cccccc7b
> volume #19 color #cccccc7c
> volume #19 color #cccccc7e
> volume #19 color #cccccc80
> volume #19 color #cccccc89
> volume #19 color #cccccc8b
> volume #19 color #cccccc90
> volume #19 color #cccccc91
> save image /Users/chunyan/2020/20200506-Figure5-6.tif pixelSize 0.1
> supersample 4 transparentBackground true
> volume #19 color #ccccb291
> volume #19 color #cca9b291
> volume #19 color #b7a9b291
> volume #19 color #a6a9b291
> volume #19 color #95a9b291
> volume #19 color #9596b291
> volume #19 color #95969b91
> volume #19 color #95968e91
> volume #19 color #95963291
> volume #19 color #9596a091
> volume #19 color #95a0a091
> volume #19 color #a0a0a091
> volume #19 color #3ca0a091
> volume #19 color #a0a0a091
> volume #19 color #a0a0a099
> save image /Users/chunyan/2020/20200506-Figure5-6.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save session /Users/chunyan/2020/gp8-asym/gp8-asym-20200507.cxs
> view
> volume #11 level 0.004921
> surface dust #11 size 40
> volume #11 level 0.005853
> volume #11 color #ffff66cd
> volume #11 color #d4ff66cd
> volume #11 color #d4d766cd
> volume #11 color #d4d7d3cd
> volume #11 color #bfd7d3cd
> volume #11 color #bfbdd3cd
> volume #11 color #bfbdc0cd
> volume #11 color #bfbdc0cc
> volume #11 color #bfbdc0c4
> volume #11 color #bfbdc088
> volume #11 color #bfbdc084
> volume #11 color #bfbdc080
> volume #11 color #bfbdc07e
> volume #11 color #bfbdc07b
> volume #11 color #bfbdc076
> volume #11 color #bfbdc075
> volume #11 color #bfbdc073
> volume #11 color #bfbdc071
> volume #11 color #bfbdc06f
> volume #11 color #bfbdc070
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 #41 level 0.009946
> volume #41 level 0.009589
> select clear
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> show sel cartoons
> show sel cartoons
> hide sel atoms
> show sel cartoons
> select clear
> volume #11 level 0.005586
> surface dust #11 size 40
> select clear
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select clear
> volume #23 color #21ffa9
> volume #23 color #21b1a9
> volume #23 color #abb1a9
> volume #23 color #abb1a9ad
> volume #23 color #abb1a996
> volume #23 color #abb1a997
> volume #10 color #fd808b
> volume #10 color #fdd48b
> volume #10 color #d7d48b
> volume #10 color #d7d4d4
> volume #10 color #d7d4d47f
> volume #10 color #d7d4d480
> volume #41 level 0.009114
> volume #10 color #d7d4d4bb
> volume #10 color #d7d4d486
> volume #10 color #d7d4d487
> volume #10 color #c9d4d487
> volume #10 color #d2d4d487
> volume #10 color #d2d3d487
> volume #10 color #d2d2d487
> volume #10 color #d2d2d387
> volume #10 color #d2d2d287
> volume #10 color #d2d2d299
> volume #23 color #abb1a999
> volume #23 color #d2b1a999
> volume #23 color #d2d2a999
> volume #23 color #d2d2d299
> surface dust #11 size 40
> surface dust #10 size 40
> surface dust #23 size 40
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 #d2ead299
> volume #23 color #d2fbd299
> volume #23 color #32fbd299
> volume #23 color #18fbd299
> volume #23 color #11fbd299
> volume #23 color #00fbd299
> volume #23 color #00fbe199
> volume #23 color #00fbe499
> volume #23 color #00fbfe99
> volume #23 color #00fbdd99
> volume #23 color #00fb8d99
> volume #23 color #00fb5e99
> volume #23 color #00fb3799
> volume #23 color #00fb1d99
> volume #23 color #00fb0e99
> volume #23 color #00fb0b99
> volume #23 color #00fb0199
> volume #23 color #00fb0099
> volume #23 color #00fb0098
> volume #23 color #00fb008a
> volume #23 color #00fb0080
> volume #23 color #00fb0076
> volume #23 color #00fb0075
> volume #23 color #00fb0076
> volume #23 color #00fb0080
> volume #23 color #d2fb0080
> volume #23 color #d2d20080
> volume #23 color #d2d2d280
> volume #23 color #d2d2d299
> select clear
> volume #11 color #d2bdc070
> volume #11 color #d2d2c070
> volume #11 color #d2d2d270
> volume #11 color #d2d2d299
> volume #11 color #d2d2d266
> volume #10 color #d2d2d266
> volume #23 color #d2d2d266
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-1.tif pixelSize 0.1
> supersample 4 transparentBackground true
> view name p1
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 #d2a0a099
> volume #19 color #d2d2a099
> volume #19 color #d2d2d299
> volume #19 color #d2d2d266
> volume #19 level 0.006746
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.
> surface dust #19 size 40
> surface dust #19 size 30
> surface dust #19 size 50
> surface dust #19 size 40
> save image /Users/chunyan/2020/20200507-Figure5-2.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37:300-400
9360 atoms, 9480 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.
> volume #19 level 0.005287
> volume #41 level 0.00953
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> hide sel cartoons
> fitmap #41 inMap #19
Fit map gp8-asym-300-400-part-genome.mrc in map gp8-asym-manmade.mrc using
7783 points
correlation = 0.9278, correlation about mean = 0.784, overlap = 1.745
steps = 1056, shift = 11.7, angle = 79.2 degrees
Position of gp8-asym-300-400-part-genome.mrc (#41) relative to gp8-asym-
manmade.mrc (#19) coordinates:
Matrix rotation and translation
0.99798290 0.06336786 -0.00382899 -12.14584535
-0.06335537 0.99798558 0.00330033 13.07674362
0.00403041 -0.00305108 0.99998723 -0.19283028
Axis -0.04996174 -0.06182390 -0.99683581
Axis point 200.09681520 198.04885876 0.00000000
Rotation angle (degrees) 3.64433341
Shift along axis -0.00940760
> select clear
> select clear
> volume #11 level 0.00572
> save image /Users/chunyan/2020/20200507-Figure5-1.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.
