The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/helical_rise_multiply.cxs"
Opened 4rise_10z.mrc as #1, grid size 288,288,288, pixel 0.83, shown at level
0.00993, step 1, values float32
Opened 4rise_50z.mrc as #2, grid size 288,288,288, pixel 0.83, shown at level
0.00993, step 1, values float32
Opened 2rise_10z.mrc as #3, grid size 288,288,288, pixel 0.83, shown at level
0.00496, step 1, values float32
Opened 2rise_50z.mrc as #4, grid size 288,288,288, pixel 0.83, shown at level
0.00315, step 1, values float32
Opened postprocess_masked.mrc as #5, grid size 288,288,288, pixel 0.83, shown
at level 0.00325, step 1, values float32
Opened postprocess_masked.mrc as #6, grid size 288,288,288, pixel 0.83, shown
at level 0.00268, step 1, values float32
Log from Tue May 21 15:52:22 2024UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:/PTB129_Tracer/mutiply_helical rise/real_FDDNP/rise_compare.cxs"
> To Restore session:
>
> * update Atomic bundle to version 1.49.1 or newer (have 1.41.5)
>
Unable to restore session: need to update bundle
> open "D:/PTB129_Tracer/mutiply_helical rise/real_FDDNP/rise_compare.cxs"
> To Restore session:
>
> * update Atomic bundle to version 1.49.1 or newer (have 1.41.5)
>
Unable to restore session: need to update bundle
> open "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/4rise/job117/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #1, grid size 288,288,288, pixel 0.83, shown
at level 0.000553, step 2, values float32
> open "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/4rise/job115/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #2, grid size 288,288,288, pixel 0.83, shown
at level 0.0034, step 2, values float32
> volume #1 step 1
> volume #2 step 1
> volume #1 level 0.006669
> volume #2 level 0.01094
> hide #!2 models
> ui tool show "Side View"
> open "D:/PTB129_Tracer/mutiply_helical rise/real_FDDNP/rise_compare.cxs"
> To Restore session:
>
> * update Atomic bundle to version 1.49.1 or newer (have 1.41.5)
>
Unable to restore session: need to update bundle
> volume #1 level 0.005302
> volume #1 level 0.005
> show #!2 models
> hide #!1 models
> volume #2 level 0.005
> volume #2 level 0.009271
> volume #2 level 0.008769
> volume #2 level 0.006507
> volume #2 level 0.01317
> rename #1 4rise_10z.mrc
> rename #2 4rise_50z.mrc
> open "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/2rise/job094/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #3, grid size 288,288,288, pixel 0.83, shown
at level 0.000603, step 2, values float32
> open "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/2rise/job105/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #4, grid size 288,288,288, pixel 0.83, shown
at level 0.00315, step 2, values float32
> volume #3 step 1
> volume #4 step 1
> hide #!2 models
> volume #3 level 0.004373
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!4 models
> volume #3 level 0.005482
> rename #3 2rise_10z.mrc
> rename #4 2rise_50z.mrc
> open "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/3rise/job090/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #5, grid size 288,288,288, pixel 0.83, shown
at level 0.00056, step 2, values float32
> open "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/3rise/job103/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #6, grid size 288,288,288, pixel 0.83, shown
at level 0.00268, step 2, values float32
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> volume #5 step 1
> volume #6 step 1
> volume #5 level 0.0005602
> volume #5 level 0.0004992
> volume #5 level 0.001659
> volume #5 level 0.001964
> volume #5 level 0.002148
> volume #5 level 0.00288
> volume #5 level 0.002941
> volume #5 level 0.003002
> volume #5 level 0.003063
> volume #5 level 0.003124
> volume #5 level 0.003247
> volume #5 level 0.003308
> volume #5 level 0.003369
> volume #5 level 0.00343
> volume #5 level 0.003491
> volume #5 level 0.003552
> volume #5 level 0.003613
> volume #5 level 0.002941
> show #!3 models
> hide #!5 models
> volume #3 level 0.004669
> volume #3 level 0.004964
> hide #!3 models
> show #!5 models
> volume #5 level 0.003247
> hide #!5 models
> show #!2 models
> show #!1 models
> hide #!1 models
> set bgColor white
> set bgColor #ffffff00
> color #2 #3791d5ff models
> color #2 #5500ffff models
> color #2 #3385ffff models
> color #2 #5555ffff models
> transparency #2.1 50
> volume #2 level 0.01161
> volume #2 level 0.009926
> save "D:/PTB129_Tracer/mutiply_helical rise/real_FDDNP/4rise/side_view.png"
> width 2000 height 1402 supersample 3 transparentBackground true
> show #!1 models
> hide #!2 models
> color #1 #5555ffff models
> select add #1
4 models selected
> transparency sel 50
> select subtract #1
Nothing selected
> volume #1 level 0.00993
> save "D:/PTB129_Tracer/mutiply_helical rise/real_FDDNP/4rise/top_view.png"
> width 2000 height 1402 supersample 3 transparentBackground true
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/helical_rise_multiply.cxs"
——— End of log from Tue May 21 15:52:22 2024 ———
opened ChimeraX session
> hide #!1 models
> open "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/1rise/job072/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #7, grid size 288,288,288, pixel 0.83, shown
at level 0.000553, step 2, values float32
> open "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/1rise/job107/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #8, grid size 288,288,288, pixel 0.83, shown
at level 0.00313, step 2, values float32
> hide #!7 models
> rename #8 1rise_50z.mrc
> rename #7 1rise_10z.mrc
> volume #8 step 1
> volume #7 step 1
> volume #8 level 0.007868
> volume #8 level 0.007
> volume #8 level 0.008
> hide #!8 models
> show #!7 models
> volume #7 level 0.0008
> volume #7 level 0.008
> open "D:/PTB129_Tracer/mutiply_helical rise/FDDNP/FDDNP_1rise_favor90.pdb"
Chain information for FDDNP_1rise_favor90.pdb #9
---
Chain | Description
A B C D E F G H I J K L | No description available
> style stick
Changed 3050 atom styles
> hide #!7 models
> show #!7 models
> color #9 #adadadff
> hide #!7 models
> hide #9 models
> show #!8 models
> select #8
4 models selected
> ui tool show "Segment Map"
Segmenting 1rise_50z.mrc, density threshold 0.008000
Showing 176 region surfaces
1919 watershed regions, grouped to 176 regions
Showing 1rise_50z.seg - 176 regions, 176 surfaces
> ui tool show "Side View"
> select #10.2
1 model selected
Ungrouped to 13 regions
Ungrouped to 28 regions
Ungrouped to 31 regions
Ungrouped to 8 regions
Ungrouped to 0 regions
> select #10.233
1 model selected
> select add #10.223
2 models selected
> select add #10.220
3 models selected
> select add #10.231
4 models selected
> select add #10.186
5 models selected
> select add #10.209
6 models selected
Grouped 6 regions
> select #10.183
1 model selected
> select #10.184
1 model selected
> select add #10.25
2 models selected
> select #10.25
1 model selected
> select add #10.46
2 models selected
> select add #10.32
3 models selected
> select add #10.21
4 models selected
Ungrouped to 17 regions
Ungrouped to 40 regions
Ungrouped to 19 regions
Ungrouped to 6 regions
Ungrouped to 0 regions
> select #10.183
1 model selected
> select add #10.184
2 models selected
> select add #10.252
3 models selected
> select add #10.185
4 models selected
> select add #10.255
5 models selected
