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Opened 3 years ago
Last modified 3 years ago
#8706 assigned defect
ArtiaX: arrays used as indices must be of integer (or boolean) type
| Reported by: | Owned by: | Utz Ermel | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.5.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/zhenhou/Desktop/Nucleosome/class1_class2_comparison_py/run_class1.mrc
Opened run_class1.mrc as #1, grid size 96,96,96, pixel 4.36, shown at level
0.0756, step 1, values float32
> volume #1 level 0.1924
> volume #1 level 0.1333
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> ui tool show "Hide Dust"
> hide target m
[Repeated 1 time(s)]
> show #!1 models
> select add #1
2 models selected
> hide target m
> show target m
> select subtract #1
Nothing selected
> surface dust #1 size 26.16
> volume #1 level 0.1575
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> volume #1 level 0.175
> volume #1 surfaceSmoothing true
> color #1 #ff7e79ff models
> set bgColor white
> color #1 #ff9300ff models
> color #1 #ff930063 models
> color #1 #ff93008f models
> color #1 #ff930080 models
> color #1 #ff930076 models
> volume #1 level 0.1477
> volume #1 level 0.1462
> volume #1 level 0.1523
> open /Users/zhenhou/Desktop/Nucleosome/Class1_py/8AAG.pdb
8AAG.pdb title:
H1-bound palindromic nucleosome, state 1 [more info...]
Chain information for 8AAG.pdb #2
---
Chain | Description | UniProt
A E | histone H3.2 |
B F | histone H4 | H4_HUMAN
C G | histone H2A type 1 |
D H | histone H2B type 1-C/E/F/G/I |
I | DNA/RNA (185-mer) |
J | DNA/RNA (185-mer) |
Z | histone H1.0-B | H10B_XENLA
> hide atoms
> show cartoons
> ui mousemode right select
> select #1
2 models selected
> ui mousemode right translate
> ui mousemode right "translate selected particles"
> mousemode rightMode "translate selected particles"
Invalid "rightMode" argument: Should be one of 'bond rotation', 'clip', 'clip
rotate', 'contour level', 'crop volume', 'delete markers', 'distance',
'identify object', 'label', 'link markers', 'map eraser', 'mark center', 'mark
maximum', 'mark plane', 'mark point', 'mark surface', 'minimize', 'move
label', 'move markers', 'move picked models', 'move planes', 'next docked',
'none', 'pick blobs', 'pivot', 'play coordinates', 'play map series', 'resize
markers', 'rotate', 'rotate and select', 'rotate independent', 'rotate
selected atoms', 'rotate selected models', 'rotate slab', 'rotate z selected
models', 'select', 'select add', 'select subtract', 'select toggle', 'swapaa',
'swipe as scroll', 'tape measure', 'translate', 'translate selected atoms',
'translate selected models', 'translate xy selected models', 'tug',
'windowing', 'zone', or 'zoom'
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,9.1476,0,1,0,-52.005,0,0,1,-91.264
> view matrix models #1,1,0,0,-85.067,0,1,0,-84.612,0,0,1,-102.79
> view matrix models #1,1,0,0,-83.094,0,1,0,-83.774,0,0,1,-111.42
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.77781,0.49957,-0.38136,-48.004,-0.52484,0.8501,0.043148,44.167,0.34575,0.16659,0.92342,-198
> view matrix models
> #1,0.34425,-0.3951,-0.8517,305.69,0.4299,0.87279,-0.23113,-101.47,0.83467,-0.28658,0.47031,-121.45
> view matrix models
> #1,0.96275,0.22661,0.14751,-147.97,-0.10623,0.81866,-0.56437,90.571,-0.24865,0.52768,0.81224,-116.76
> view matrix models
> #1,0.93398,0.083993,-0.3473,-11.547,-0.28072,0.77383,-0.56779,135.93,0.22106,0.6278,0.74632,-219.26
> view matrix models
> #1,0.93416,0.064469,-0.35099,-7.2247,-0.26651,0.78013,-0.56601,131.43,0.23733,0.62228,0.74595,-221.57
> view matrix models
> #1,0.94028,0.14767,-0.30669,-33.098,-0.30849,0.75049,-0.58446,149.52,0.14387,0.64417,0.75123,-207.19
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.94028,0.14767,-0.30669,-32.774,-0.30849,0.75049,-0.58446,150.04,0.14387,0.64417,0.75123,-198.06
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 8AAG.pdb (#2) to map run_class1.mrc (#1) using 14180 atoms
average map value = 0.3236, steps = 76
shifted from previous position = 12.8
rotated from previous position = 14.3 degrees
atoms outside contour = 1331, contour level = 0.15225
Position of 8AAG.pdb (#2) relative to run_class1.mrc (#1) coordinates:
Matrix rotation and translation
0.95507333 -0.22078452 0.19770971 98.77516627
-0.01702488 0.62513200 0.78033335 32.00034996
-0.29588019 -0.74864155 0.59328807 261.99515317
Axis -0.94407912 0.30477147 0.12581320
Axis point 0.00000000 310.43660489 88.38577416
Rotation angle (degrees) 54.07351746
Shift along axis -50.53633033
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.49227,0.26943,-0.82769,148.17,-0.69164,0.6984,-0.18401,155.18,0.52848,0.66305,0.53016,-235.22
> view matrix models
> #1,-0.66918,0.28657,-0.68562,357.49,-0.48918,0.52464,0.69674,-40.773,0.55937,0.80164,-0.2109,-110.95
> view matrix models
> #1,-0.87324,0.03338,0.48615,199.63,0.43637,0.4976,0.74965,-240.13,-0.21689,0.86676,-0.44909,89.304
> fitmap #2 inMap #1
Fit molecule 8AAG.pdb (#2) to map run_class1.mrc (#1) using 14180 atoms
average map value = 0.3225, steps = 68
shifted from previous position = 6.03
rotated from previous position = 9.49 degrees
atoms outside contour = 1417, contour level = 0.15225
Position of 8AAG.pdb (#2) relative to run_class1.mrc (#1) coordinates:
Matrix rotation and translation
-0.95654446 0.22108153 -0.19012012 318.43185506
-0.10689626 0.34074480 0.93405898 57.69328172
0.27128563 0.91379207 -0.30230476 106.63709721
Axis -0.03577827 -0.81454440 -0.57899684
Axis point 154.65793226 0.00000000 60.69173255
Rotation angle (degrees) 163.54696292
Shift along axis -120.12922248
> color #2 #ff2f92ff
> color #2 #ff40ffff
> color #2 #0433ffff
> color #2 #00fa92ff
> color #2 #929292ff
> color #2 #919191ff
> color #2 #424242ff
> color #2 #ff7e79ff
> color #2 #008f00ff
> color #2 #73fa79ff
> ui mousemode right select
> select clear
> hide #!1 models
> select /Z:69
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /Z:73
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /Z:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /Z:82
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 59 residues
Drag select of 15 residues
Drag select of 75 residues
> color #2 #ff7e79ff
> select clear
Drag select of 33 residues
Drag select of 7 residues
Drag select of 41 residues
Drag select of 11 residues
Drag select of 19 residues
Drag select of 21 residues
Drag select of 6 residues
> select subtract /I:2
354 atoms, 44 residues, 1 model selected
> select subtract /I:3
335 atoms, 43 residues, 1 model selected
Drag select of 21 residues
Drag select of 39 residues
> select subtract /I:1
408 atoms, 48 residues, 1 model selected
> select subtract /I:4
386 atoms, 47 residues, 1 model selected
> select subtract /I:2
367 atoms, 46 residues, 1 model selected
> select subtract /I:3
348 atoms, 45 residues, 1 model selected
Drag select of 37 residues
Drag select of 14 residues
Drag select of 20 residues
Drag select of 12 residues
Drag select of 9 residues
> ui mousemode right "pick blobs"
[Repeated 1 time(s)]
> ui mousemode right "contour level"
> color sel bychain
[Repeated 2 time(s)]
> color sel byhetero
> color sel bypolymer
> color bfactor sel
321 atoms, 45 residues, atom bfactor range 315 to 463
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 8AAG.pdb_Z SES surface #2.1: minimum, -8.65, mean 4.81,
maximum 19.83
To also show corresponding color key, enter the above coulombic command and
add key true
> rainbow sel
[Repeated 2 time(s)]
> select add #2
14180 atoms, 15189 bonds, 1203 residues, 2 models selected
> select subtract #2
1 model selected
> select add #2
14180 atoms, 15189 bonds, 1203 residues, 1 model selected
> select subtract #2
1 model selected
> close
> open /Users/zhenhou/Desktop/Nucleosome/Class1_py/8AAG.pdb
8AAG.pdb title:
H1-bound palindromic nucleosome, state 1 [more info...]