> surface dust #19 size 50
> surface dust #19 size 20
> surface dust #19 size 10
> surface dust #19 size 15
> surface dust #19 size 19
> save image /Users/chunyan/2020/20200507-Figure5-2.tif pixelSize 0.1
> supersample 4 transparentBackground true
> open /Users/chunyan/2020/gp8-asym/part/gp8-asym-360-383-part.mrc
Opened gp8-asym-360-383-part.mrc, grid size 400,400,400, pixel 1.05, shown at
level 5.35e-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 #34 level 0.004485
> volume #34 step 1
> select #34
2 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> volume #34 color #b2b254
> volume #34 color #f0b254
> volume #34 color #f1b254
> volume #34 color #f4b254
> volume #34 color #f5b254
> volume #34 color #f9b254
> volume #34 color #feb254
> volume #34 color #ffb254
> volume #34 color #ffff54
> volume #34 color #ffff53
> volume #34 color #ffff51
> volume #34 color #ffff4c
> volume #34 color #ffff44
> volume #34 color #ffff3e
> volume #34 color #ffff37
> volume #34 color #ffff32
> volume #34 color #ffff2f
> volume #34 color #ffff2d
> volume #34 color #ffff2c
> volume #34 color #ffff26
> volume #34 color #ffff21
> volume #34 color #ffff1e
> volume #34 color #ffff1b
> volume #34 color #ffff19
> volume #34 color #ffff17
> volume #34 color #ffff15
> volume #34 color #ffff14
> volume #34 color #ffff13
> volume #34 color #ffff12
> volume #34 color #ffff10
> volume #34 color #ffff0e
> volume #34 color #ffff0d
> lighting flat
> volume #34 color #ffff05
> volume #34 color yellow
> lighting flat
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate 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 #34 inMap #19
Fit map gp8-asym-360-383-part.mrc in map gp8-asym-manmade.mrc using 28648
points
correlation = 0.557, correlation about mean = 0.3042, overlap = 1.757
steps = 76, shift = 6.81, angle = 6.29 degrees
Position of gp8-asym-360-383-part.mrc (#34) relative to gp8-asym-manmade.mrc
(#19) coordinates:
Matrix rotation and translation
0.06655295 0.97230064 -0.22405845 27.34578043
-0.84899906 -0.06278820 -0.52465060 488.71519810
-0.52418634 0.22514246 0.82130358 100.13786168
Axis 0.37633884 0.15064127 -0.91415332
Axis point 279.72434579 237.46857280 0.00000000
Rotation angle (degrees) 95.01783476
Shift along axis -7.62940078
> volume #19 color #d2d2d2b9
> volume #19 color #d2d2d2da
> volume #19 color #d2d2d2d9
> lighting soft
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"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #34 inMap #19
Fit map gp8-asym-360-383-part.mrc in map gp8-asym-manmade.mrc using 28648
points
correlation = 0.8733, correlation about mean = 0.6888, overlap = 3.359
steps = 112, shift = 9.76, angle = 4.84 degrees
Position of gp8-asym-360-383-part.mrc (#34) relative to gp8-asym-manmade.mrc
(#19) coordinates:
Matrix rotation and translation
0.50448478 0.86341311 -0.00359559 -76.70631138
-0.86341923 0.50448701 -0.00032550 285.28025861
0.00153289 0.00326871 0.99999349 -1.24790332
Axis 0.00208137 -0.00296986 -0.99999342
Axis point 210.19328550 209.47190344 0.00000000
Rotation angle (degrees) 59.70298563
Shift along axis 0.24099930
> ui mousemode rightMode "rotate selected models"
> fitmap #34 inMap #19
Fit map gp8-asym-360-383-part.mrc in map gp8-asym-manmade.mrc using 28648
points
correlation = 0.9353, correlation about mean = 0.8283, overlap = 3.769
steps = 56, shift = 0.772, angle = 2.52 degrees
Position of gp8-asym-360-383-part.mrc (#34) relative to gp8-asym-manmade.mrc
(#19) coordinates:
Matrix rotation and translation
0.86730538 0.49777078 -0.00237426 -76.24261085
-0.49777315 0.86730713 -0.00050043 132.39955696
0.00181011 0.00161587 0.99999706 -0.81475401
Axis 0.00212575 -0.00420305 -0.99998891
Axis point 210.21552119 209.20730927 0.00000000
Rotation angle (degrees) 29.85306801
Shift along axis 0.09619043
> ui mousemode rightMode "rotate selected models"
> fitmap #34 inMap #19
Fit map gp8-asym-360-383-part.mrc in map gp8-asym-manmade.mrc using 28648
points
correlation = 0.9994, correlation about mean = 0.9978, overlap = 4.311
steps = 76, shift = 0.751, angle = 3.2 degrees
Position of gp8-asym-360-383-part.mrc (#34) relative to gp8-asym-manmade.mrc
(#19) coordinates:
Matrix rotation and translation
0.99999991 0.00033577 0.00029514 -0.11132430
-0.00033564 0.99999987 -0.00041694 0.16480008
-0.00029528 0.00041684 0.99999988 0.08422849
Axis 0.68201519 0.48294647 -0.54919759
Axis point 0.00000000 -145.80624871 444.64506118
Rotation angle (degrees) 0.03502295
Shift along axis -0.04259333
> surface dust #34 size 40
> surface dust #19 size 40
> select #19
3 models selected
> 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.
> volume #19 color #d2d2bbd9
> volume #19 color #d2d2acd9
> volume #19 color #d2d2ddd9
> volume #19 color #d2d2d2d9
> volume #19 color #d2d2d266
> volume #34 level 0.003799
> volume #34 level 0.002151
> volume #34 level 0.003799
> volume #34 level 0.003661
> volume #34 level 0.003661
> volume #34 level 0.003387
> volume #34 level 0.0007783
> volume #34 level 0.0002292
> volume #34 level 0.002151
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 #34 level 0.003524
> volume #34 level 0.003799
> open /Users/chunyan/2020/gp8-asym/part/gp8-asym-360-383-part-lp.mrc
Opened gp8-asym-360-383-part-lp.mrc, grid size 400,400,400, pixel 1.05, shown
at level 2.07e-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 0.004534
> volume #40 step 1
> select #40
2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate 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.