> select add #10.274
6 models selected
> select add #10.220
7 models selected
> select add #10.266
8 models selected
Grouped 8 regions
> select #10.209
1 model selected
> select add #10.183
2 models selected
Grouped 2 regions
> select #10.85
1 model selected
> select add #10.44
2 models selected
> select add #10.24
3 models selected
> select add #10.41
4 models selected
> select add #10.1
5 models selected
> select subtract #10.1
4 models selected
> select add #10.1
5 models selected
Ungrouped to 25 regions
Ungrouped to 47 regions
Ungrouped to 59 regions
Ungrouped to 22 regions
Ungrouped to 0 regions
> select #10.183
1 model selected
> select add #10.345
2 models selected
> select add #10.371
3 models selected
> select add #10.209
4 models selected
> select add #10.360
5 models selected
> select add #10.357
6 models selected
> select add #10.274
7 models selected
Grouped 7 regions
> select #10.368
1 model selected
> select add #10.286
2 models selected
> select add #10.365
3 models selected
> select add #10.338
4 models selected
> select add #10.185
5 models selected
> select add #10.282
6 models selected
> select add #10.183
7 models selected
Grouped 7 regions
> select #10.335
1 model selected
> select add #10.316
2 models selected
> select add #10.183
3 models selected
> select #10.335
1 model selected
> select add #10.183
2 models selected
Grouped 2 regions
> select #10.12
1 model selected
Ungrouped to 6 regions
Ungrouped to 18 regions
Ungrouped to 30 regions
Ungrouped to 4 regions
Ungrouped to 0 regions
Ungrouped to 206 regions
> select #10.378
1 model selected
> select add #10.387
2 models selected
> select add #10.273
3 models selected
> select add #10.185
4 models selected
Grouped 4 regions
> select add #10.380
2 models selected
> select #10.455
1 model selected
> select add #10.510
2 models selected
> select add #10.508
3 models selected
> select add #10.402
4 models selected
> select add #10.400
5 models selected
> select add #10.408
6 models selected
> select add #10.407
7 models selected
> select add #10.572
8 models selected
Ungrouped to 19 regions
Ungrouped to 30 regions
Ungrouped to 8 regions
Ungrouped to 0 regions
Ungrouped to 474 regions
> select #10.380
1 model selected
> select #10.3
1 model selected
> select add #10.380
2 models selected
> select add #10.83
3 models selected
> select add #10.18
4 models selected
> select add #10.87
5 models selected
> select add #10.73
6 models selected
> select add #10.78
7 models selected
Grouped 7 regions
> select #10.15
1 model selected
> select add #10.50
2 models selected
> select add #10.29
3 models selected
> select add #10.837
4 models selected
> select add #10.817
5 models selected
Drag select of 899, 10 of 760 triangles, 2428, 9 of 1468 triangles, 893, 12 of
588 triangles, 2427, 15 of 1268 triangles, 8 1rise_50z.mrc
> select #10.50
1 model selected
> select add #10.15
2 models selected
> select add #10.3
3 models selected
Grouped 3 regions
> select #10.29
1 model selected
> select #10.837
1 model selected
> select add #10.817
2 models selected
> select add #10.1000
3 models selected
> select add #10.1023
4 models selected
> select add #10.747
5 models selected
> select add #10.845
6 models selected
> select add #10.847
7 models selected
> select add #10.768
8 models selected
Ungrouped to 27 regions
Ungrouped to 8 regions
Ungrouped to 0 regions
Ungrouped to 954 regions
> select #10.3
1 model selected
> select #10.3
1 model selected
> select #10.3
1 model selected
> select add #10.29
2 models selected
> select add #10.68
3 models selected
> select add #10.48
4 models selected
> select add #10.45
5 models selected
> select add #10.56
6 models selected
> select add #10.65
7 models selected
> select add #10.52
8 models selected
> select add #10.64
9 models selected
> select add #10.15
10 models selected
> select subtract #10.64
9 models selected
> select add #10.61
10 models selected
> select add #10.1333
11 models selected
> select add #10.1229
12 models selected
> select add #10.1061
13 models selected
Grouped 13 regions
> select #10.1559
1 model selected
> select add #10.1211
2 models selected
> select add #10.3
3 models selected
Grouped 3 regions
> select add #10.183
2 models selected
Grouped 2 regions
Opened 1rise_50z_imasked as #11, grid size 288,288,288, pixel 0.83, shown at
step 1, values float32
> close #11
> close #10
> close #12-1514
> hide #8.1 models
> show #8.1 models
> hide #!8 models
> show #!8 models
Segmenting 1rise_50z.mrc, density threshold 0.008000
Showing 176 region surfaces
1919 watershed regions, grouped to 176 regions
Showing 1rise_50z.seg - 176 regions, 176 surfaces
> select #10.2
1 model selected
Ungrouped to 13 regions
Ungrouped to 28 regions
Ungrouped to 31 regions
Ungrouped to 8 regions
Ungrouped to 0 regions
> select #10.233
1 model selected
> select add #10.226
2 models selected
> select add #10.180
3 models selected
> select add #10.227
4 models selected
> select add #10.232
5 models selected
> select add #10.216
6 models selected
> select add #10.220
7 models selected
> select add #10.25
8 models selected
> select subtract #10.25
7 models selected
Grouped 7 regions
> select #10.40
1 model selected
> select #10.25
1 model selected
> select add #10.46
2 models selected
> select add #10.32
3 models selected
> select add #10.21
4 models selected
> select add #10.85
5 models selected
> select add #10.44
6 models selected
Ungrouped to 22 regions
Ungrouped to 47 regions
Ungrouped to 27 regions
Ungrouped to 10 regions
Ungrouped to 0 regions
> select #10.259
1 model selected
> select add #10.285
2 models selected
> select add #10.284
3 models selected
> select add #10.272
4 models selected
> select add #10.223
5 models selected
> select add #10.266
6 models selected
> select add #10.288
7 models selected
> select add #10.238
8 models selected
> select add #10.208
9 models selected
> select add #10.179
10 models selected
Grouped 10 regions
> select #10.24
1 model selected
> select add #10.41
2 models selected
> select add #10.1
3 models selected
Ungrouped to 20 regions
Ungrouped to 40 regions
Ungrouped to 51 regions
Ungrouped to 18 regions
Ungrouped to 0 regions
> select #10.272
1 model selected
> select #10.179
1 model selected
> select add #10.272
2 models selected
> select add #10.294
3 models selected
> select add #10.369
4 models selected
> select add #10.341
5 models selected
> select add #10.285
6 models selected
> select add #10.230
7 models selected
> select add #10.351
8 models selected
> select add #10.336
9 models selected
> select add #10.357
10 models selected
> select add #10.363
11 models selected
> select add #10.339
12 models selected
Grouped 12 regions
> select #10.10
1 model selected
> select add #10.19
2 models selected
Ungrouped to 15 regions
Ungrouped to 31 regions
Ungrouped to 33 regions
Ungrouped to 10 regions
Ungrouped to 0 regions
> select #10.351
1 model selected
> select add #10.10
2 models selected
> select add #10.413
3 models selected
> select add #10.395
4 models selected
> select add #10.376
5 models selected
> select add #10.332
6 models selected
Grouped 6 regions
> select #10.405
1 model selected
> select #10.18
1 model selected
> select add #10.83
2 models selected
> select add #10.20
3 models selected
> select add #10.87
4 models selected
Ungrouped to 12 regions
Ungrouped to 23 regions
Ungrouped to 30 regions