Chain information for 8AAG.pdb #1
---
Chain | Description | UniProt
A E | histone H3.2 |
B F | histone H4 | H4_HUMAN
C G | histone H2A type 1 |
D H | histone H2B type 1-C/E/F/G/I |
I | DNA/RNA (185-mer) |
J | DNA/RNA (185-mer) |
Z | histone H1.0-B | H10B_XENLA
> hide atoms
> show cartoons
> ui mousemode right select
Drag select of 43 residues
> volume hide
No volumes specified
> volume style surface
No volumes specified
> show sel surfaces
> hide sel surfaces
Drag select of 1198 residues
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> show sel surfaces
> select /Z:87@O
1 atom, 1 residue, 1 model selected
> select /Z:85@CA
1 atom, 1 residue, 1 model selected
Drag select of 8AAG.pdb_Z SES surface, 3161 of 76110 triangles, 5 residues
Drag select of 8AAG.pdb_Z SES surface, 23625 of 76110 triangles, 32 residues
Drag select of 8AAG.pdb_Z SES surface, 2902 of 76110 triangles, 8AAG.pdb_J SES
surface, 28 of 577034 triangles, 8 residues
Drag select of 8AAG.pdb_Z SES surface, 7051 of 76110 triangles, 14 residues
Drag select of 8AAG.pdb_Z SES surface, 841 of 76110 triangles, 10 residues
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
Drag select of 8AAG.pdb_Z SES surface, 4355 of 76110 triangles, 8AAG.pdb_A SES
surface, 69360 of 129148 triangles, 8AAG.pdb_B SES surface, 28358 of 105756
triangles, 8AAG.pdb_E SES surface, 24367 of 130746 triangles, 8AAG.pdb_F SES
surface, 27005 of 105214 triangles, 8AAG.pdb_G SES surface, 85791 of 122002
triangles, 8AAG.pdb_H SES surface, 58455 of 123086 triangles, 8AAG.pdb_I SES
surface, 192315 of 574266 triangles, 8AAG.pdb_J SES surface, 203276 of 577034
triangles, 400 residues
> select /I:13@C7
1 atom, 1 residue, 1 model selected
> select /G:109@CG
1 atom, 1 residue, 1 model selected
Drag select of 8AAG.pdb_Z SES surface, 44498 of 76110 triangles, 8AAG.pdb_A
SES surface, 8AAG.pdb_B SES surface, 8AAG.pdb_C SES surface, 8AAG.pdb_D SES
surface, 8AAG.pdb_E SES surface, 8AAG.pdb_F SES surface, 8AAG.pdb_G SES
surface, 8AAG.pdb_H SES surface, 8AAG.pdb_I SES surface, 567854 of 574266
triangles, 8AAG.pdb_J SES surface, 567873 of 577034 triangles, 1203 residues
> hide sel surfaces
> select clear
> select /Z:77
7 atoms, 6 bonds, 1 residue, 1 model selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> color #1 indian red
> color #1 cornflower blue
> select clear
> open /Users/zhenhou/Desktop/Nucleosome/Class1_py/run_class001.mrc
Opened run_class001.mrc as #2, grid size 96,96,96, pixel 4.36, shown at level
0.0756, step 1, values float32
> volume #2 level 0.15
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> volume #2 surfaceSmoothing true
> ui tool show "Hide Dust"
> surface dust #2 size 26.16
> volume #2 level 0.1379
> volume #2 level 0.2713
> volume #2 level 0.1758
> volume #2 level 0.15
> volume #2 level 0.1591
> select #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-18.537,0,1,0,-63.57,0,0,1,-109.98
> view matrix models #2,1,0,0,-21.729,0,1,0,-86.21,0,0,1,-105.52
> view matrix models #2,1,0,0,-81.117,0,1,0,-88.006,0,0,1,-102.97
> view matrix models #2,1,0,0,-93.427,0,1,0,-87.35,0,0,1,-104.14
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.60942,0.61364,0.50204,-229.99,-0.57286,0.77857,-0.25625,127.22,-0.54812,-0.13143,0.82601,71.409
> view matrix models
> #2,0.36438,0.61555,-0.6988,74.006,-0.78614,0.60558,0.12351,123.59,0.49921,0.50436,0.70457,-238.94
> view matrix models
> #2,0.7217,-0.46868,-0.50939,158.16,0.070386,0.78177,-0.61958,68.497,0.68861,0.4113,0.5972,-238.9
> view matrix models
> #2,0.91569,0.40007,0.038196,-157.21,-0.26442,0.67132,-0.69239,174.21,-0.30265,0.62392,0.72051,-96.32
> view matrix models
> #2,0.96155,0.27286,-0.031286,-128.83,-0.22293,0.70888,-0.66917,153.74,-0.16041,0.65041,0.74245,-135.59
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.96155,0.27286,-0.031286,-128.05,-0.22293,0.70888,-0.66917,159.05,-0.16041,0.65041,0.74245,-131.97
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule 8AAG.pdb (#1) to map run_class001.mrc (#2) using 14180 atoms
average map value = 0.3236, steps = 80
shifted from previous position = 6.64
rotated from previous position = 23.6 degrees
atoms outside contour = 1399, contour level = 0.1591
Position of 8AAG.pdb (#1) relative to run_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.95509982 -0.22115952 0.19716187 98.97187127
-0.01640303 0.62495838 0.78048573 31.92843815
-0.29582981 -0.74867583 0.59326995 262.00050111
Axis -0.94412458 0.30437958 0.12641936
Axis point 0.00000000 310.40847626 88.51616644
Rotation angle (degrees) 54.07936359
Shift along axis -50.60147448
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.86035,0.20901,0.46488,-199.7,0.28945,0.55038,-0.78314,104.85,-0.41955,0.80833,0.41302,-37.255
> view matrix models
> #2,0.25704,0.005403,0.96639,-141.69,0.94367,0.21422,-0.25219,-82.354,-0.20838,0.97677,0.049964,-35.869
> view matrix models
> #2,-0.70413,0.30557,0.64096,73.086,0.55498,-0.32624,0.76522,-116.21,0.44294,0.89453,0.060125,-159.31
> view matrix models
> #2,-0.86065,0.1571,-0.48435,370.22,-0.50918,-0.25925,0.82069,82.643,0.0033671,0.95295,0.30311,-129.18
> view matrix models
> #2,-0.90617,0.26457,0.32993,188.45,0.27898,-0.21236,0.93652,-115.4,0.31784,0.94069,0.11863,-153.91
> view matrix models
> #2,-0.86854,0.48761,-0.088736,227.88,0.074012,0.30464,0.94959,-170.07,0.49006,0.81819,-0.30068,-79.145
> fitmap #1 inMap #2
Fit molecule 8AAG.pdb (#1) to map run_class001.mrc (#2) using 14180 atoms
average map value = 0.3225, steps = 72
shifted from previous position = 7.68
rotated from previous position = 22.1 degrees
atoms outside contour = 1481, contour level = 0.1591
Position of 8AAG.pdb (#1) relative to run_class001.mrc (#2) coordinates:
Matrix rotation and translation