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> volume #40 color #ffff4a
> volume #40 color #ffff1b
> volume #40 color #ffff13
> volume #40 color #ffff02
> volume #40 color yellow
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 #34 inMap #19
No atoms or maps for #34
> fitmap #40 inMap #19
Fit map gp8-asym-360-383-part-lp.mrc in map gp8-asym-manmade.mrc using 24638
points
correlation = 0.9649, correlation about mean = 0.8708, overlap = 3.272
steps = 76, shift = 3.71, angle = 8.87 degrees
Position of gp8-asym-360-383-part-lp.mrc (#40) relative to gp8-asym-
manmade.mrc (#19) coordinates:
Matrix rotation and translation
0.99999967 -0.00007102 0.00082066 -0.11388253
0.00007134 0.99999993 -0.00038619 0.04669667
-0.00082063 0.00038625 0.99999960 0.21626464
Axis 0.42452417 0.90202945 0.07824381
Axis point 262.44281744 0.00000000 144.41216470
Rotation angle (degrees) 0.05212622
Shift along axis 0.01069726
> volume #40 level 0.003573
> select clear
> ui mousemode rightMode "rotate selected models"
> select #40
3 models selected
> ui mousemode rightMode "rotate selected models"
> fitmap #40 inMap #19
Fit map gp8-asym-360-383-part-lp.mrc in map gp8-asym-manmade.mrc using 31658
points
correlation = 0.9581, correlation about mean = 0.8663, overlap = 3.415
steps = 72, shift = 0.559, angle = 8.92 degrees
Position of gp8-asym-360-383-part-lp.mrc (#40) relative to gp8-asym-
manmade.mrc (#19) coordinates:
Matrix rotation and translation
0.99999938 -0.00026360 0.00108789 -0.11845285
0.00026436 0.99999973 -0.00070115 0.07206661
-0.00108771 0.00070144 0.99999917 0.21903891
Axis 0.53091701 0.82352231 0.19984529
Axis point 193.88534095 0.00000000 128.62943191
Rotation angle (degrees) 0.07568272
Shift along axis 0.04023372
> select clear
> volume #40 level 0.003786
> save image /Users/chunyan/2020/20200507-Figure5-3.tif pixelSize 0.1
> supersample 4 transparentBackground true
> volume #19 color #d2d2d2af
> volume #19 color #d2d2d2d0
> volume #19 color #d2d2d2d1
> volume #19 color #d2d2d2d4
> volume #19 color #d2d2d2e3
> volume #19 color #d2d2d2ed
> volume #19 color #d2d2d2f1
> volume #19 color #d2d2d2f2
> volume #19 color #d2d2d2f4
> volume #19 color #d2d2d2f6
> volume #19 color #d2d2d2f8
> volume #19 color #d2d2d2fa
> volume #19 color #d2d2d2fb
> volume #19 color #d2d2d2fa
> volume #19 color #d2d2d2f8
> volume #19 color #d2d2d2e3
> volume #19 color #d2d2d2c7
> volume #19 color #d2d2d2b0
> volume #19 color #d2d2d2a8
> volume #19 color #d2d2d29e
> volume #19 color #d2d2d297
> volume #19 color #d2d2d292
> volume #19 color #d2d2d28f
> volume #19 color #d2d2d28c
> volume #19 color #d2d2d28a
> volume #19 color #d2d2d288
> volume #19 color #d2d2d285
> volume #19 color #d2d2d282
> volume #19 color #d2d2d280
> volume #19 color #d2d2d275
> volume #19 color #d2d2d274
> volume #19 color #d2d2d272
> volume #19 color #d2d2d271
> volume #19 color #d2d2d272
> volume #19 color #d2d2d274
> volume #19 color #d2d2d276
> volume #19 color #d2d2d277
> volume #19 color #d2d2d279
> volume #19 color #d2d2d27a
> volume #19 color #d2d2d27c
> volume #19 color #d2d2d27e
> volume #19 color #d2d2d28a
> volume #19 color #d2d2d29b
> volume #19 color #d2d2d2a5
> volume #19 color #d2d2d2a6
> volume #19 color #d2d2d2ac
> volume #19 color #d2d2d2d9
> volume #19 color #d2d2d2db
> volume #19 color #d2d2d2dc
> volume #19 color #d2d2d2df
> volume #19 color #d2d2d2e1
> volume #19 color #d2d2d2e3
> volume #19 color #d2d2d2e4
> volume #19 color #d2d2d2e3
> volume #19 color #d2d2d2db
> volume #19 color #d2d2d2d3
> volume #19 color #d2d2d2d0
> volume #19 color #d2d2d2cd
> volume #19 color #d2d2d2ca
> volume #19 color #d2d2d2c8
> volume #19 color #d2d2d2c5
> volume #19 color #d2d2d2c2
> volume #19 color #d2d2d2c1
> volume #19 color #d2d2d2c0
> volume #19 color #d2d2d2bf
> volume #19 color #d2d2d2bd
> volume #19 color #d2d2d2bb
> volume #19 color #d2d2d2ba
> surface dust #19 size 40
> surface dust #40 size 40
> surface dust #40 size 10
> surface dust #19 size 40
> volume #40 level 0.004213
> volume #19 level 0.006891
> save image /Users/chunyan/2020/20200507-Figure5-3.tif pixelSize 0.1
> supersample 4 transparentBackground true
> volume #19 color #d2d2d2cc
> volume #19 color #b4d2d2cc
> volume #19 color #b4b4d2cc
> volume #19 color #b4b4b4cc
> volume #19 color #b4b4b4cb
> volume #19 color #b4b4b4b4
> volume #19 color #b4b4b49c
> volume #19 color #b4b4b49a
> volume #19 color #b4b4b498
> volume #19 color #b4b4b497
> volume #19 color #b4b4b496
> volume #19 color #b4b4b494
> volume #19 color #b4b4b493
> volume #19 color #b4b4b492
> volume #19 color #b4b4b491
> volume #19 color #b4b4b490
> volume #19 color #b4b4b48f
> volume #19 color #b4b4b48e
> volume #19 color #b4b4b487
> volume #19 color #b4b4b485
> volume #19 color #b4b4b484
> volume #19 color #b4b4b482
> volume #19 color #b4b4b481
> volume #19 color #b4b4b480
> volume #19 color #b4b4b47f
> volume #19 color #b4b4b47d
> volume #19 color #b4b4b47c
> volume #19 color #b4b4b47b
> volume #19 color #b4b4b47a
> volume #19 color #b4b4b479
> volume #19 color #b4b4b475
> volume #19 color #b4b4b466
> save image /Users/chunyan/2020/20200507-Figure5-3.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save image /Users/chunyan/2020/20200507-Figure5-3.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-4.tif pixelSize 0.1
> supersample 4 transparentBackground true
> lighting flat
> open /Users/chunyan/2020/gp8-asym/terminal-genome-remodeling/Ideal-B-form-
> DNA-coot-0.pdb
Chain information for Ideal-B-form-DNA-coot-0.pdb #34
---
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.
> select #34
1640 atoms, 1838 bonds, 1 model selected
> 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.