Ungrouped to 6 regions
Ungrouped to 0 regions
Ungrouped to 185 regions
> select #10.10
1 model selected
Drag select of 2734, 13 of 2444 triangles, 460, 9 of 472 triangles, 2378, 6 of
3328 triangles, 2745, 17 of 2484 triangles, 8 1rise_50z.mrc
> select add #10.444
8 models selected
> select clear
> select #10.405
1 model selected
> select add #10.10
2 models selected
> select add #10.444
3 models selected
> select add #10.433
4 models selected
> select add #10.442
5 models selected
> select add #10.437
6 models selected
> select add #10.394
7 models selected
> select add #10.447
8 models selected
> select add #10.388
9 models selected
Grouped 9 regions
> select #10.600
1 model selected
> select add #10.604
2 models selected
> select add #10.590
3 models selected
> select add #10.591
4 models selected
> select add #10.573
5 models selected
> select add #10.572
6 models selected
> select add #10.477
7 models selected
> select add #10.460
8 models selected
Ungrouped to 20 regions
Ungrouped to 28 regions
Ungrouped to 8 regions
Ungrouped to 0 regions
Ungrouped to 452 regions
> select #10.3
1 model selected
> select #10.3
1 model selected
> select add #10.90
2 models selected
> select add #10.10
3 models selected
> select add #10.39
4 models selected
> select add #10.75
5 models selected
> select add #10.80
6 models selected
> select add #10.6
7 models selected
> select add #10.63
8 models selected
Grouped 8 regions
> select #10.779
1 model selected
> select add #10.123
2 models selected
> select add #10.635
3 models selected
> select add #10.630
4 models selected
Ungrouped to 13 regions
Ungrouped to 2 regions
Ungrouped to 0 regions
Ungrouped to 934 regions
> select #10.50
1 model selected
> select #10.50
1 model selected
> select add #10.39
2 models selected
> select add #10.10
3 models selected
> select add #10.51
4 models selected
> select add #10.30
5 models selected
> select add #10.3
6 models selected
Grouped 6 regions
> select #10.179
1 model selected
> select add #10.3
2 models selected
Grouped 2 regions
Opened 1rise_50z_imasked as #11, grid size 288,288,288, pixel 0.83, shown at
step 1, values float32
Opened 1rise_50z_imasked as #12, grid size 288,288,288, pixel 0.83, shown at
step 1, values float32
> hide #!10 models
> hide #!8 models
> hide #8.1 models
> color #11 #aaff00ff models
> color #12 #ffaa7fff models
> show #9 models
> color #9 #aaff00ff
> color #9,11-12 lime
> color #12 #ffaa7fff models
> color #11 #aaff00ff models
> select add #10
1514 models selected
> select subtract #10
Nothing selected
> select add #11
2 models selected
> transparency sel 50
> transparency sel 90
> transparency sel 100
> graphics silhouettes true
> select clear
> select add #9
3050 atoms, 3099 bonds, 409 residues, 1 model selected
> color sel lime
> color sel byhetero
> select clear
> select add #12
2 models selected
> transparency sel 50
> select /M:1@H122
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 39 bonds, 1 residue, 1 model selected
> select up
3050 atoms, 3099 bonds, 409 residues, 1 model selected
> hide H
> color sel orange
> color sel lime
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
38 atoms, 39 bonds, 1 residue, 1 model selected
> color sel orange
> color sel byhetero
> select /M:1@C08
1 atom, 1 residue, 1 model selected
> select /M:1@C08
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 39 bonds, 1 residue, 1 model selected
> combine sel
> hide #9 models
> select add #9
3050 atoms, 3099 bonds, 409 residues, 1 model selected
> select subtract #9
Nothing selected
> select add #13
3050 atoms, 3099 bonds, 409 residues, 1 model selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #13,1,0,0,-0.0791,0,1,0,0.31015,0,0,1,-4.4418
> ui tool show "Fit in Map"
> fitmap #13 inMap #12
Fit molecule copy of FDDNP_1rise_favor90.pdb (#13) to map 1rise_50z_imasked
(#12) using 3050 atoms
average map value = 0.001092, steps = 64
shifted from previous position = 0.668
rotated from previous position = 2.44 degrees
atoms outside contour = 3039, contour level = 0.008
Position of copy of FDDNP_1rise_favor90.pdb (#13) relative to
1rise_50z_imasked (#12) coordinates:
Matrix rotation and translation
0.99911079 -0.04196330 0.00408738 5.16899461
0.04193728 0.99910065 0.00625669 -5.45418359
-0.00434626 -0.00607972 0.99997207 -3.44104713
Axis -0.14475786 0.09896195 0.98450581
Axis point 121.26268057 104.47979130 0.00000000
Rotation angle (degrees) 2.44214139
Shift along axis -4.67574015
> fitmap #13 inMap #12
Fit molecule copy of FDDNP_1rise_favor90.pdb (#13) to map 1rise_50z_imasked
(#12) using 3050 atoms
average map value = 0.001094, steps = 28
shifted from previous position = 0.0209
rotated from previous position = 0.0481 degrees
atoms outside contour = 3040, contour level = 0.008
Position of copy of FDDNP_1rise_favor90.pdb (#13) relative to
1rise_50z_imasked (#12) coordinates:
Matrix rotation and translation
0.99910194 -0.04223026 0.00345214 5.27966429
0.04220633 0.99908621 0.00673569 -5.53972106
-0.00373344 -0.00658394 0.99997136 -3.43321978
Axis -0.15527277 0.08376548 0.98431383
Axis point 124.27679533 105.23234611 0.00000000
Rotation angle (degrees) 2.45823262
Shift along axis -4.66319119
> fitmap #13 inMap #12
Fit molecule copy of FDDNP_1rise_favor90.pdb (#13) to map 1rise_50z_imasked
(#12) using 3050 atoms
average map value = 0.001092, steps = 48
shifted from previous position = 0.0235
rotated from previous position = 0.051 degrees
atoms outside contour = 3039, contour level = 0.008
Position of copy of FDDNP_1rise_favor90.pdb (#13) relative to
1rise_50z_imasked (#12) coordinates:
Matrix rotation and translation
0.99911104 -0.04195193 0.00414289 5.16125221
0.04192562 0.99910121 0.00624690 -5.45068059
-0.00440123 -0.00606765 0.99997191 -3.43856783
Axis -0.14452645 0.10027586 0.98440686
Axis point 121.05802671 104.34847552 0.00000000
Rotation angle (degrees) 2.44171621
Shift along axis -4.67745884
> hide #!11 models
Drag select of 215 atoms, 210 bonds
> select up
237 atoms, 211 bonds, 50 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 17 atoms, 10 bonds, 3 pseudobonds
> select up
20 atoms, 10 bonds, 3 pseudobonds, 9 residues, 2 models selected
> select up
44 atoms, 32 bonds, 3 pseudobonds, 9 residues, 2 models selected
> select up
77 atoms, 66 bonds, 3 pseudobonds, 15 residues, 2 models selected
> select up
355 atoms, 349 bonds, 3 pseudobonds, 57 residues, 2 models selected
> delete atoms (#!13 & sel)
> delete bonds (#!13 & sel)
Drag select of 10 atoms, 3 bonds, 5 pseudobonds
> select up
16 atoms, 7 bonds, 5 pseudobonds, 6 residues, 2 models selected
> select up
124 atoms, 109 bonds, 5 pseudobonds, 23 residues, 2 models selected
> select up
338 atoms, 333 bonds, 5 pseudobonds, 47 residues, 2 models selected
> select up
497 atoms, 495 bonds, 5 pseudobonds, 67 residues, 2 models selected
> delete atoms (#!13 & sel)
> delete bonds (#!13 & sel)
Drag select of 284 atoms, 309 bonds
> select up
316 atoms, 312 bonds, 53 residues, 1 model selected
> select up
412 atoms, 411 bonds, 53 residues, 1 model selected
> select up
818 atoms, 822 bonds, 112 residues, 1 model selected
> select up
1502 atoms, 1525 bonds, 204 residues, 1 model selected
> select up
1961 atoms, 1987 bonds, 264 residues, 1 model selected
> select down
1502 atoms, 1525 bonds, 204 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 11 atoms, 8 bonds