-0.95663731 0.22161923 -0.18902374 318.13742593
-0.10580335 0.34023466 0.93436932 57.58959123
0.27138664 0.91385190 -0.30203311 106.58030364
Axis -0.03629247 -0.81440202 -0.57916509
Axis point 154.50997431 0.00000000 60.60619743
Rotation angle (degrees) 163.58051094
Shift along axis -120.17466498
> view matrix models
> #2,-0.86675,0.4956,-0.055851,219.11,0.11295,0.30414,0.94591,-177.36,0.48578,0.81356,-0.31959,-73.413
> fitmap #1 inMap #2
Fit molecule 8AAG.pdb (#1) to map run_class001.mrc (#2) using 14180 atoms
average map value = 0.3225, steps = 48
shifted from previous position = 0.0235
rotated from previous position = 2.26 degrees
atoms outside contour = 1477, contour level = 0.1591
Position of 8AAG.pdb (#1) relative to run_class001.mrc (#2) coordinates:
Matrix rotation and translation
-0.95659386 0.22141140 -0.18948664 318.26303413
-0.10621651 0.34059178 0.93419232 57.60239635
0.27137842 0.91376924 -0.30229046 106.62555602
Axis -0.03609457 -0.81450637 -0.57903070
Axis point 154.57015230 0.00000000 60.66632256
Rotation angle (degrees) 163.56600125
Shift along axis -120.14455726
> view matrix models
> #2,-0.89448,0.44453,-0.047957,232.62,0.10396,0.3111,0.94467,-176.49,0.43486,0.84,-0.32449,-66.57
> ui mousemode right select
> select clear
> fitmap #1 inMap #2
Fit molecule 8AAG.pdb (#1) to map run_class001.mrc (#2) using 14180 atoms
average map value = 0.3225, steps = 64
shifted from previous position = 0.665
rotated from previous position = 3.33 degrees
atoms outside contour = 1478, contour level = 0.1591
Position of 8AAG.pdb (#1) relative to run_class001.mrc (#2) coordinates:
Matrix rotation and translation
-0.95654498 0.22110443 -0.19009088 318.42538876
-0.10686123 0.34074169 0.93406412 57.68910945
0.27129760 0.91378769 -0.30230726 106.63671765
Axis -0.03579639 -0.81454375 -0.57899663
Axis point 154.65439814 0.00000000 60.69120095
Rotation angle (degrees) 163.54758285
Shift along axis -120.13108456
> color #2 indian red
> volume #2 color #cd5c5c80
> volume #2 color #cd5c5c72
> color #2 light coral
> volume #2 color indianred
> lighting soft
> color #2 dark salmon
> volume #2 color #cd5c5ccd
> volume #2 color indianred
> color #2 dark salmon
> volume #2 color indianred
> color #2 dark salmon
> lighting simple
> volume #2 color #cd5c5c82
> volume #2 color indianred
> color #2 dark salmon
> volume #2 color #e9967aa9
> volume #2 color #e9967aa8
> color #2 light coral
> volume #2 color lightcoral
> volume #2 color #f0808080
> volume #2 level 0.1212
> volume #2 level 0.15
> volume #2 color #ff9300
> volume #2 color #ff2600
> color #2 light coral
> color #2 indian red
> color #2 salmon
> volume #2 color #fa807284
> volume #2 color #fa807285
> hide #!2 models
Drag select of 36 residues
Drag select of 10 residues
Drag select of 32 residues
Drag select of 18 residues
Drag select of 17 residues
Drag select of 7 residues
Drag select of 16 residues
> select subtract /J:80
439 atoms, 53 residues, 3 models selected
> select subtract /J:79
417 atoms, 52 residues, 3 models selected
Drag select of 55 residues
[Repeated 1 time(s)]
> select subtract /Z:73
391 atoms, 49 residues, 2 models selected
> select subtract /Z:71
385 atoms, 48 residues, 2 models selected
> select subtract /Z:72
377 atoms, 47 residues, 2 models selected
> select subtract /Z:74
366 atoms, 46 residues, 2 models selected
> select add /Z:74
377 atoms, 10 bonds, 47 residues, 2 models selected
> select subtract /Z:74
366 atoms, 46 residues, 2 models selected
> select subtract /Z:75
358 atoms, 45 residues, 2 models selected
> select subtract /Z:76
351 atoms, 44 residues, 2 models selected
> select subtract /Z:77
344 atoms, 43 residues, 2 models selected
> select subtract /Z:78
338 atoms, 42 residues, 2 models selected
> select subtract /Z:79
334 atoms, 41 residues, 2 models selected
> select add /Z:79
338 atoms, 3 bonds, 42 residues, 2 models selected
> select add /Z:78
344 atoms, 8 bonds, 43 residues, 2 models selected
Drag select of 57 residues
Drag select of 59 residues
> select clear
Drag select of 59 residues
Drag select of 8 residues
Drag select of 11 residues
> select clear
Drag select of 85 residues
> select subtract /J:-85
784 atoms, 84 residues, 4 models selected
> select add /I:88
804 atoms, 21 bonds, 85 residues, 4 models selected
> select subtract /J:-86
784 atoms, 21 bonds, 84 residues, 4 models selected
> select subtract /I:88
764 atoms, 83 residues, 4 models selected
> select subtract /J:80
745 atoms, 82 residues, 4 models selected
> select subtract /I:-78
725 atoms, 81 residues, 4 models selected
> select subtract /J:81
705 atoms, 80 residues, 4 models selected
> select add /J:80
724 atoms, 20 bonds, 81 residues, 4 models selected
> select subtract /I:-77
703 atoms, 20 bonds, 80 residues, 4 models selected
> select subtract /I:-76
681 atoms, 20 bonds, 79 residues, 4 models selected
> select subtract /I:-75
659 atoms, 20 bonds, 78 residues, 4 models selected
> select subtract /J:78
638 atoms, 20 bonds, 77 residues, 4 models selected
> select subtract /J:80
619 atoms, 76 residues, 4 models selected
> select subtract /J:79
597 atoms, 75 residues, 4 models selected
> select subtract /I:1
577 atoms, 74 residues, 3 models selected
> select subtract /I:2
558 atoms, 73 residues, 3 models selected
> select /Z:84
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
Drag select of 84 residues
> select subtract /I:1
763 atoms, 83 residues, 4 models selected
> select subtract /I:3
744 atoms, 82 residues, 4 models selected
> select add /I:3
763 atoms, 20 bonds, 83 residues, 4 models selected
> select subtract /I:3
744 atoms, 82 residues, 4 models selected
> select subtract /I:2
725 atoms, 81 residues, 4 models selected
> select subtract /I:-76
703 atoms, 80 residues, 4 models selected