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> select #34/B:40
20 atoms, 21 bonds, 1 model selected
> select #34/A:31
21 atoms, 23 bonds, 1 model selected
> select #34/A:31
21 atoms, 23 bonds, 1 model selected
> select #37/G:344
7 atoms, 6 bonds, 1 model selected
> select #34/B:1
20 atoms, 21 bonds, 1 model selected
> select #34/B:1
20 atoms, 21 bonds, 1 model selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #34 inMap #41
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
genome.mrc (#41) using 1640 atoms
average map value = 0.004446, steps = 84
shifted from previous position = 8.22
rotated from previous position = 6.66 degrees
atoms outside contour = 1231, contour level = 0.0095301
Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
gp8-asym-300-400-part-genome.mrc (#41) coordinates:
Matrix rotation and translation
0.42625311 -0.90240860 0.06298412 299.64749259
0.90453614 0.42433433 -0.04188980 -62.82850166
0.01107539 0.07482708 0.99713502 -23.89254867
Axis 0.06443269 0.02865583 0.99751054
Axis point 199.96101362 205.37050398 0.00000000
Rotation angle (degrees) 64.92139561
Shift along axis -6.32637712
> lighting soft
> lighting simple
> lighting soft
> lighting full
> select clear
> select clear
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-5.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save image /Users/chunyan/2020/20200507-Figure5-5.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #34:300-400
Nothing 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
> show sel cartoons
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-6.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37/F
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/K
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
> save image /Users/chunyan/2020/20200507-Figure5-7.tif pixelSize 0.1
> supersample 4 transparentBackground true
#34
Unknown command: sequence #34
#34/A
Unknown command: sequence #34/A
#34/A
Unknown command: sequence #34/A
> select #34/B:27
20 atoms, 21 bonds, 1 model selected
> select #34/B:28
21 atoms, 23 bonds, 1 model selected
#34/G
Unknown command: sequence #34/G
> select #34/G
Nothing selected
> select #37/G
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/H-J:368
33 atoms, 30 bonds, 1 model selected
> color #37/H-J:368 red
> show sel atoms
> style sel stick
Changed 33 atom styles
> style sel sphere
Changed 33 atom styles
> style sel stick
Changed 33 atom styles
> style sel ball
Changed 33 atom styles
> color sel byhetero
> hide sel atoms
> select clear
> color #37/H-J:368 blue
> color #37/H-J:368 magenta
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-7.tif pixelSize 0.1
> supersample 4 transparentBackground true
Expected an objects specifier or a keyword
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> select clear
> hide #32,34,37#17.1,3#!25,27#!17.2 cartoons
> select #34
1640 atoms, 1838 bonds, 1 model selected
> hide sel atoms
> show sel cartoons
> show sel atoms
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> fitmap #34 inMap #41
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
genome.mrc (#41) using 1640 atoms
average map value = 0.004451, steps = 44
shifted from previous position = 0.0135
rotated from previous position = 1.03 degrees
atoms outside contour = 1230, contour level = 0.0095301
Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
gp8-asym-300-400-part-genome.mrc (#41) coordinates:
Matrix rotation and translation
0.41007729 -0.90966944 0.06586455 304.05920833
0.91199125 0.40815477 -0.04100800 -61.13699070
0.01042080 0.07688434 0.99698556 -24.16858650
Axis 0.06455209 0.03035829 0.99745246
Axis point 199.90398960 205.06379451 0.00000000
Rotation angle (degrees) 65.94528781
Shift along axis -6.33537287
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select #34
1640 atoms, 1838 bonds, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> ui mousemode rightMode "rotate selected models"
> volume #41 level 0.008283
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #34 inMap #41
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
genome.mrc (#41) using 1640 atoms
average map value = 0.004447, steps = 100
shifted from previous position = 3.3
rotated from previous position = 2.64 degrees
atoms outside contour = 1202, contour level = 0.0082828
Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
gp8-asym-300-400-part-genome.mrc (#41) coordinates:
Matrix rotation and translation
0.42063165 -0.90497669 0.06392350 301.19950201
0.90716627 0.41871105 -0.04159828 -62.24577642
0.01087999 0.07548680 0.99708745 -23.98488873
Axis 0.06444946 0.02919779 0.99749374
Axis point 199.94459682 205.27147824 0.00000000
Rotation angle (degrees) 65.27805103
Shift along axis -6.33007116
> ui mousemode rightMode "rotate selected models"
> fitmap #34 inMap #41
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
genome.mrc (#41) using 1640 atoms
average map value = 0.004519, steps = 132
shifted from previous position = 5.13
rotated from previous position = 10.6 degrees
atoms outside contour = 1186, contour level = 0.0082828
Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
gp8-asym-300-400-part-genome.mrc (#41) coordinates:
Matrix rotation and translation
0.93547549 0.34489143 -0.07704237 -44.40030068
-0.34464527 0.93858102 0.01689126 83.03529378
0.07813616 0.01075093 0.99688473 -19.50503015
Axis -0.00868740 -0.21954805 -0.97556301
Axis point 211.68923829 168.31140960 0.00000000
Rotation angle (degrees) 20.69569092
Shift along axis 1.18387280
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #34 inMap #41
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
genome.mrc (#41) using 1640 atoms
average map value = 0.004556, steps = 96
shifted from previous position = 1.91
rotated from previous position = 4.58 degrees
atoms outside contour = 1170, contour level = 0.0082828
Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
gp8-asym-300-400-part-genome.mrc (#41) coordinates:
Matrix rotation and translation
0.82117216 0.56991607 -0.02952885 -77.47602396
-0.56802441 0.82124170 0.05394755 147.54016646
0.05499590 -0.02752711 0.99810707 -9.14699464
Axis -0.07122033 -0.07388654 -0.99472028
Axis point 198.03521668 197.61791594 0.00000000
Rotation angle (degrees) 34.88912441
Shift along axis 3.71533704
> ui mousemode rightMode "translate selected models"
> fitmap #34 inMap #41
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
genome.mrc (#41) using 1640 atoms
average map value = 0.003983, steps = 156
shifted from previous position = 3.49
rotated from previous position = 8.74 degrees
atoms outside contour = 1257, contour level = 0.0082828
Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
gp8-asym-300-400-part-genome.mrc (#41) coordinates:
Matrix rotation and translation
0.66300924 0.74771230 0.03667518 -96.77980539
-0.74781153 0.65924187 0.07860078 212.81848276
0.03459296 -0.07953916 0.99623133 -26.82893429
Axis -0.10515581 0.00138458 -0.99445479
Axis point 189.08756419 209.43060811 0.00000000
Rotation angle (degrees) 48.75797096
Shift along axis 37.15178598
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate 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 #34 inMap #41
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
genome.mrc (#41) using 1640 atoms
average map value = 0.004543, steps = 72
shifted from previous position = 5.04
rotated from previous position = 3.4 degrees
atoms outside contour = 1185, contour level = 0.0082828
Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
gp8-asym-300-400-part-genome.mrc (#41) coordinates:
Matrix rotation and translation
-0.08772293 0.99467753 -0.05404914 30.40851684
-0.98904511 -0.08050292 0.12372979 414.18108330
0.11872013 0.06431098 0.99084289 -44.92164954
Axis -0.02982695 -0.08672641 -0.99578556
Axis point 206.46391414 194.96895401 0.00000000
Rotation angle (degrees) 95.08833309
Shift along axis 7.90489774
> fitmap #34 inMap #41
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
genome.mrc (#41) using 1640 atoms
average map value = 0.004505, steps = 224
shifted from previous position = 2.63
rotated from previous position = 7.74 degrees
atoms outside contour = 1185, contour level = 0.0082828
Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
gp8-asym-300-400-part-genome.mrc (#41) coordinates:
Matrix rotation and translation
-0.31789315 0.94775299 0.02661256 72.56060229
-0.93584472 -0.31815481 0.15156576 447.23106988
0.15211382 0.02327649 0.98808886 -45.04347688
Axis -0.06780157 -0.06632810 -0.99549160
Axis point 198.56896202 198.82464526 0.00000000
Rotation angle (degrees) 108.90376267
Shift along axis 10.25669493
> show sel atoms
> hide sel cartoons
> hide sel atoms
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select #34
1640 atoms, 1838 bonds, 1 model selected
> ui mousemode rightMode "rotate selected models"
> fitmap #34 inMap #41
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
genome.mrc (#41) using 1640 atoms
average map value = 0.004508, steps = 68
shifted from previous position = 0.488
rotated from previous position = 3.5 degrees
atoms outside contour = 1183, contour level = 0.0082828
Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
gp8-asym-300-400-part-genome.mrc (#41) coordinates:
Matrix rotation and translation
-0.28987221 0.95681841 0.02174035 65.63628670
-0.94513990 -0.28976119 0.15082779 443.36651320
0.15061432 0.02317312 0.98832097 -44.70401392