> select up
14 atoms, 8 bonds, 7 residues, 1 model selected
> select up
35 atoms, 27 bonds, 7 residues, 1 model selected
> select up
98 atoms, 93 bonds, 18 residues, 1 model selected
> select up
421 atoms, 423 bonds, 59 residues, 1 model selected
> select up
459 atoms, 462 bonds, 60 residues, 1 model selected
> select down
421 atoms, 423 bonds, 59 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #9 models
> show #!11 models
> select #9/M:1@C08
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 39 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> graphics silhouettes true width 5
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/1rise_sideview_mode.png" width 2000 height 1426 supersample
> 3
> hide #!12 models
> hide #!13 models
> hide #!11 models
> hide #9 models
> show #!5 models
> hide #!5 models
> show #!4 models
> volume #4 level 0.007373
> volume #4 level 0.006967
> volume #4 level 0.006642
> volume #4 level 0.006317
> volume #4 level 0.005749
> volume #5 level 0.00575
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!4 models
Segmenting 2rise_50z.mrc, density threshold 0.005749
Showing 171 region surfaces
1994 watershed regions, grouped to 171 regions
Showing 2rise_50z.seg - 171 regions, 171 surfaces
> select #10.12
1 model selected
> select add #10.34
2 models selected
Ungrouped to 7 regions
Ungrouped to 20 regions
Ungrouped to 40 regions
Ungrouped to 10 regions
Ungrouped to 0 regions
> select #10.208
1 model selected
> select add #10.197
2 models selected
> select add #10.203
3 models selected
> select add #10.224
4 models selected
> select add #10.201
5 models selected
Drag select of 3004, 6 of 1536 triangles, 4 2rise_50z.mrc
> select add #10.1
9 models selected
> select #10.172
1 model selected
> select add #10.201
2 models selected
> select add #10.224
3 models selected
> select add #10.203
4 models selected
> select add #10.197
5 models selected
> select add #10.208
6 models selected
Grouped 6 regions
> select #10.26
1 model selected
> select add #10.30
2 models selected
> select add #10.36
3 models selected
Ungrouped to 11 regions
Ungrouped to 29 regions
Ungrouped to 30 regions
Ungrouped to 6 regions
Ungrouped to 0 regions
> select #10.264
1 model selected
> select add #10.172
2 models selected
> select add #10.237
3 models selected
> select add #10.252
4 models selected
> select add #10.244
5 models selected
> select add #10.262
6 models selected
> select add #10.255
7 models selected
Grouped 7 regions
> select #10.28
1 model selected
> select add #10.33
2 models selected
Ungrouped to 8 regions
Ungrouped to 18 regions
Ungrouped to 25 regions
Ungrouped to 0 regions
Ungrouped to 258 regions
> select #10.172
1 model selected
> select add #10.287
2 models selected
> select add #10.270
3 models selected
> select add #10.237
4 models selected
> select add #10.277
5 models selected
> select add #10.440
6 models selected
> select subtract #10.440
5 models selected
Grouped 5 regions
> select #10.440
1 model selected
> select add #10.439
2 models selected
> select add #10.538
3 models selected
> select add #10.539
4 models selected
> select add #10.452
5 models selected
> select add #10.449
6 models selected
> select add #10.490
7 models selected
> select add #10.491
8 models selected
Ungrouped to 17 regions
Ungrouped to 36 regions
Ungrouped to 9 regions
Ungrouped to 0 regions
> select #10.56
1 model selected
> select add #10.61
2 models selected
> select add #10.1
3 models selected
> select add #10.42
4 models selected
> select add #10.24
5 models selected
> select add #10.47
6 models selected
> select add #10.60
7 models selected
> select add #10.32
8 models selected
> select add #10.64
9 models selected
> select add #10.487
10 models selected
> select subtract #10.487
9 models selected
Grouped 9 regions
> select #10.487
1 model selected
> select add #10.489
2 models selected
Ungrouped to 6 regions
Ungrouped to 13 regions
Ungrouped to 0 regions
> select #10.1
1 model selected
> select add #10.66
2 models selected
> select add #10.56
3 models selected
> select add #10.51
4 models selected
Grouped 4 regions
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> select #10.422
1 model selected
Ungrouped to 7 regions
Ungrouped to 12 regions
Ungrouped to 4 regions
> select #10.56
1 model selected
> select add #10.71
2 models selected
> select add #10.73
3 models selected
Grouped 3 regions
> select #10.423
1 model selected
> select add #10.421
2 models selected
> select add #10.301
3 models selected
> select add #10.300
4 models selected
> select add #10.314
5 models selected
> select add #10.315
6 models selected
> select add #10.475
7 models selected
Ungrouped to 14 regions
Ungrouped to 37 regions
Ungrouped to 4 regions
Ungrouped to 0 regions
> select #10.421
1 model selected
> select add #10.108
2 models selected
> select add #10.96
3 models selected
> select add #10.300
4 models selected
> select add #10.142
5 models selected
> select add #10.95
6 models selected
> select add #10.315
7 models selected
> select add #10.16
8 models selected
Grouped 8 regions
> select #10.478
1 model selected
> select add #10.406
2 models selected
> select add #10.404
3 models selected
> select add #10.321
4 models selected
Ungrouped to 10 regions
Ungrouped to 16 regions
Ungrouped to 2 regions
> select #10.85
1 model selected
> select add #10.487
2 models selected
> select add #10.108
3 models selected
> select add #10.475
4 models selected
> select add #10.16
5 models selected
Grouped 5 regions
> select #10.319
1 model selected
> select add #10.431
2 models selected
> select add #10.429
3 models selected
> select add #10.375
4 models selected
Ungrouped to 11 regions
Ungrouped to 17 regions
Ungrouped to 4 regions
> select #10.16
1 model selected
> select add #10.319
2 models selected
> select add #10.340
3 models selected
> select add #10.548
4 models selected
> select #10.548
1 model selected
> select add #10.319
2 models selected
> select add #10.16
3 models selected
> select add #10.546
4 models selected
> select add #10.552
5 models selected
Grouped 5 regions
> select #10.374
1 model selected
> select add #10.356
2 models selected
> select add #10.355
3 models selected
> select add #10.353
4 models selected
> select add #10.352
5 models selected
Ungrouped to 12 regions
Ungrouped to 21 regions
Ungrouped to 8 regions
> select #10.16
1 model selected
> select add #10.564
2 models selected
> select add #10.352
3 models selected
> select add #10.561
4 models selected
> select add #10.555
5 models selected
> select add #10.569
6 models selected
> select add #10.467
7 models selected
Grouped 7 regions
> select #10.464
1 model selected
> select add #10.466
2 models selected
Ungrouped to 7 regions
Ungrouped to 14 regions
Ungrouped to 0 regions
> select #10.570
1 model selected
> select add #10.561
2 models selected
> select add #10.575
3 models selected
> select add #10.16
4 models selected
Grouped 4 regions
Grouped 1 regions
> select #10.16
1 model selected
Ungrouped to 1 regions
Ungrouped to 4 regions
Ungrouped to 7 regions
[Repeated 1 time(s)]
> select #10.467
1 model selected
> select add #10.374
2 models selected
> select add #10.16
3 models selected
> select add #10.353
4 models selected
> select subtract #10.353
3 models selected
> select add #10.561
4 models selected
> select add #10.575
5 models selected