> select subtract /I:-77
682 atoms, 79 residues, 4 models selected
> select subtract /I:-78
662 atoms, 78 residues, 4 models selected
> select subtract /J:81
642 atoms, 77 residues, 4 models selected
> select subtract /J:80
623 atoms, 76 residues, 4 models selected
> select subtract /J:79
601 atoms, 75 residues, 4 models selected
> select subtract /J:78
580 atoms, 74 residues, 4 models selected
> select subtract /I:-75
558 atoms, 73 residues, 3 models selected
> color selected salmon
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color selected green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color selected bychain
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color selected bychain green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color selection green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color (#!1 & sel) orange
> color (#!1 & sel) purple
> color (#!1 & sel) blue
[Repeated 1 time(s)]
> color #1 black
> color (#!1 & sel) blue
> select clear
> undo
> color #1 #ff40ffff
> color #1 black
> color (#!1 & sel) forest green
> color (#!1 & sel) cornflower blue
> select clear
> undo
> color (#!1 & sel) lime
> color (#!1 & sel) cyan
> select clear
> color #1 #929292ff
> color #1 #919191ff
> color #1 #797979ff
> undo
[Repeated 3 time(s)]
> color #1 darkgrey
> color #1 #919191ff
> color #1 #797979ff
> color (#!1 & sel) blue
> select clear
> undo
> color (#!1 & sel) medium blue
> color (#!1 & sel) cyan
> color (#!1 & sel) blue
> select clear
> undo
> color (#!1 & sel) magenta
> color (#!1 & sel) orange
> color (#!1 & sel) blue
> select clear
> color #2 #ff9300ff models
> color #2 #ff930076 models
> color #2 #ff930080 models
> color #2 #ffd479ff models
> color #2 #ffd47983 models
> color #2 #ffd47981 models
> color #2 #ff2f92ff models
> color #2 #ff9300ff models
> color #2 #ff93004b models
> color #2 #ff930080 models
> undo
[Repeated 2 time(s)]
> color #2 #ff7e79ff models
> color #2 #ff7e7967 models
> color #2 #ff7e7964 models
> color #2 #ff7e797d models
> color #2 #ff7e7980 models
> save /Users/zhenhou/Desktop/image1.png supersample 3
> volume #2 level 0.2289
> save /Users/zhenhou/Desktop/image2.png supersample 3
> volume #2 level 0.15
> view orient
> save /Users/zhenhou/Desktop/image3.png supersample 3
> volume #2 level 0.23
> save /Users/zhenhou/Desktop/image4.png supersample 3
> view orient
> hide #!1 models
> open /Users/zhenhou/Desktop/Nucleosome/class2_py/run_class001.mrc
Opened run_class001.mrc as #3, grid size 96,96,96, pixel 4.36, shown at level
0.0796, step 1, values float32
> volume #3 color #76d6ff
> volume #3 surfaceSmoothing true
> surface dust #3 size 26.16
> volume #3 level 0.15
> volume #3 level 0.1029
> volume #3 level 0.08431
> volume #3 level 0.15
> lighting soft
> volume #3 color #73fdff
> volume #3 color #76d6ff
> color #3 sky blue
> lighting simple
> volume #3 color #87ceeb80
> open /Users/zhenhou/Desktop/Nucleosome/class2_py/6ESF.pdb
6ESF.pdb title:
Nucleosome : class 1 [more info...]
Chain information for 6ESF.pdb #4
---
Chain | Description | UniProt
A E | histone H3.2 | H32_XENLA
B F | histone H4 | H4_XENLA
C G | histone H2A | Q6AZJ8_XENLA
D H | H2B1.1 | H2B11_XENLA
I | DNA (147-mer) |
J | DNA (147-mer) |
> hide #4 cartoons
> hide #4 atoms
> show #4 cartoons
> color #4 #797979ff
> select #3
2 models selected
> select #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-6.9482,0,1,0,-95.841,0,0,1,-118.47
> view matrix models #3,1,0,0,-78.669,0,1,0,-115.95,0,0,1,-124.91
> view matrix models #3,1,0,0,-93.222,0,1,0,-109.64,0,0,1,-96.897
> view matrix models #3,1,0,0,-92.865,0,1,0,-108.92,0,0,1,-97.314
> view matrix models #3,1,0,0,-86.262,0,1,0,-95.62,0,0,1,-105.21
> view matrix models #3,1,0,0,8.7221,0,1,0,-144.72,0,0,1,-102.87
> view matrix models #3,1,0,0,-2.7348,0,1,0,-143.5,0,0,1,-70.651
> view matrix models #3,1,0,0,-66.776,0,1,0,-90.76,0,0,1,-112.2
> view matrix models #3,1,0,0,-87.464,0,1,0,-92.379,0,0,1,-113.44
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.99749,-0.054565,0.045035,-85.59,0.070739,0.75835,-0.648,78.998,0.0012056,0.64956,0.76031,-192.79
> view matrix models
> #3,0.99242,0.12154,-0.018345,-106.32,-0.00074365,-0.14331,-0.98968,346.97,-0.12291,0.98219,-0.14214,-41.776
> fitmap #4 inMap #3
Fit molecule 6ESF.pdb (#4) to map run_class001.mrc (#3) using 12091 atoms
average map value = 0.3212, steps = 64
shifted from previous position = 11.7
rotated from previous position = 17.8 degrees
atoms outside contour = 423, contour level = 0.15
Position of 6ESF.pdb (#4) relative to run_class001.mrc (#3) coordinates:
Matrix rotation and translation
0.99821454 0.05434950 0.02477646 85.60453462
-0.03118691 0.12046747 0.99222727 86.50676855
0.05094230 -0.99122839 0.12194737 306.58553917
Axis -0.99898465 -0.01317865 -0.04308116
Axis point 0.00000000 213.42727229 103.32870091
Rotation angle (degrees) 83.08973541
Shift along axis -99.86571820
> volume #3 level 0.19
> volume #3 level 0.1229
> volume #3 level 0.15
> ui mousemode right select
> select clear
> color #3 royal blue
> lighting soft
> volume #3 color royalblue
> undo
> lighting soft
> lighting simple
> color #3 cornflower blue
> save /Users/zhenhou/Desktop/image5.png supersample 3
> volume #3 level 0.17
> save /Users/zhenhou/Desktop/image6.png supersample 3
> hide #4 models
> artiax start
Using preset: ArtiaX / Artiax Default
> set bgColor transparent
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> open /Users/zhenhou/Desktop/Nucleosome/refine_class13456789/run_data.star
> format star
Summary of feedback from opening
/Users/zhenhou/Desktop/Nucleosome/refine_class13456789/run_data.star
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list run_data.star with 5578 particles.