Axis -0.06681431 -0.06745249 -0.99548280
Axis point 198.76335963 198.63836369 0.00000000
Rotation angle (degrees) 107.19689109
Shift along axis 10.21045962
> hide sel cartoons
> hide sel atoms
> volume #8 color #ce5c00e2
> volume #8 color #cec000e2
> volume #8 color #cebf00e2
> volume #8 color #cebfb7e2
> volume #8 color #cebfb7e1
> save image /Users/chunyan/2020/20200507-Figure5-8.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37
49008 atoms, 49740 bonds, 1 model selected
> volume #19 color #b4b4b4de
> volume #19 color #b4b4b4f4
> volume #19 color #b4b4b4
> volume #19 color #b4b4b47c
> volume #19 color #b4b4b461
> volume #19 color #b4b4b4c9
> volume #19 color #b4b4b499
> volume #19 color #b4b4b495
> volume #41 level 0.01001
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-9.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> select clear
> 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 clear
> select #37/E:393
6 atoms, 5 bonds, 1 model selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/I:509
5 atoms, 4 bonds, 1 model selected
> select #37/K:504
4 atoms, 3 bonds, 1 model selected
> select #37/K:495
9 atoms, 8 bonds, 1 model selected
> select #37/K
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> hide sel cartoons
> select #37/H:381
8 atoms, 7 bonds, 1 model selected
> select #37/H
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/I:377
7 atoms, 6 bonds, 1 model selected
> select #37/I
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> select #37/J:376
12 atoms, 12 bonds, 1 model selected
> select #37/J
4084 atoms, 4145 bonds, 1 model selected
> hide sel cartoons
> save image /Users/chunyan/2020/20200507-Figure5-9.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel cartoons
> show sel atoms
> volume #41 level 0.008699
> show sel cartoons
> select clear
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #34/A #3DC5D3
> color #34/B #3DC5D3
> show #32,34,37#17.1,3#!25,27#!17.2 atoms
> show #32,34,37#17.1,3#!25,27#!17.2 cartoons
> hide #32,34,37#17.1,3#!25,27#!17.2 atoms
> hide #32,34,37#17.1,3#!25,27#!17.2 atoms
> 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 #27
6313 atoms, 6474 bonds, 1 model selected
> hide sel cartoons
> select #17
60992 atoms, 61568 bonds, 64 pseudobonds, 5 models selected
> hide sel cartoons
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel cartoons
> show sel atoms
Expected a keyword
> color #34/A green
> select clear
> color #34/A pink
> volume #41 color #3debd3
> volume #41 color #3dbcd3
> volume #41 color #ccbcd3
> volume #41 color #ccc9d3
> volume #41 color #3dc5d3
> color #34/A #3DC5DD
> color #34/A #3DC500
> save image /Users/chunyan/2020/20200507-Figure5-A1.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> hide sel cartoons
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> select #37:A368
Nothing selected
> select #37:368
132 atoms, 120 bonds, 1 model selected
> color #37:368 yellow
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-A2.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.
> save image /Users/chunyan/2020/20200507-Figure5-A3.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-A4.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select #37:300-4--
Nothing selected
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-A5.tif pixelSize 0.1
> supersample 4 transparentBackground true
> lighting soft
> lighting simple
> lighting soft
> lighting full
> save image /Users/chunyan/2020/20200507-Figure5-A5.tif pixelSize 0.1
> supersample 4 transparentBackground true
> save image /Users/chunyan/2020/20200507-Figure5-A6.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 #41 level 0.009649
> select #34
1640 atoms, 1838 bonds, 1 model selected
> hide sel cartoons
> hide sel atoms
> 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.
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 #44
Nothing selected
> select #41
3 models selected
> ui mousemode rightMode "rotate selected models"
> volume #41 level 0.008699
> ui mousemode rightMode "translate selected models"
> 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 = 0.9787, correlation about mean = 0.8204, overlap = 1.878
steps = 828, shift = 2.58, angle = 63.6 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
0.99967047 0.02564450 -0.00115134 -5.11732562
-0.02564356 0.99967083 0.00081819 5.31212695
0.00117194 -0.00078840 0.99999901 -0.11592871
Axis -0.03127735 -0.04523009 -0.99848684
Axis point 204.62035890 202.13476675 0.00000000
Rotation angle (degrees) 1.47168305
Shift along axis 0.03554170
> select #34
1640 atoms, 1838 bonds, 1 model selected
> hide sel cartoons
> hide sel cartoons
> hide sel atoms
> select #34
1640 atoms, 1838 bonds, 1 model selected
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel cartoons
> ui mousemode rightMode "rotate selected models"
> lighting flat
> fitmap #34 inMap #41
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
genome.mrc (#41) using 1640 atoms
average map value = 0.004499, steps = 156
shifted from previous position = 3.15
rotated from previous position = 7.9 degrees
atoms outside contour = 1193, contour level = 0.0086986
Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
gp8-asym-300-400-part-genome.mrc (#41) coordinates:
Matrix rotation and translation
0.30568357 0.95194111 -0.01912283 -51.34197856
-0.94579986 0.30590167 0.10902665 325.68893073
0.10963665 -0.01524129 0.99385488 -25.83545717
Axis -0.06519285 -0.06754918 -0.99558375
Axis point 199.07452745 198.64871664 0.00000000
Rotation angle (degrees) 72.37895029
Shift along axis 7.06847102
> lighting soft
> hide sel cartoons
> lighting soft
> select #37:300-400
9360 atoms, 9480 bonds, 1 model selected
> show sel cartoons
> 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
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-A7.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> hide sel cartoons
> select #34/B:39
21 atoms, 23 bonds, 1 model selected
> select #34/A:31
21 atoms, 23 bonds, 1 model selected
> hide sel cartoons
> volume #41 color #3dc5d355
> volume #41 level 0.008283
> volume #41 color #b2c5d355
> volume #41 color #d2c5d355
> volume #41 color #d2d2d355
> volume #41 color #d2d2d255
> volume #41 color #d2b3d255
> volume #41 color #d2b3b855
> volume #41 color #b6b3b855
> volume #41 color #b6b3b755
> volume #41 color #b6b4b755
> volume #41 color #b4b4b755
> volume #41 color #b4b4b455
> volume #41 level 0.009768
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel atoms
> select clear
> select clear
> select clear
> hide sel atoms
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 atoms
> hide sel atoms
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
> hide sel atoms
> hide sel atoms
> select clear
> volume #41 level 0.009649
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-A8.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37:36
108 atoms, 96 bonds, 1 model selected
> select #37:368
132 atoms, 120 bonds, 1 model selected
> color #37:368 magenta
> select clear
> select #37/L:371
5 atoms, 4 bonds, 1 model selected
> select #37/F:371
5 atoms, 4 bonds, 1 model selected
> select #37/F:371
5 atoms, 4 bonds, 1 model selected
> select clear
> view name p1
> save image /Users/chunyan/2020/20200507-Figure5-A9.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #34
1640 atoms, 1838 bonds, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> select #37/B
4084 atoms, 4145 bonds, 1 model selected
> show sel cartoons
> select #37/C
4084 atoms, 4145 bonds, 1 model selected
> show sel cartoons
> show sel cartoons
> hide sel cartoons
> select #37/H
4084 atoms, 4145 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #37/He
Nothing selected
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #37/H
4084 atoms, 4145 bonds, 1 model selected
> show sel cartoons
Expected an objects specifier or a keyword
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #37/A-B
8168 atoms, 8290 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #37/A,C
8168 atoms, 8290 bonds, 1 model selected
> show sel cartoons
Expected an objects specifier or a keyword
> select #37
49008 atoms, 49740 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> hide sel cartoons
> select #37/E
4084 atoms, 4145 bonds, 1 model selected
> show sel cartoons
> select #37/G
4084 atoms, 4145 bonds, 1 model selected
> show sel cartoons
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel cartoons
> hide sel atoms
> save image /Users/chunyan/2020/20200507-Figure5-A10.tif pixelSize 0.1
> supersample 4 transparentBackground true
> color #37:368 yellow
> hide sel cartoons
> save image /Users/chunyan/2020/20200507-Figure5-A10.tif pixelSize 0.1
> supersample 4 transparentBackground true
> select #37/E:384
7 atoms, 6 bonds, 1 model selected
> select #37/E:355
5 atoms, 4 bonds, 1 model selected
> select #37/E:356
11 atoms, 11 bonds, 1 model selected
> select #37/E:383
8 atoms, 7 bonds, 1 model selected
> open /Users/chunyan/2020/gp8-asym/terminal-genome-
> remodeling/gp8-asym-300-400-part-genome-lp.mrc
> /Users/chunyan/2020/gp8-asym/terminal-genome-remodeling/Ideal-B-form-DNA-
> coot-0.pdb
Opened gp8-asym-300-400-part-genome-lp.mrc, grid size 400,400,400, pixel 1.05,
shown at level 1.54e-06, step 2, values float32
Chain information for Ideal-B-form-DNA-coot-0.pdb
---
Chain | Description
42.2/A | No description available
42.2/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.