> select add #10.554
6 models selected
Grouped 6 regions
> select #10.352
1 model selected
> select add #10.555
2 models selected
> select add #10.583
3 models selected
> select add #10.581
4 models selected
> select add #10.585
5 models selected
> select add #10.16
6 models selected
Grouped 6 regions
> select #10.582
1 model selected
> select add #10.16
2 models selected
Grouped 2 regions
> select #10.584
1 model selected
> select add #10.16
2 models selected
Grouped 2 regions
> select #10.468
1 model selected
Ungrouped to 2 regions
Ungrouped to 8 regions
Ungrouped to 5 regions
> select #10.16
1 model selected
> select add #10.353
2 models selected
> select #10.353
1 model selected
Ungrouped to 3 regions
Ungrouped to 0 regions
Ungrouped to 442 regions
> select #10.16
1 model selected
> select #10.579
1 model selected
> select add #10.16
2 models selected
Grouped 2 regions
> select add #10.1
2 models selected
Grouped 2 regions
Opened 2rise_50z_imasked as #14, grid size 288,288,288, pixel 0.83, shown at
step 1, values float32
Opened 2rise_50z_imasked as #15, grid size 288,288,288, pixel 0.83, shown at
step 1, values float32
> hide #!10 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!4 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> select add #15
875 models selected
> select subtract #15
873 models selected
> select add #15
875 models selected
> select subtract #15
873 models selected
> select add #14
875 models selected
> surface dust #14 size 8.3
> color #14 #aaff00ff models
> color #15 #ffaa7fff models
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/2rise_sideview_mode.png" width 2000 height 1426 supersample
> 3
> graphics silhouettes true width 1
> graphics silhouettes true width 3
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/2rise_sideview_mode.png" width 2000 height 1426 supersample
> 3
> hide #!14 models
> hide #!15 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!3 models
Segmenting 2rise_10z.mrc, density threshold 0.004964
Showing 28 region surfaces
543 watershed regions, grouped to 28 regions
Showing 2rise_10z.seg - 28 regions, 28 surfaces
> select clear
> select #10.1
1 model selected
Ungrouped to 10 regions
Ungrouped to 33 regions
Ungrouped to 43 regions
Ungrouped to 5 regions
> select #10.76
1 model selected
> select add #10.79
2 models selected
> select add #10.84
3 models selected
> select add #10.70
4 models selected
> select add #10.75
5 models selected
> select add #10.30
6 models selected
Grouped 6 regions
> select #10.30
1 model selected
> select #10.87
1 model selected
> select add #10.30
2 models selected
Grouped 2 regions
> select #10.9
1 model selected
> select add #10.3
2 models selected
Ungrouped to 7 regions
Ungrouped to 28 regions
Ungrouped to 50 regions
Ungrouped to 15 regions
Ungrouped to 0 regions
Ungrouped to 40 regions
> select #10.134
1 model selected
> select #10.135
1 model selected
> select add #10.157
2 models selected
> select add #10.141
3 models selected
> select add #10.154
4 models selected
> select add #10.127
5 models selected
> select add #10.120
6 models selected
> select add #10.134
7 models selected
Grouped 7 regions
> select add #10.30
2 models selected
Grouped 2 regions
Opened 2rise_10z_imasked as #16, grid size 288,288,288, pixel 0.83, shown at
step 1, values float32
Opened 2rise_10z_imasked as #17, grid size 288,288,288, pixel 0.83, shown at
step 1, values float32
> hide #!10 models
> hide #!3 models
> select add #16
167 models selected
> select subtract #16
165 models selected
> select add #16
167 models selected
> surface dust #16 size 8.3
> color #16 #aaff00ff models
> color #17 #ffaa7fff models
> select clear
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/2rise_topview_mode.png" width 1318 height 940 supersample 3
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/2rise_topview_mode.png" width 2000 height 1426 supersample 3
> hide #!17 models
> hide #!16 models
> show #!1 models
> show #!2 models
> hide #!1 models
Segmenting 4rise_50z.mrc, density threshold 0.009926
Showing 90 region surfaces
1414 watershed regions, grouped to 90 regions
Showing 4rise_50z.seg - 90 regions, 90 surfaces
> select #10.19
1 model selected
> select add #10.53
2 models selected
> select add #10.9
3 models selected
Ungrouped to 16 regions
Ungrouped to 41 regions
Ungrouped to 26 regions
Ungrouped to 6 regions
> select #10.101
1 model selected
> select add #10.131
2 models selected
> select add #10.96
3 models selected
Grouped 3 regions
> select #10.97
1 model selected
> select add #10.74
2 models selected
> select add #10.156
3 models selected
> select add #10.3
4 models selected
> select add #10.71
5 models selected
Ungrouped to 16 regions
Ungrouped to 28 regions
Ungrouped to 20 regions
Ungrouped to 10 regions
Ungrouped to 0 regions
Ungrouped to 267 regions
> select #10.174
1 model selected
> select add #10.156
2 models selected
> select add #10.163
3 models selected
> select add #10.181
4 models selected
> select add #10.162
5 models selected
> select add #10.184
6 models selected
> select add #10.91
7 models selected
Grouped 7 regions
> select #10.137
1 model selected
Ungrouped to 0 regions
Ungrouped to 584 regions
> select #10.25
1 model selected
> select add #10.566
2 models selected
> select add #10.755
3 models selected
> select add #10.275
4 models selected
> select subtract #10.275
3 models selected
> select add #10.275
4 models selected
> select add #10.547
5 models selected
> select add #10.950
6 models selected
> select add #10.849
7 models selected
> select add #10.306
8 models selected
> select add #10.918
9 models selected
Ungrouped to 19 regions
Ungrouped to 2 regions
Ungrouped to 0 regions
> select #10.1
1 model selected
> select add #10.84
2 models selected
> select add #10.82
3 models selected
> select add #10.755
4 models selected
> select add #10.68
5 models selected
> select add #10.73
6 models selected
> select add #10.849
7 models selected
> select add #10.79
8 models selected
> select add #10.608
9 models selected
> select subtract #10.608
8 models selected
Grouped 8 regions
> select #10.608
1 model selected
> select add #10.468
2 models selected
> select add #10.649
3 models selected
Ungrouped to 6 regions
Ungrouped to 0 regions
> select #10.82
1 model selected
> select add #10.468
2 models selected
> select add #10.68
3 models selected
Grouped 3 regions
> select #10.5
1 model selected
> select #10.524
1 model selected
Ungrouped to 2 regions
> select #10.82
1 model selected
> select add #10.5
2 models selected
Grouped 2 regions
> select #10.112
1 model selected
> select add #10.141
2 models selected
> select #10.141
1 model selected
Ungrouped to 0 regions
Ungrouped to 696 regions
> select #10.543
1 model selected
> select #10.112
1 model selected
> select add #10.141
2 models selected
Grouped 2 regions
> select #10.880
1 model selected
> select add #10.1035
2 models selected
> select add #10.1484
3 models selected
> select add #10.918
4 models selected
Grouped 4 regions
> select add #10.892
2 models selected
> select add #10.1132
3 models selected
> select add #10.500
4 models selected
Grouped 4 regions
> select #10.1485
1 model selected
> select add #10.7
2 models selected
> select add #10.451
3 models selected
> select add #10.1280
4 models selected
Grouped 4 regions
> select #10.1022
1 model selected
Grouped 1 regions