set axis size 32.7
32.7
['.arrow', '0', '0', '0', '32.7', '0', '0', '2.18', '8.72']
> artiax particles #5.2.1 originScaleFactor 2.18
> artiax view xy
> open
> /Users/zhenhou/Desktop/Nucleosome/refine_class2_bin2_masked/run_data.star
> format star
Summary of feedback from opening
/Users/zhenhou/Desktop/Nucleosome/refine_class2_bin2_masked/run_data.star
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list run_data.star with 1212 particles.
set axis size 32.7
32.7
['.arrow', '0', '0', '0', '32.7', '0', '0', '2.18', '8.72']
> artiax particles #5.2.2 originScaleFactor 2.18
> artiax view xy
set axis size 15.00003
15.00003
['.arrow', '0', '0', '0', '15.00003', '0', '0', '1.000002', '4.000008']
set axis size 15.00006
15.00006
['.arrow', '0', '0', '0', '15.00006', '0', '0', '1.000004', '4.000016']
set axis size 15.00009
15.00009
['.arrow', '0', '0', '0', '15.00009', '0', '0', '1.000006', '4.000024']
set axis size 15.00012
15.00012
['.arrow', '0', '0', '0', '15.00012', '0', '0', '1.000008', '4.000032']
set axis size 15.00009
15.00009
['.arrow', '0', '0', '0', '15.00009', '0', '0', '1.000006', '4.000024']
set axis size 15.00006
15.00006
['.arrow', '0', '0', '0', '15.00006', '0', '0', '1.000004', '4.000016']
set axis size 15.00003
15.00003
['.arrow', '0', '0', '0', '15.00003', '0', '0', '1.000002', '4.000008']
> artiax attach #3 toParticleList #5.2.2
Opened run_class001.mrc as #5.2.2.1.1, grid size 96,96,96, pixel 4.36, shown
at level 0.0796, step 1, values float32
> volume #5.2.2.1.1 capFaces false
> open /Users/zhenhou/Desktop/Nucleosome/class2_py/run_class001.mrc
Opened run_class001.mrc as #3, grid size 96,96,96, pixel 4.36, shown at level
0.0796, step 1, values float32
> artiax attach #3 toParticleList #5.2.2
Opened run_class001.mrc as #5.2.2.1.1, grid size 96,96,96, pixel 4.36, shown
at level 0.0796, step 1, values float32
> volume #5.2.2.1.1 capFaces false
> artiax show #5.2.2 surfaces
> artiax particles #5.2.2 surfaceLevel 0.15
> open /Users/zhenhou/Desktop/Nucleosome/Class1_py/run_class001.mrc
Opened run_class001.mrc as #3, grid size 96,96,96, pixel 4.36, shown at level
0.0756, step 1, values float32
> artiax attach #3 toParticleList #5.2.2
Opened run_class001.mrc as #5.2.2.1.1, grid size 96,96,96, pixel 4.36, shown
at level 0.0756, step 1, values float32
> volume #5.2.2.1.1 capFaces false
> artiax show #5.2.2 surfaces
> open /Users/zhenhou/Desktop/Nucleosome/class2_py/run_class001.mrc
Opened run_class001.mrc as #3, grid size 96,96,96, pixel 4.36, shown at level
0.0796, step 1, values float32
> artiax attach #3 toParticleList #5.2.2
Opened run_class001.mrc as #5.2.2.1.1, grid size 96,96,96, pixel 4.36, shown
at level 0.0796, step 1, values float32
> volume #5.2.2.1.1 capFaces false
> artiax show #5.2.2 surfaces
> artiax particles #5.2.2 surfaceLevel 0.15
> open /Users/zhenhou/Desktop/Nucleosome/Class1_py/run_class001.mrc
Opened run_class001.mrc as #3, grid size 96,96,96, pixel 4.36, shown at level
0.0756, step 1, values float32
> artiax attach #3 toParticleList #5.2.1
Opened run_class001.mrc as #5.2.1.1.1, grid size 96,96,96, pixel 4.36, shown
at level 0.0756, step 1, values float32
> volume #5.2.1.1.1 capFaces false
> artiax show #5.2.1 surfaces
> artiax particles #5.2.1 surfaceLevel 0.66648
> artiax particles #5.2.1 surfaceLevel 0.15
> artiax particles #5.2.1 color 94,64,100,100
> artiax particles #5.2.1 color 100,49,47,100
> artiax particles #5.2.2 color 0,46,86,100
> artiax particles #5.2.2 color 46,84,100,100
> color #5.2.2 cornflower blue
> lighting soft
> set bgColor white
> set bgColor #ffffff00
> hide #!5.2.1 models
> hide #!5.2.2 models
> view orient
> volume #2 color #ff7e79
> volume #2 color #b87e79
> volume #2 color #b88079
> volume #2 color #b88089
> volume #2 color #b78089
> volume #2 color #c58089
> volume #2 color #c78089
> volume #2 level 0.1783
> volume #2 level 0.15
> lighting simple
> volume #2 color #c7808980
> show #!1 models
> color #2 #e87e7980 models
> color #2 #ff7e7980 models
> color #2 #ac7e7980 models
> color #2 #b57e7980 models
> color #2 #b07e7980 models
> color #2 #a37e7980 models
> color #2 #a97e7980 models
> color #2 #a87e7980 models
> color #2 #b47e7980 models
> fitmap #1 inMap #2
Fit molecule 8AAG.pdb (#1) to map run_class001.mrc (#2) using 14180 atoms
average map value = 0.0001813, steps = 48
shifted from previous position = 24
rotated from previous position = 7.43 degrees
atoms outside contour = 14180, contour level = 0.15
Position of 8AAG.pdb (#1) relative to run_class001.mrc (#2) coordinates:
Matrix rotation and translation
-0.94648074 0.17020315 -0.27423547 347.66223131
-0.17745662 0.43529273 0.88262642 73.27269381
0.26959850 0.88405380 -0.38179251 133.98483955
Axis 0.00221141 -0.84254636 -0.53861930
Axis point 167.79967088 0.00000000 77.80837721
Rotation angle (degrees) 161.17175210
Shift along axis -133.13363688
> show #4 models
> hide #4 models
> view orient
> color #2 #c67e7980 models
> select #2
2 models selected
Drag select of 2 run_class001.mrc
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.89448,0.44453,-0.047957,255.43,0.10396,0.3111,0.94467,137.76,0.43486,0.84,-0.32449,85.862
> view matrix models