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide 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
Expected an objects specifier or a keyword
> select #42
1640 atoms, 1838 bonds, 4 models selected
> select #42.2/B:39
21 atoms, 23 bonds, 1 model selected
> select clear
> volume #42.1 level 0.0007187
> select #42.1
2 models selected
> volume #42.1 color #b2ffffd0
> volume #42.1 color #b2ffffcc
> volume #42.1 color #b2ffffba
> 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.
> toolshed show "Side View"
> view
> 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 "translate selected models"
> select clear
> select clear
> volume #42.1 color #b2fffff6
> volume #42.1 color #b2fffff8
> volume #42.1 color #b2fffffe
> volume #42.1 color #b2ffff
> volume #41 color #3dc5db55
> volume #41 color #3dc5dbca
> volume #41 color #3dc5dbcc
> volume #41 color #3dc5db
> volume #42.1 color #3dc5db
> select #42.2
1640 atoms, 1838 bonds, 1 model selected
> ui mousemode rightMode "rotate selected models"
> fitmap #42.2 inMap #42.1
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#42.2) to map gp8-asym-300-400-part-
genome-lp.mrc (#42.1) using 1640 atoms
average map value = 0.004499, steps = 136
shifted from previous position = 0.239
rotated from previous position = 8.4 degrees
atoms outside contour = 709, contour level = 0.00071868
Position of Ideal-B-form-DNA-coot-0.pdb (#42.2) relative to
gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates:
Matrix rotation and translation
0.99873794 -0.05021764 0.00084651 10.69268753
0.05021922 0.99873630 -0.00196013 -9.89928782
-0.00074701 0.00200016 0.99999772 -0.15730335
Axis 0.03939510 0.01585163 0.99909797
Axis point 202.38327616 207.75661272 0.00000000
Rotation angle (degrees) 2.88111567
Shift along axis 0.10715811
> 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.
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 #41 level 0.01066
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 #42.2
1640 atoms, 1838 bonds, 1 model selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> volume #15 level 0.01821
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 0.01276
> lighting flat
> fitmap #42.2 inMap #42.1
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#42.2) to map gp8-asym-300-400-part-
genome-lp.mrc (#42.1) using 1640 atoms
average map value = 0.004347, steps = 320
shifted from previous position = 0.6
rotated from previous position = 15.1 degrees
atoms outside contour = 823, contour level = 0.00071868
Position of Ideal-B-form-DNA-coot-0.pdb (#42.2) relative to
gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates:
Matrix rotation and translation
-0.18236091 -0.97704616 0.11011492 435.41937537
0.98291778 -0.18398541 -0.00469014 42.41735540
0.02484202 0.10737861 0.99390779 -29.77959578
Axis 0.05703197 0.04339552 0.99742879
Axis point 200.89472016 202.71517927 0.00000000
Rotation angle (degrees) 100.73222639
Shift along axis -3.02948046
> fitmap #42.2 inMap #42.1
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#42.2) to map gp8-asym-300-400-part-
genome-lp.mrc (#42.1) using 1640 atoms
average map value = 0.004504, steps = 120
shifted from previous position = 3.2
rotated from previous position = 4.01 degrees
atoms outside contour = 706, contour level = 0.00071868
Position of Ideal-B-form-DNA-coot-0.pdb (#42.2) relative to
gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates:
Matrix rotation and translation
0.99944996 -0.03316067 0.00036586 7.02156618
0.03316116 0.99944901 -0.00141842 -6.58165157
-0.00031862 0.00142977 0.99999892 -0.16636008
Axis 0.04290318 0.01031048 0.99902603
Axis point 201.95672256 208.30701193 0.00000000
Rotation angle (degrees) 1.90218229
Shift along axis 0.06718951
> volume #42.1 color #4dddd3
> lighting soft
> volume #42.1 color #dfddd3
> volume #42.1 color #dfddd39d
> volume #42.1 color #c8ddd39d
> volume #42.1 color #c8c2d39d
> volume #42.1 color #c8c1d39d
> volume #42.1 color #c8c1d3ca
> volume #42.1 color #c8c1d3d6
Missing or invalid "chains" argument: only initial part "#42" of atom
specifier valid
> sequence chain #42.1
Chains must have same sequence
> select #42.2/A
820 atoms, 922 bonds, 1 model selected
> color #42.2/A green
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel cartoons
> volume #42.1 color #8fc1d3d6
> volume #42.1 color #7fc1d3d6
> volume #42.1 color #7fced3d6
> volume #42.1 color #7fced3d9
> volume #42.1 color #7fced3
> volume #42.1 color #4aced3
> volume #42.1 color #08ced3
> volume #42.1 color #08ce35
> volume #42.1 color #08ce07
> select #42.2/A
820 atoms, 922 bonds, 1 model selected
> color #42.2/A green
> volume #42.1 color #08ced6
> volume #42.1 color #cbced6
> volume #42.1 color #cbced698
> select #42.2/B
820 atoms, 916 bonds, 1 model selected
> select #34
1640 atoms, 1838 bonds, 1 model selected
> hide sel cartoons
> select #42.2/a
820 atoms, 922 bonds, 1 model selected
> select #42.2/A
820 atoms, 922 bonds, 1 model selected
> color #42.2/A green
> color #42.2/B #4DDDD3
> select clear
> select #42.2
1640 atoms, 1838 bonds, 1 model selected
> show sel atoms
> show sel atoms
> show sel cartoons
> show sel atoms
> select clear
> select #34
1640 atoms, 1838 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> volume #42.1 color #cb50d698
> volume #42.1 color #5750d698
> volume #42.1 color #57a7d698
> volume #42.1 color #57e8d698
> volume #42.1 color #57e80298
> volume #42.1 color #57e80198
> volume #42.1 color #57e80098
> volume #42.1 color #57e90098
> volume #42.1 color #57f60098
> volume #42.1 color #57ff0098
> volume #42.1 color #57ff00
> volume #42.1 color #57de00
> volume #42.1 color #57df00
> volume #42.1 color #d8df00
> volume #42.1 color #d8dfdf
> volume #42.1 color #d8dfdf9a
> volume #42.1 color #d8dfde9a
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #42.2/A #D58F00
> volume #42.1 color #56dfde9a
> volume #42.1 color #56df059a
> volume #42.1 color #56df049a
> volume #42.1 color #56df009a
> volume #42.1 color #04df009a
> volume #42.1 color #03df009a
> volume #42.1 color #00df009a
> volume #42.1 color #00e0009a
> volume #42.1 color #00e5009a
> volume #42.1 color #00ee009a
> volume #42.1 color #00f6009a
> volume #42.1 color #00fd009a
> volume #42.1 color #00ff009a
> color #42.2/A #00FF00
> volume #42.1 color #00d5009a
> volume #42.1 color #ced5009a
> volume #42.1 color #ced5d49a
> select clear
> save image /Users/chunyan/2020/20200507-Figure5-A11.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.