> select add #10.597
2 models selected
> select add #10.1281
3 models selected
> select #10.7
1 model selected
> select add #10.15
2 models selected
Grouped 2 regions
> select #10.334
1 model selected
> select #10.806
1 model selected
> select add #10.36
2 models selected
> select add #10.1045
3 models selected
> select add #10.1009
4 models selected
> select add #10.641
5 models selected
> select add #10.645
6 models selected
> select add #10.1087
7 models selected
> select add #10.310
8 models selected
> select subtract #10.310
7 models selected
> select add #10.7
8 models selected
Grouped 8 regions
Ungrouped to 8 regions
> select subtract #10.29
7 models selected
Grouped 7 regions
> select #10.1404
1 model selected
> select add #10.1385
2 models selected
> select add #10.321
3 models selected
> select subtract #10.321
2 models selected
> select add #10.7
3 models selected
Grouped 3 regions
> select #10.1135
1 model selected
> select add #10.5
2 models selected
Ungrouped to 4 regions
Ungrouped to 0 regions
Ungrouped to 356 regions
Ungrouped to 16 regions
> select #10.17
1 model selected
> select add #10.18
2 models selected
> select add #10.16
3 models selected
> select subtract #10.16
2 models selected
> select add #10.28
3 models selected
> select add #10.34
4 models selected
> select add #10.556
5 models selected
> hide #!2 models
> select #10.23
1 model selected
> select #10.181
1 model selected
> select add #10.23
2 models selected
Grouped 2 regions
> select #10.1008
1 model selected
Ungrouped to 0 regions
> select #10.1
1 model selected
> select #10.822
1 model selected
Ungrouped to 0 regions
> select #10.556
1 model selected
> select add #10.1
2 models selected
Grouped 2 regions
> select #10.34
1 model selected
> select add #10.28
2 models selected
> select add #10.1
3 models selected
Grouped 3 regions
> select #10.18
1 model selected
> select add #10.17
2 models selected
> select add #10.16
3 models selected
> select subtract #10.16
2 models selected
> select add #10.689
3 models selected
> select add #10.1
4 models selected
> select subtract #10.1
3 models selected
> select subtract #10.689
2 models selected
> select add #10.1
3 models selected
Grouped 3 regions
> select #10.16
1 model selected
Ungrouped to 0 regions
> select #10.1
1 model selected
Opened 4rise_50z_imasked as #18, grid size 288,288,288, pixel 0.83, shown at
step 1, values float32
Opened 4rise_50z_imasked as #19, grid size 288,288,288, pixel 0.83, shown at
step 1, values float32
> hide #!10 models
> color #18 #ffaa7f80 models
> color #18 #aaff7f80 models
> color #18 #aaff0080 models
> color #19 #ffaa7f80 models
> select add #19
1386 models selected
> select add #18
1389 models selected
> transparency sel & #18.1#19.1 0
> graphics silhouettes true width 1
> select clear
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/4rise_sideview_mode.png" width 2000 height 1426 supersample
> 3
> hide #14.1 models
> hide #!18 models
> show #!16 models
> hide #!19 models
> show #!14 models
> hide #!14 models
> hide #!16 models
> show #!1 models
Segmenting 4rise_10z.mrc, density threshold 0.009930
Showing 24 region surfaces
365 watershed regions, grouped to 24 regions
Showing 4rise_10z.seg - 24 regions, 24 surfaces
> select #10.7
1 model selected
> select add #10.2
2 models selected
> select add #10.15
3 models selected
> select add #10.3
4 models selected
Ungrouped to 26 regions
Ungrouped to 42 regions
Ungrouped to 39 regions
Ungrouped to 8 regions
> select #10.77
1 model selected
> select add #10.69
2 models selected
> select add #10.50
3 models selected
> select add #10.89
4 models selected
> select add #10.92
5 models selected
Grouped 5 regions
> select #10.66
1 model selected
> select add #10.25
2 models selected
Grouped 2 regions
> select #10.13
1 model selected
> select add #10.8
2 models selected
> select #10.1
1 model selected
> select subtract #10.1
Nothing selected
> select #10.13
1 model selected
> select add #10.1
2 models selected
Ungrouped to 9 regions
Ungrouped to 33 regions
Ungrouped to 31 regions
Ungrouped to 8 regions
Ungrouped to 0 regions
> select #10.50
1 model selected
> select add #10.132
2 models selected
> select add #10.83
3 models selected
> select add #10.145
4 models selected
> select add #10.17
5 models selected
> select #10.17
1 model selected
Ungrouped to 2 regions
Ungrouped to 5 regions
Ungrouped to 0 regions
> select #10.83
1 model selected
> select add #10.145
2 models selected
> select add #10.134
3 models selected
> select add #10.132
4 models selected
> select add #10.50
5 models selected
Grouped 5 regions
> select #10.142
1 model selected
Ungrouped to 0 regions
Ungrouped to 27 regions
> select #10.142
1 model selected
> select #10.34
1 model selected
> select add #10.25
2 models selected
Grouped 2 regions
Opened 4rise_10z_imasked as #20, grid size 288,288,288, pixel 0.83, shown at
step 1, values float32
Opened 4rise_10z_imasked as #21, grid size 288,288,288, pixel 0.83, shown at
step 1, values float32
> hide #!10 models
> color #20 #ffaa7f80 models
> color #20 #aaff7f80 models
> color #20 #aaff0080 models
> color #21 #ffaa7f80 models
> hide #!1 models
> select add #20
167 models selected
> surface dust #20 size 8.3
> select add #21
169 models selected
> transparency sel & #20.1#21.1 0
> select clear
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/4rise_topview_mode.png" width 2000 height 1426 supersample 3
> show #!5 models
> show #!6 models
> hide #!20 models
> hide #!21 models
> hide #!6 models
> show #!6 models
> close #6
> open "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/3rise/job103/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #6, grid size 288,288,288, pixel 0.83, shown
at level 0.00268, step 2, values float32
> volume #6 step 1
> volume #6 level 0.0057
> hide #!15 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #6
2 models selected
> ui tool show "Segment Map"
Segmenting postprocess_masked.mrc, density threshold 0.005700
Showing 100 region surfaces
1643 watershed regions, grouped to 100 regions
Showing postprocess_masked.seg - 100 regions, 100 surfaces
> select #10.4
1 model selected
> select add #10.3
2 models selected
Ungrouped to 8 regions
Ungrouped to 25 regions
Ungrouped to 31 regions
Ungrouped to 16 regions
Ungrouped to 0 regions
> select #10.140
1 model selected
> select add #10.142
2 models selected
> select add #10.144
3 models selected
> select add #10.130
4 models selected
Drag select of 2471, 19 of 13844 triangles, 2451, 20 of 13236 triangles, 2423,
13 of 12620 triangles, 2370, 12 of 8956 triangles, 2454, 6 of 7948 triangles,
2286, 5 of 7328 triangles, 2472, 26 of 5384 triangles, 2318, 13 of 3992
triangles, 228, 6 of 444 triangles, 6 postprocess_masked.mrc
> select add #10.101
16 models selected
> select subtract #10.134
15 models selected
> select subtract #10.101
14 models selected
> select subtract #10.8
13 models selected
> select add #10.134
14 models selected
> select add #10.101
15 models selected
Grouped 13 regions
> select #10.27
1 model selected
> select add #10.26
2 models selected
> select add #10.38
3 models selected
> select add #10.28
4 models selected
Ungrouped to 19 regions
Ungrouped to 47 regions
Ungrouped to 71 regions
Ungrouped to 15 regions
Ungrouped to 0 regions
> select #10.13
1 model selected
> select #10.13
1 model selected
> select #10.13