> #2,-0.89448,0.44453,-0.047957,176.99,0.10396,0.3111,0.94467,181.69,0.43486,0.84,-0.32449,152.51
> view matrix models
> #2,-0.89448,0.44453,-0.047957,112.78,0.10396,0.3111,0.94467,129.44,0.43486,0.84,-0.32449,152.04
> fitmap #1 inMap #2
Fit molecule 8AAG.pdb (#1) to map run_class001.mrc (#2) using 14180 atoms
average map value = 0.3225, steps = 60
shifted from previous position = 10.9
rotated from previous position = 7.41 degrees
atoms outside contour = 1402, contour level = 0.15
Position of 8AAG.pdb (#1) relative to run_class001.mrc (#2) coordinates:
Matrix rotation and translation
-0.95652266 0.22096395 -0.19036635 109.20572683
-0.10710874 0.34096690 0.93395358 -151.57449603
0.27127869 0.91373766 -0.30247539 -102.61478577
Axis -0.03567264 -0.81461013 -0.57891088
Axis point 57.83283644 0.00000000 12.81359908
Rotation angle (degrees) 163.53955372
Shift along axis 178.98327869
> view orient
> view matrix models
> #2,-0.89448,0.44453,-0.047957,112.83,0.10396,0.3111,0.94467,129.31,0.43486,0.84,-0.32449,152.27
> ui mousemode right select
> select clear
> color #2 #ff2600ff models
> color #2 #b02600ff models
> color #2 #b04700ff models
> color #2 #b37020ff models
> color #2 indian red
[Repeated 1 time(s)]
> volume #2 level 0.147
> volume #2 level 0.15
> volume #2 color #af5c5c
> lighting soft
> volume #2 color #a65c5c
> volume #2 color #aa5c5c
> lighting simple
> volume #2 color #aa5c5c80
> save /Users/zhenhou/Desktop/image7.png supersample 3
> volume #2 level 0.23
> save /Users/zhenhou/Desktop/image8.png supersample 3
> hide #!1 models
> show #!5.2.1 models
> show #!5.2.2 models
> view orient
> lighting soft
set axis size 32.69997
32.69997
['.arrow', '0', '0', '0', '32.69997', '0', '0', '2.179998', '8.719992']
set axis size 32.69994
32.69994
['.arrow', '0', '0', '0', '32.69994', '0', '0', '2.179996', '8.719984']
set axis size 32.69991
32.69991
['.arrow', '0', '0', '0', '32.69991', '0', '0', '2.179994', '8.719976']
set axis size 32.69988
32.69988
['.arrow', '0', '0', '0', '32.69988', '0', '0', '2.179992', '8.719968']
set axis size 32.69985
32.69985
['.arrow', '0', '0', '0', '32.69985', '0', '0', '2.1799899999999997',
'8.719959999999999']
set axis size 32.69982
32.69982
['.arrow', '0', '0', '0', '32.69982', '0', '0', '2.1799880000000003',
'8.719952000000001']
> lighting simple
> artiax hide markers
> artiax hide axes
[Repeated 1 time(s)]
> artiax hide markers
> artiax particles #5.2.1 color 100,49,47,100
> artiax particles #5.2.1 color 67,36,36,100
> lighting soft
> hide #!5.2.2 models
> save /Users/zhenhou/Desktop/image9.png supersample 3
> hide #!5.2.1 models
> show #!5.2.2 models
> save /Users/zhenhou/Desktop/image10.png supersample 3
> show #!5.2.1 models
> hide #!5.2.1 models
> lighting simple
> hide #!5.2.2 models
> view orient
> volume #2 color #ac5c5c80
> volume #2 color #b26c5c80
> lighting soft
> volume #2 color #b26c5c80
> lighting simple
> volume #2 color #b26c5c
[Repeated 1 time(s)]
> volume #2 color #b2585c
> volume #2 color #a6595c
> volume #2 color #a65957
> volume #2 color #be7f86
> volume #2 color #be7f860d
> volume #2 color #be7f8680
> show #!1 models
> volume #2 level 0.15
> save /Users/zhenhou/Desktop/image11.png supersample 3
> volume #2 level 0.23
> save /Users/zhenhou/Desktop/image12.png supersample 3
> hide #!1 models
> show #!5.2.1 models
> show #!5.2.2 models
> view orient
> artiax particles #5.2.1 color 67,36,36,100
> artiax particles #5.2.1 color 69,46,44,100
> artiax particles #5.2.1 color 75,50,53,100
> lighting soft
> save /Users/zhenhou/Desktop/image13.png supersample 3
> hide #!5.2.2 models
> save /Users/zhenhou/Desktop/image14.png supersample 3
> artiax particles #5.2.1 color 75,50,53,100
> artiax particles #5.2.1 color 71,51,41,100
[Repeated 2 time(s)]
> artiax particles #5.2.1 color 72,52,42,100
> undo
[Repeated 1 time(s)]
> view orient
[Repeated 1 time(s)]
> artiax particles #5.2.1 color 72,52,42,100
> artiax particles #5.2.1 color 74,50,52,100
> hide #!5.2.1 models
> hide #!5.2.2 models
> view orient
[Repeated 1 time(s)]
> show #!2 models
> view orient
> color #2 #bebb8680 models
> color #2 #bebb8a80 models
> color #2 #93bb8a80 models
> color #2 #99bb8a80 models
> lighting soft
> color #2 #99bb8aff models
> color #2 #97bb8aff models
> color #2 #97bb80ff models
> color #2 #97bb8dff models
> color #2 #97bb8bff models
> color #2 #97bb80ff models
> color #2 #97bb8aff models
> color #2 #97b88aff models
> color #2 #97b58aff models
> open /Users/zhenhou/Desktop/Nucleosome/class2_py/run_class001.mrc
Opened run_class001.mrc as #3, grid size 96,96,96, pixel 4.36, shown at level
0.0796, step 1, values float32
> volume #3 color #0096ff
> volume #3 color #009eff
> volume #3 color #009cff
> volume #3 color #009ca9
> volume #3 color #5d9ca9
> view orient
> volume #3 level 0.1616
> volume #3 level 0.1881
> lighting simple
> volume #3 color #5d9ca980
> open
> /Users/zhenhou/Desktop/Nucleosome/template_sirt_final/lamellae_014_1_bin6.em
> format motl
Summary of feedback from opening
/Users/zhenhou/Desktop/Nucleosome/template_sirt_final/lamellae_014_1_bin6.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list lamellae_014_1_bin6.em with 361 particles.