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 #d2d2d28f
> lighting flat
> volume #42.1 color #ced5d4f9
> volume #42.1 color #ced5d4
> volume #42.1 color #4dddd3
> lighting soft
> 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
> open /Users/chunyan/2020/gp8-asym/part/gp8-asym-lp.mrc
Opened gp8-asym-lp.mrc, grid size 400,400,400, pixel 1.05, shown at level
0.02, 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.
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 #43 level 0.008651
> lighting flat
> select #43
3 models selected
> 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.
> ui mousemode rightMode "rotate 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"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #43 inMap #23
Fit map gp8-asym-lp.mrc in map gp12-new.mrc using 1456064 points
correlation = 0.1995, correlation about mean = 0.124, overlap = 10.24
steps = 2000, shift = 51.6, angle = 23.8 degrees
Position of gp8-asym-lp.mrc (#43) relative to gp12-new.mrc (#23) coordinates:
Matrix rotation and translation
0.40696140 -0.91344510 -0.00066381 106.40439805
-0.91344420 -0.40695962 -0.00188189 277.92196286
0.00144886 0.00137221 -0.99999800 210.81785650
Axis 0.83873705 -0.54453659 0.00023232
Axis point 0.00000000 173.37975011 105.53535540
Rotation angle (degrees) 179.88885292
Shift along axis -62.04438986
> volume #43 color #b2b2b6
> volume #43 color #b2b2b6a2
> volume #43 color #b2b2b680
> volume #43 color #b2b2b580
> volume #43 color #b2b2b480
> volume #43 color #b2b2b380
> fitmap #42.1 inMap #43
Fit map gp8-asym-300-400-part-genome-lp.mrc in map gp8-asym-lp.mrc using 1667
points
correlation = 0.9298, correlation about mean = 0.9033, overlap = 0.1757
steps = 1056, shift = 1.89, angle = 79.6 degrees
Position of gp8-asym-300-400-part-genome-lp.mrc (#42.1) relative to gp8-asym-
lp.mrc (#43) coordinates:
Matrix rotation and translation
0.99082847 -0.13499437 0.00595422 29.27059608
0.13502393 0.99083033 -0.00487730 -25.60878619
-0.00524121 0.00563653 0.99997037 0.24372855
Axis 0.03887465 0.04139482 0.99838631
Axis point 203.53926969 202.90732245 0.00000000
Rotation angle (degrees) 7.77176754
Shift along axis 0.32114826
> fitmap #42.2 inMap #42.1
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#42.2) to map gp8-asym-300-400-part-
genome-lp.mrc (#42.1) using 1640 atoms
average map value = 0.004369, steps = 348
shifted from previous position = 6.57
rotated from previous position = 17.7 degrees
atoms outside contour = 813, contour level = 0.00071868
Position of Ideal-B-form-DNA-coot-0.pdb (#42.2) relative to
gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates:
Matrix rotation and translation
0.39874175 -0.91455788 0.06774138 307.15876655
0.91700257 0.39677637 -0.04092407 -59.81831363
0.01054925 0.07843715 0.99686324 -24.46895053
Axis 0.06499965 0.03114469 0.99739915
Axis point 199.82629197 204.93099831 0.00000000
Rotation angle (degrees) 66.65974546
Shift along axis -6.30312184
> fitmap #37 inMap #43
Fit molecule gp8-new-assembled.pdb (#37) to map gp8-asym-lp.mrc (#43) using
49008 atoms
average map value = 0.007408, steps = 52
shifted from previous position = 0.589
rotated from previous position = 0.379 degrees
atoms outside contour = 32763, contour level = 0.0086506
Position of gp8-new-assembled.pdb (#37) relative to gp8-asym-lp.mrc (#43)
coordinates:
Matrix rotation and translation
-0.00550842 -0.99998038 0.00297801 420.47849047
0.99998479 -0.00550910 -0.00022072 1.20334395
0.00023713 0.00297674 0.99999553 -2.23188863
Axis 0.00159876 0.00137046 0.99999778
Axis point 209.64160107 209.68869631 0.00000000
Rotation angle (degrees) 90.31575837
Shift along axis -1.55799090
> select #42.2
1640 atoms, 1838 bonds, 1 model selected
> ui mousemode rightMode "rotate selected models"
> fitmap #42.2 inMap #42.1
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#42.2) to map gp8-asym-300-400-part-
genome-lp.mrc (#42.1) using 1640 atoms
average map value = 0.004365, steps = 252
shifted from previous position = 0.144
rotated from previous position = 16.1 degrees
atoms outside contour = 811, contour level = 0.00071868
Position of Ideal-B-form-DNA-coot-0.pdb (#42.2) relative to
gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates:
Matrix rotation and translation
0.43194805 -0.89974929 0.06222611 298.03003881
0.90182219 0.42998487 -0.04277546 -63.30728183
0.01173090 0.07459366 0.99714501 -23.97935667
Axis 0.06498496 0.02795820 0.99749451
Axis point 199.88992538 205.49390475 0.00000000
Rotation angle (degrees) 64.56169474
Shift along axis -6.32176333
> volume #43 step 1
> lighting soft
> lighting flat
> volume #43 step 2
> select #42.3
Nothing selected
> select #43
4 models selected
> ui mousemode rightMode "rotate selected models"
> fitmap #43 inMap #23
Fit map gp8-asym-lp.mrc in map gp12-new.mrc using 1456064 points
correlation = 0.1995, correlation about mean = 0.1245, overlap = 10.27
steps = 2000, shift = 2.89, angle = 27.9 degrees
Position of gp8-asym-lp.mrc (#43) relative to gp12-new.mrc (#23) coordinates:
Matrix rotation and translation
-0.58760139 -0.80914968 0.00117414 293.10936819
-0.80915053 0.58760087 -0.00078318 46.88503539
-0.00005622 -0.00141025 -0.99999900 211.67207040
Axis -0.45409174 0.89095472 -0.00061587
Axis point 158.54360138 0.00000000 105.80349757
Rotation angle (degrees) 179.96043891