1 model selected
Ungrouped to 13 regions
Ungrouped to 29 regions
Ungrouped to 62 regions
Ungrouped to 46 regions
Ungrouped to 22 regions
> select #10.193
1 model selected
> select add #10.69
2 models selected
> select add #10.180
3 models selected
> select add #10.182
4 models selected
> select add #10.195
5 models selected
> select add #10.181
6 models selected
> select add #10.210
7 models selected
Drag select of 415, 5 of 452 triangles
Drag select of 2388, 12 of 2880 triangles, 582, 14 of 1032 triangles, 595, 6
of 720 triangles, 6 postprocess_masked.mrc
> select add #10.224
14 models selected
> select add #10.23
15 models selected
Drag select of 2442, 6 of 8848 triangles
> select #10.224
1 model selected
> select #10.237
1 model selected
> select add #10.224
2 models selected
> select add #10.240
3 models selected
> select add #10.218
4 models selected
> select add #10.210
5 models selected
> select add #10.181
6 models selected
> select add #10.195
7 models selected
> select add #10.182
8 models selected
> select add #10.180
9 models selected
> select add #10.69
10 models selected
> select add #10.193
11 models selected
Grouped 11 regions
> select add #10.251
2 models selected
> select add #10.154
3 models selected
> select add #10.101
4 models selected
> select add #10.217
5 models selected
Grouped 5 regions
> select add #10.31
2 models selected
> select add #10.22
3 models selected
> select add #10.41
4 models selected
Ungrouped to 18 regions
Ungrouped to 49 regions
Ungrouped to 46 regions
Ungrouped to 10 regions
Ungrouped to 0 regions
> select #10.193
1 model selected
> select #10.402
1 model selected
> select add #10.395
2 models selected
> select add #10.398
3 models selected
> select add #10.399
4 models selected
> select add #10.403
5 models selected
> select add #10.400
6 models selected
> select add #10.396
7 models selected
> select add #10.394
8 models selected
> select add #10.404
9 models selected
> select add #10.401
10 models selected
> select add #10.397
11 models selected
> select add #10.182
12 models selected
> select add #10.195
13 models selected
Grouped 13 regions
> select add #10.217
2 models selected
> select add #10.193
3 models selected
> select add #10.237
4 models selected
> select add #10.424
5 models selected
> select add #10.413
6 models selected
> select add #10.407
7 models selected
> select add #10.375
8 models selected
> select add #10.210
9 models selected
> select add #10.433
10 models selected
> select add #10.418
11 models selected
> select add #10.410
12 models selected
> select add #10.20
13 models selected
> select subtract #10.20
12 models selected
Grouped 12 regions
> select #10.20
1 model selected
> select add #10.50
2 models selected
Ungrouped to 9 regions
Ungrouped to 36 regions
Ungrouped to 18 regions
Ungrouped to 7 regions
Ungrouped to 0 regions
> select #10.423
1 model selected
Drag select of 6 postprocess_masked.mrc
> select add #10.418
4 models selected
> select #10.423
1 model selected
> select add #10.452
2 models selected
> select add #10.418
3 models selected
> select add #10.182
4 models selected
Grouped 4 regions
> view matrix models #10.182,1,0,0,-38.62,0,1,0,19.924,0,0,1,6.4525
> view matrix models #10.182,1,0,0,-50.591,0,1,0,22.235,0,0,1,8.0171
> view matrix models #10.182,1,0,0,-57.967,0,1,0,22.058,0,0,1,8.801
> view matrix models #10.182,1,0,0,-70.67,0,1,0,25.968,0,0,1,10.625
> undo
[Repeated 3 time(s)]
> select clear
> select #10.1
1 model selected
> select add #10.12
2 models selected
> select subtract #10.1
1 model selected
Ungrouped to 5 regions
Ungrouped to 14 regions
Ungrouped to 18 regions
Ungrouped to 11 regions
Ungrouped to 0 regions
> select #10.1
1 model selected
Ungrouped to 3 regions
Ungrouped to 16 regions
Ungrouped to 29 regions
Ungrouped to 21 regions
> select #10.498
1 model selected
> select add #10.473
2 models selected
> select add #10.468
3 models selected
> select add #10.513
4 models selected
> select add #10.24
5 models selected
> select subtract #10.24
4 models selected
Grouped 4 regions
> select #10.24
1 model selected
> select add #10.25
2 models selected
Ungrouped to 9 regions
Ungrouped to 30 regions
Ungrouped to 32 regions
Ungrouped to 8 regions
Ungrouped to 0 regions
Ungrouped to 144 regions
> select #10.423
1 model selected
> select add #10.573
2 models selected
> select add #10.580
3 models selected
> select add #10.582
4 models selected
> select add #10.568
5 models selected
> select add #10.500
6 models selected
> select add #10.577
7 models selected
> select add #10.277
8 models selected
> select add #10.341
9 models selected
Grouped 9 regions
> select #10.660
1 model selected
> select add #10.682
2 models selected
> select add #10.685
3 models selected
> select add #10.643
4 models selected
Ungrouped to 17 regions
Ungrouped to 33 regions
Ungrouped to 19 regions
Ungrouped to 0 regions
Ungrouped to 337 regions
> select #10.66
1 model selected
> select add #10.72
2 models selected
> select add #10.46
3 models selected
> select add #10.52
4 models selected
> select add #10.56
5 models selected
> select add #10.915
6 models selected
> select add #10.740
7 models selected
> select add #10.34
8 models selected
> select subtract #10.915
7 models selected
> select subtract #10.740
6 models selected
> select add #10.2
7 models selected
Grouped 7 regions
> select #10.916
1 model selected
> select add #10.835
2 models selected
> select add #10.831
3 models selected
> select add #10.832
4 models selected
> select add #10.1040
5 models selected
Ungrouped to 18 regions
Ungrouped to 8 regions
Ungrouped to 0 regions
Ungrouped to 581 regions
Ungrouped to 466 regions
> select #10.81
1 model selected
> select #10.81
1 model selected
> select #10.72
1 model selected
> select add #10.81
2 models selected
> select add #10.2
3 models selected
> select add #10.49
4 models selected
> select add #10.60
5 models selected
> select add #10.52
6 models selected
Grouped 6 regions
> select #10.1210
1 model selected
> select add #10.2
2 models selected
Grouped 2 regions
> select #10.663
1 model selected
> select #10.719
1 model selected
> select add #10.663
2 models selected
> select add #10.2
3 models selected
Grouped 3 regions
> select clear
> select #10.2
1 model selected
> select add #10.182
2 models selected
Grouped 2 regions
Opened postprocess_masked_imasked as #22, grid size 288,288,288, pixel 0.83,
shown at step 1, values float32
Opened postprocess_masked_imasked as #23, grid size 288,288,288, pixel 0.83,
shown at step 1, values float32
> hide #!10 models
> hide #!6 models
> select add #23
1592 models selected
> select subtract #23
1590 models selected
> select add #22
1592 models selected
> surface dust #22 size 8.3
> color #22 #aaff00ff models
> color #23 #ffaa7fff models
> select clear
> graphics silhouettes true width 3
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/3rise_sideview_mode.png" width 2000 height 1426 supersample
> 3
> hide #!22 models
> hide #!23 models
> show #!5 models
Segmenting postprocess_masked.mrc, density threshold 0.005750
Showing 21 region surfaces
359 watershed regions, grouped to 21 regions
Showing postprocess_masked.seg - 21 regions, 21 surfaces
> select #10.7
1 model selected
> select add #10.2
2 models selected
> select add #10.8
3 models selected
Ungrouped to 17 regions
Ungrouped to 38 regions