> view orient
> artiax hide axes
Opened lamellae_014_1_bin6.rec as #5.1.1, grid size 166,212,33, pixel
13.1,13.1,13.1, shown at level 1.74, step 1, values float32
> artiax tomo #5.1.1 sliceDirection 0,0,1
> artiax view xy
> volume #5.1.1 region 0,0,16,165,211,16 step 1 showOutlineBox true imageMode
> "full region"
> volume #5.1.1 level -4.709,0 level 1.263,0.8441 level 4.761,1
> open
> /Users/zhenhou/Desktop/Nucleosome/template_sirt_final/lamellae_014_1_bin6.em
> format motl
Summary of feedback from opening
/Users/zhenhou/Desktop/Nucleosome/template_sirt_final/lamellae_014_1_bin6.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list lamellae_014_1_bin6.em with 361 particles.
set axis size 196.2
196.2
['.arrow', '0', '0', '0', '196.2', '0', '0', '13.08', '52.32']
> artiax particles #5.2.3 originScaleFactor 13.08
> artiax view xy
> artiax hide axes
> artiax particles #5.2.3 radius 19.1019
> open /Users/zhenhou/Desktop/Nucleosome/STA/postprocess_masked.mrc
Opened postprocess_masked.mrc as #6, grid size 96,96,96, pixel 4.36, shown at
level 0.00656, step 1, values float32
> artiax attach #6 toParticleList #5.2.3
Opened postprocess_masked.mrc as #5.2.3.1.1, grid size 96,96,96, pixel 4.36,
shown at level 0.00656, step 1, values float32
> volume #5.2.3.1.1 capFaces false
> artiax show #5.2.3 surfaces
> artiax particles #5.2.3 surfaceLevel 0.29067
> artiax show markers
set axis size 196.20003
196.20003
['.arrow', '0', '0', '0', '196.20003', '0', '0', '13.080002', '52.320008']
set axis size 196.20006
196.20006
['.arrow', '0', '0', '0', '196.20006', '0', '0', '13.080004', '52.320016']
set axis size 196.20009
196.20009
['.arrow', '0', '0', '0', '196.20009', '0', '0', '13.080006', '52.320024']
set axis size 196.20012
196.20012
['.arrow', '0', '0', '0', '196.20012', '0', '0', '13.080008', '52.320032']
set axis size 196.20009
196.20009
['.arrow', '0', '0', '0', '196.20009', '0', '0', '13.080006', '52.320024']
set axis size 196.20006
196.20006
['.arrow', '0', '0', '0', '196.20006', '0', '0', '13.080004', '52.320016']
set axis size 196.20003
196.20003
['.arrow', '0', '0', '0', '196.20003', '0', '0', '13.080002', '52.320008']
set axis size 196.2
196.2
['.arrow', '0', '0', '0', '196.2', '0', '0', '13.08', '52.32']
set axis size 196.19997
196.19997
['.arrow', '0', '0', '0', '196.19997', '0', '0', '13.079998', '52.319992']
> artiax particles #5.2.3 radius 37.34373
set axis size 196.19994
196.19994
['.arrow', '0', '0', '0', '196.19994', '0', '0', '13.079996', '52.319984']
set axis size 196.19991
196.19991
['.arrow', '0', '0', '0', '196.19991', '0', '0', '13.079994', '52.319976']
set axis size 196.19994
196.19994
['.arrow', '0', '0', '0', '196.19994', '0', '0', '13.079996', '52.319984']
set axis size 196.19997
196.19997
['.arrow', '0', '0', '0', '196.19997', '0', '0', '13.079998', '52.319992']
set axis size 196.19994
196.19994
['.arrow', '0', '0', '0', '196.19994', '0', '0', '13.079996', '52.319984']
set axis size 196.19991
196.19991
['.arrow', '0', '0', '0', '196.19991', '0', '0', '13.079994', '52.319976']
set axis size 196.19988
196.19988
['.arrow', '0', '0', '0', '196.19988', '0', '0', '13.079992', '52.319968']
> volume #5.1.1 region 0,0,29,165,211,29
> ui mousemode right select
> select #5.2.3.3/M:74@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right rotate
> ui mousemode right "rotate selected particles"
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:139@M
1 atom, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:220@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right "translate selected particles"
> artiax hide surfaces
> artiax particles #5.2.3 radius 28.98289
> ui mousemode right select
> select #5.1.1
3 models selected
> select #5.2.3.3/M:109@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui tool show "Side View"
> view orient
> hide #!5.2.3 models
> show #!5.2.3 models
> ui mousemode right select
> select #5.2.3.3/M:355@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> ui mousemode right select
> select #5.2.3.3/M:353@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> ui mousemode right select
> select #5.1.1
3 models selected
> select #5.1.1
3 models selected
> select #5.1.1
3 models selected
> select #5.2.3.3/M:327@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
[Repeated 1 time(s)]
> volume #5.1.1 level -3.397,0 level 1.263,0.8441 level 4.761,1
> volume #5.1.1 level -3.397,0 level 1.319,0.7826 level 4.761,1
> ui mousemode right select
> select #5.2.3.3/M:215@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:346@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:117@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:199@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:230@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> ui mousemode right select
> select #5.2.3.3/M:359@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:212@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> ui mousemode right select
> select #5.2.3.3/M:84@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:61@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> ui mousemode right select
> select #5.2.3.3/M:48@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:304@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.1.1
3 models selected
> select #5.1.1
3 models selected
> select #5.2.3.3/M:290@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:195@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:120@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:176@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:317@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> ui mousemode right select
> select #5.2.3.3/M:330@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:329@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> artiax particles #5.2.3 radius 16.82167
> view orient
> artiax particles #5.2.3 radius 25.94259
> ui mousemode right select
> select #5.2.3.3/M:350@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> ui mousemode right select
> select #5.2.3.3/M:86@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> artiax show surfaces
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:106@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:158@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> view orient
[Repeated 1 time(s)]
> ui mousemode right select
> select #5.2.3.3/M:205@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> artiax hide surfaces
> view orient
> ui mousemode right select
> select #5.2.3.3/M:48@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> artiax show surfaces
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.1.1
3 models selected
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:190@M
1 atom, 1 residue, 1 model selected
> artiax hide surfaces
> artiax show surfaces
> ui mousemode right "rotate selected particles"
> view orient
> ui mousemode right select
> select #5.1.1
3 models selected
> select #5.2.3.3/M:138@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right "translate selected particles"
> artiax hide surfaces
> artiax show surfaces
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:100@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:123@M
1 atom, 1 residue, 1 model selected
> view orient
> artiax hide surfaces
> ui mousemode right "translate selected particles"
> view orient
> artiax hide markers
> artiax show markers
> artiax hide markers
[Repeated 1 time(s)]
> artiax show markers
> artiax hide markers
> artiax show markers
> ui mousemode right select
> select #5.2.3.3/M:111@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:107@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:132@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> artiax hide markers
[Repeated 2 time(s)]
> artiax show markers
> ui mousemode right select
> select #5.2.3.3/M:127@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> artiax hide markers
> artiax show markers
> artiax hide markers
> artiax show markers
> artiax hide markers
> artiax show markers
> ui mousemode right select
> select #5.2.3.3/M:124@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:343@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:52@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> artiax hide markers
[Repeated 1 time(s)]
> artiax show markers
> view orient
> ui mousemode right select
> select #5.2.3.3/M:348@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> ui mousemode right select
> select #5.2.3.3/M:334@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> artiax show surfaces
> ui mousemode right "rotate selected particles"
> view orient
> ui mousemode right select
> select #5.2.3.3/M:124@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:113@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:115@M
1 atom, 1 residue, 1 model selected
> select clear
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:115@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:150@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> view orient
> ui mousemode right select
> view orient
> select #5.2.3.3/M:124@M
1 atom, 1 residue, 1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:104@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:101@M
1 atom, 1 residue, 1 model selected
> select clear
> select #5.2.3.3/M:101@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:174@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:185@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:177@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:168@M
1 atom, 1 residue, 1 model selected
fine
> ui mousemode right select
> select #5.2.3.3/M:167@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:252@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:270@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:240@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> view orient
> ui mousemode right select
> select #5.2.3.3/M:124@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> artiax hide surfaces
> artiax hide markers
> artiax show markers
> artiax show surfaces
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:14@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:10@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:77@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> artiax hide surfaces
> ui mousemode right select
> select #5.2.3.3/M:155@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> artiax show surfaces