Shift along axis -91.45646384
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> volume #43 level 0.004727
> show sel cartoons
> show sel cartoons
> fitmap #37 inMap #43
Fit molecule gp8-new-assembled.pdb (#37) to map gp8-asym-lp.mrc (#43) using
49008 atoms
average map value = 0.007438, steps = 48
shifted from previous position = 0.201
rotated from previous position = 0.0765 degrees
atoms outside contour = 14728, contour level = 0.004727
Position of gp8-new-assembled.pdb (#37) relative to gp8-asym-lp.mrc (#43)
coordinates:
Matrix rotation and translation
0.86332314 -0.50464305 0.00292023 134.01356052
0.50464654 0.86332586 -0.00056369 -77.09876795
-0.00223665 0.00196033 0.99999557 -1.50301816
Axis 0.00250074 0.00510934 0.99998382
Axis point 209.33152145 208.87376160 0.00000000
Rotation angle (degrees) 30.30831817
Shift along axis -1.56178425
> fitmap #42.1 inMap #43
Fit map gp8-asym-300-400-part-genome-lp.mrc in map gp8-asym-lp.mrc using 1667
points
correlation = 0.931, correlation about mean = 0.9059, overlap = 0.1758
steps = 852, shift = 0.704, angle = 45.8 degrees
Position of gp8-asym-300-400-part-genome-lp.mrc (#42.1) relative to gp8-asym-
lp.mrc (#43) coordinates:
Matrix rotation and translation
0.99360833 0.11286291 -0.00210474 -21.97002251
-0.11285188 0.99360031 0.00478170 24.19417980
0.00263095 -0.00451361 0.99998634 0.14833026
Axis -0.04113774 -0.02095848 -0.99893365
Axis point 202.74999257 206.05268258 0.00000000
Rotation angle (degrees) 6.48700546
Shift along axis 0.24855187
> volume #43 level 0.005539
> select #37
49008 atoms, 49740 bonds, 1 model selected
> hide sel cartoons
> save session /Users/chunyan/2020/gp8-asym/gp8-asym-20200507.cxs
> select clear
> lighting soft
> select #37
49008 atoms, 49740 bonds, 1 model selected
> select #42.2
1640 atoms, 1838 bonds, 1 model selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #42.2 inMap #42.1
Fit molecule Ideal-B-form-DNA-coot-0.pdb (#42.2) to map gp8-asym-300-400-part-
genome-lp.mrc (#42.1) using 1640 atoms
average map value = 0.004498, steps = 172
shifted from previous position = 3.86
rotated from previous position = 11.7 degrees
atoms outside contour = 708, contour level = 0.00071868
Position of Ideal-B-form-DNA-coot-0.pdb (#42.2) relative to
gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates:
Matrix rotation and translation
0.99843386 -0.05593555 0.00101059 11.93622326
0.05593765 0.99843186 -0.00218753 -10.99074593
-0.00088665 0.00224063 0.99999709 -0.16246687
Axis 0.03954532 0.01694311 0.99907412
Axis point 202.34037066 207.63984332 0.00000000
Rotation angle (degrees) 3.20957956
Shift along axis 0.12348789
> 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-B1.tif pixelSize 0.1
> supersample 4 transparentBackground true
> lighting soft
> fitmap #40 inMap #43
Fit map gp8-asym-360-383-part-lp.mrc in map gp8-asym-lp.mrc using 26754 points
correlation = 0.95, correlation about mean = 0.8047, overlap = 2.207
steps = 60, shift = 0.465, angle = 0.272 degrees
Position of gp8-asym-360-383-part-lp.mrc (#40) relative to gp8-asym-lp.mrc
(#43) coordinates:
Matrix rotation and translation
0.99999867 -0.00116975 0.00113122 0.05528665
0.00117189 0.99999751 -0.00189750 0.10726151
-0.00112899 0.00189883 0.99999755 -0.00322989
Axis 0.75920582 0.45200683 0.46829087
Axis point 0.00000000 23.68192431 35.30910081
Rotation angle (degrees) 0.14325100
Shift along axis 0.08894435
> volume #10 color #d2d2d268
> volume #10 color #d2d2d274
> volume #10 color #d2d2d277
> volume #10 color #d2d2d27d
> volume #10 color #d2d2d281
> volume #10 color #d2d2d285
> volume #10 color #d2d2d288
> volume #10 color #d2d2d28d
> volume #10 color #d2d2d28f
> volume #10 color #d2d2d291
> volume #10 color #d2d2d294
> volume #10 color #d2d2d298
> volume #10 color #d2d2d299
> volume #10 color #d2d2d2a0
> volume #10 color #d2d2d2b4
> volume #10 color #d2d2d2b7
> volume #10 color #d2d2d2ba
> volume #10 color #d2d2d2c6
> volume #10 color #d2d2d2d3
> volume #10 color #d2d2d2d7
> volume #10 color #d2d2d2da
> volume #10 color #d2d2d2df
> volume #10 color #d2d2d2eb
> volume #10 color #d2d2d2ef
> volume #10 color #d2d2d2
> volume #10 color #d2d2d2f6
> volume #10 color #d2d2d2ec
> volume #10 color #d2d2d2d7
> volume #10 color #d2d2d2c6
> volume #10 color #d2d2d273
> volume #10 color #d2d2d271
> volume #10 color #d2d2d26f
> volume #10 color #d2d2d25e
> volume #10 color #d2d2d25c
> volume #10 color #d2d2d25b
> volume #10 color #d2d2d252
> volume #10 color #d2d2d250
> volume #10 color #d2d2d24d
> volume #10 color #d2d2d247
> volume #10 color #d2d2d246
> volume #10 color #d2d2d244
> volume #10 color #d2d2d243
> volume #10 color #d2d2d240
> volume #10 color #d2d2d23f
> volume #10 color #d2d2d23e
> volume #10 color #d2d2d23c
> volume #10 color #d2d2d23b
> volume #10 color #d2d2d23a
> volume #10 color #d2d2d235
> volume #10 color #d2d2d230
> volume #10 color #d2d2d22a
> volume #10 color #d2d2d227
> volume #10 color #d2d2d228
> volume #10 color #d2d2d233
> volume #10 color #d2d2d24e
> volume #10 color #d2d2d259
> volume #10 color #d2d2d26f
> volume #10 color #d2d2d271
> volume #10 color #d2d2d276
> volume #10 color #d2d2d279
> volume #10 color #d2d2d27a
> volume #10 color #d2d2d27d
> volume #10 color #d2d2d280
> volume #10 color #a2d2d280
> 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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