Ungrouped to 65 regions
Ungrouped to 20 regions
Ungrouped to 0 regions
Ungrouped to 28 regions
> select #10.78
1 model selected
> select add #10.74
2 models selected
> select add #10.36
3 models selected
> select add #10.37
4 models selected
> select subtract #10.37
3 models selected
> select add #10.112
4 models selected
> select add #10.35
5 models selected
> select subtract #10.35
4 models selected
> select add #10.83
5 models selected
> select add #10.135
6 models selected
> select add #10.92
7 models selected
> select subtract #10.135
6 models selected
> select add #10.114
7 models selected
> select subtract #10.114
6 models selected
> select add #10.134
7 models selected
> select add #10.100
8 models selected
> select subtract #10.100
7 models selected
Grouped 7 regions
> select #10.37
1 model selected
Ungrouped to 3 regions
[Repeated 1 time(s)]Ungrouped to 0 regions
> select #10.5
1 model selected
> select #10.35
1 model selected
Ungrouped to 5 regions
Ungrouped to 12 regions
Ungrouped to 4 regions
> select #10.93
1 model selected
> select add #10.35
2 models selected
> select add #10.1
3 models selected
> select subtract #10.1
2 models selected
> select add #10.5
3 models selected
> select add #10.1
4 models selected
Grouped 4 regions
> select #10.100
1 model selected
Ungrouped to 4 regions
Ungrouped to 10 regions
Ungrouped to 2 regions
Ungrouped to 0 regions
> select #10.1
1 model selected
Ungrouped to 4 regions
Ungrouped to 7 regions
Ungrouped to 5 regions
Ungrouped to 6 regions
> select #10.100
1 model selected
> select add #10.168
2 models selected
> select add #10.159
3 models selected
> select add #10.135
4 models selected
> select subtract #10.135
3 models selected
> select add #10.1
4 models selected
Grouped 4 regions
> select #10.135
1 model selected
Ungrouped to 4 regions
Ungrouped to 16 regions
Ungrouped to 7 regions
Ungrouped to 0 regions
> select #10.1
1 model selected
> select add #10.183
2 models selected
Grouped 2 regions
> select #10.114
1 model selected
Ungrouped to 2 regions
Ungrouped to 4 regions
Ungrouped to 2 regions
Ungrouped to 0 regions
> select #10.114
1 model selected
> select add #10.1
2 models selected
> select subtract #10.1
1 model selected
> select add #10.1
2 models selected
> select add #10.83
3 models selected
> select add #10.158
4 models selected
> select add #10.92
5 models selected
> select add #10.157
6 models selected
> select add #10.160
7 models selected
> select add #10.156
8 models selected
Grouped 8 regions
> select add #10.153
2 models selected
Grouped 2 regions
Opened postprocess_masked_imasked as #24, grid size 288,288,288, pixel 0.83,
shown at step 1, values float32
Opened postprocess_masked_imasked as #25, grid size 288,288,288, pixel 0.83,
shown at step 1, values float32
> hide #!5 models
> hide #!10 models
> color #24 #aaff7fff models
> hide #!25 models
> show #!25 models
> color #25 #ffaa7fff models
> select clear
> select add #24
2 models selected
> surface dust #24 size 8.3
> select clear
> select add #25
2 models selected
> select add #24
4 models selected
> transparency sel 50
> transparency sel 0
> select clear
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/3rise_topview_mode.png" width 2000 height 1426 supersample 3
> hide #!25 models
> hide #!24 models
> show #!23 models
> show #!22 models
> hide #!23 models
> hide #!22 models
> show #!21 models
> show #!20 models
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/4rise_topview_mode.png" width 2000 height 1426 supersample 3
> hide #!21 models
> hide #!20 models
> show #!24 models
> color #24 #aaff00ff models
> show #!25 models
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/3rise_topview_mode.png" width 2000 height 1426 supersample 3
> save "D:/PTB129_Tracer/mutiply_helical
> rise/real_FDDNP/helical_rise_multiply_NEW.cxs"
Traceback (most recent call last):
File "msgpack\\_packer.pyx", line 177, in msgpack._cmsgpack.Packer._pack
OverflowError: int too big to convert
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack\\_packer.pyx", line 184, in msgpack._cmsgpack.Packer._pack
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap
File "src\\_serialize.pyx", line 251, in chimerax.core._serialize._encode_ext
RuntimeError: Can't convert object of type: <class 'int'>
RuntimeError: Can't convert object of type:
File "src\\_serialize.pyx", line 251, in chimerax.core._serialize._encode_ext
See log for complete Python traceback.
Traceback (most recent call last):
File "msgpack\\_packer.pyx", line 177, in msgpack._cmsgpack.Packer._pack
OverflowError: int too big to convert
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack\\_packer.pyx", line 184, in msgpack._cmsgpack.Packer._pack
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap
File "src\\_serialize.pyx", line 251, in chimerax.core._serialize._encode_ext
RuntimeError: Can't convert object of type: <class 'int'>
RuntimeError: Can't convert object of type:
File "src\\_serialize.pyx", line 251, in chimerax.core._serialize._encode_ext
See log for complete Python traceback.
> save "D:/PTB129_Tracer/mutiply_helical rise/real_FDDNP/1.cxs" includeMaps
> true
Traceback (most recent call last):
File "msgpack\\_packer.pyx", line 177, in msgpack._cmsgpack.Packer._pack
OverflowError: int too big to convert
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack\\_packer.pyx", line 184, in msgpack._cmsgpack.Packer._pack
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap
File "src\\_serialize.pyx", line 251, in chimerax.core._serialize._encode_ext
RuntimeError: Can't convert object of type: <class 'int'>
RuntimeError: Can't convert object of type:
File "src\\_serialize.pyx", line 251, in chimerax.core._serialize._encode_ext
See log for complete Python traceback.
Traceback (most recent call last):
File "msgpack\\_packer.pyx", line 177, in msgpack._cmsgpack.Packer._pack
OverflowError: int too big to convert
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack\\_packer.pyx", line 184, in msgpack._cmsgpack.Packer._pack
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap
File "src\\_serialize.pyx", line 251, in chimerax.core._serialize._encode_ext
RuntimeError: Can't convert object of type: <class 'int'>
RuntimeError: Can't convert object of type:
File "src\\_serialize.pyx", line 251, in chimerax.core._serialize._encode_ext
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 474.80
OpenGL renderer: NVIDIA GeForce GT 730/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: LENOVO
Model: 90L0CTO1WW
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 17,106,743,296
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 3600 6-Core Processor
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
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-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
comtypes: 1.1.10
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
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
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
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
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
pywin32: 303
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
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
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
msgpack supports 64-bit integers. This is probably related to the volume data.