> ui mousemode right "rotate selected particles"
> artiax hide surfaces
> artiax hide markers
[Repeated 1 time(s)]
> artiax show markers
> artiax hide markers
> artiax show markers
> ui mousemode right select
> select #5.2.3.3/M:146@M
1 atom, 1 residue, 1 model selected
fine
> artiax hide markers
> artiax show markers
> select #5.2.3.3/M:356@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> artiax show surfaces
> ui mousemode right "rotate selected particles"
> artiax hide markers
> artiax show markers
> artiax hide surfaces
> ui mousemode right select
> select #5.2.3.3/M:357@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> artiax show surfaces
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:109@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:212@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:85@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.1.1
3 models selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:73@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:97@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> view orient
> ui mousemode right select
> select #5.2.3.3/M:176@M
1 atom, 1 residue, 1 model selected
> select #5.2.3.3/M:67@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:18@M
1 atom, 1 residue, 1 model selected
> view orient
> ui mousemode right "rotate selected particles"
fine
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:6@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> artiax hide markers
> artiax hide surfaces
> artiax show markers
> artiax hide markers
> artiax show markers
> artiax hide markers
> artiax show markers
> artiax hide markers
> artiax show markers
> ui mousemode right select
> select #5.2.3.3/M:354@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> artiax show surfaces
> ui mousemode right "rotate selected particles"
> view orient
> artiax hide surfaces
> artiax hide markers
> artiax show markers
> ui mousemode right select
> select #5.2.3.3/M:358@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> artiax show surfaces
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:72@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.1.1
3 models selected
> select #5.2.3.3/M:346@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> artiax hide surfaces
> ui mousemode right select
> select #5.2.3.3/M:339@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> artiax show surfaces
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:328@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> view orient
[Repeated 1 time(s)]
> ui mousemode right select
> select #5.2.3.3/M:193@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> view orient
> artiax hide surfaces
> artiax show surfaces
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:80@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:54@M
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:54@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:63@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:58@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:51@M
1 atom, 1 residue, 1 model selected
fine
> ui mousemode right select
> select #5.2.3.3/M:83@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:50@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:44@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:41@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:11@M
1 atom, 1 residue, 1 model selected
fine
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:19@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:21@M
1 atom, 1 residue, 1 model selected
fine
> ui mousemode right select
> select #5.2.3.3/M:7@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:40@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:254@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:265@M
1 atom, 1 residue, 1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:273@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:269@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:164@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:56@M
1 atom, 1 residue, 1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:88@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:85@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> view orient
> ui mousemode right select
> select #5.2.3.3/M:151@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:84@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:98@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:49@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> artiax hide surfaces
> artiax hide markers
> artiax show surfaces
> artiax hide surfaces
> artiax show surfaces
> artiax show markers
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:118@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:58@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:355@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:353@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:122@M
1 atom, 1 residue, 1 model selected
fine
> select #5.1.1
3 models selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:327@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> view orient
> open /Users/zhenhou/Desktop/Nucleosome/manuscript/command_list.cxc
> graphics selection color dodger blue width 4
> graphics selection color dark violet width 4
> movie record
> volume #1.1.2 planes z,75,0
Failed opening file
/Users/zhenhou/Desktop/Nucleosome/manuscript/command_list.cxc:
No volumes specified
> open /Users/zhenhou/Desktop/Nucleosome/manuscript/command_list.cxc
> graphics selection color dodger blue width 4
> graphics selection color dark violet width 4
> movie record
Failed opening file
/Users/zhenhou/Desktop/Nucleosome/manuscript/command_list.cxc:
Already recording a movie
> open /Users/zhenhou/Desktop/Nucleosome/manuscript/command_list.cxc
> graphics selection color dodger blue width 4
> graphics selection color dark violet width 4
> movie record
Already recording a movie
> movie stop
> artiax particles #5.2.3 radius 0.1
> artiax particles #5.2.3 surfaceLevel 0.21558
> artiax particles #5.2.3 surfaceLevel 0.17514
> artiax particles #5.2.3 color 100,80,60,100
> lighting soft
> view orient
> lighting simple
> artiax particles #5.2.3 radius 33.54335
> ui mousemode right select
> select #5.2.3.3/M:169@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:184@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:189@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:52@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:98@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:57@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:111@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:200@M
1 atom, 1 residue, 1 model selected
> select #5.2.3.3/M:161@M
1 atom, 1 residue, 1 model selected
> select #5.2.3.3/M:179@M
1 atom, 1 residue, 1 model selected
fine
> ui mousemode right select
> select #5.2.3.3/M:203@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:187@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:119@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:339@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:196@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select clear
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:196@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:161@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:192@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> view orient
> artiax hide surfaces
> artiax hide markers
> view orient
> artiax show surfaces
> ui mousemode right select
> artiax show markers
> select #5.2.3.3/M:155@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:213@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:200@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:360@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right "translate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:212@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> view orient
> ui mousemode right select
> select #5.2.3.3/M:170@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:166@M
1 atom, 1 residue, 1 model selected
fine
> view orient
> select #5.2.3.3/M:182@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.2
1 model selected
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:235@M
1 atom, 1 residue, 1 model selected
fine
> select #5.2.3.3/M:238@M
1 atom, 1 residue, 1 model selected
fine
> view orient
> select #5.2.3.3/M:190@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.2
1 model selected
> select #5.2.3.3/M:289@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> volume #5.2.3.1.1 level 0.1818
> artiax hide surfaces
> artiax hide markers
[Repeated 1 time(s)]
> artiax show markers
> artiax hide markers
> view orient
> artiax show markers
> ui mousemode right select
> select #5.2.3.3/M:298@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected particles"
> artiax show surfaces
> ui mousemode right "rotate selected particles"
> ui mousemode right "translate selected particles"
> ui mousemode right "rotate selected particles"
> ui mousemode right select
> select #5.2.3.3/M:298@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "rotate selected particles"
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag
self._rotate(axis, angle)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate
rotate_instances(saxis, angle, self._collections, self._masks)
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds
spos = self.child_positions.masked(mask)
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked
p = Places(place_array=self.array()[mask])
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 7459.141.1
OS Loader Version: 7459.141.1
Software:
System Software Overview:
System Version: macOS 12.5.1 (21G83)
Kernel Version: Darwin 21.6.0
Time since boot: 29 days 3:20
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-ArtiaX: 0.3
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
geomdl: 5.3.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
pandas: 1.5.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
starfile: 0.4.11
superqt: 0.4.1
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ArtiaX: arrays used as indices must be of integer (or boolean) type |
comment:2 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|
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