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Opened 5 years ago
Last modified 5 years ago
#3605 assigned defect
wrapped C/C++ object of type SideViewCanvas has been deleted
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | 1.0 |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open D:\RuvAB_figures\Sessions\Tests\1_Rings.cxs format session
Log from Mon Aug 3 16:55:01 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open D:/RuvAB_figures/Maps/RuvB/Post_processed/RuvB/Zoned/1a/A.mrc
> D:/RuvAB_figures/Maps/RuvB/Post_processed/RuvB/Zoned/1a/B.mrc
> D:/RuvAB_figures/Maps/RuvB/Post_processed/RuvB/Zoned/1a/C.mrc
> D:/RuvAB_figures/Maps/RuvB/Post_processed/RuvB/Zoned/1a/D.mrc
> D:/RuvAB_figures/Maps/RuvB/Post_processed/RuvB/Zoned/1a/E.mrc
> D:/RuvAB_figures/Maps/RuvB/Post_processed/RuvB/Zoned/1a/F.mrc
> D:/RuvAB_figures/Maps/RuvB/Post_processed/RuvB/Zoned/1a/G.mrc
> D:/RuvAB_figures/Maps/RuvB/Post_processed/RuvB/Zoned/1a/H.mrc
> D:/RuvAB_figures/Maps/RuvB/Post_processed/RuvB/Zoned/1a/U.mrc
> D:/RuvAB_figures/Maps/RuvB/Post_processed/RuvB/Zoned/1a/V.mrc
Opened A.mrc, grid size 360,360,360, pixel 1.09, shown at level 9.5e-06, step
2, values float32
Opened B.mrc, grid size 360,360,360, pixel 1.09, shown at level 8.41e-06, step
2, values float32
Opened C.mrc, grid size 360,360,360, pixel 1.09, shown at level 9.96e-06, step
2, values float32
Opened D.mrc, grid size 360,360,360, pixel 1.09, shown at level 1.25e-05, step
2, values float32
Opened E.mrc, grid size 360,360,360, pixel 1.09, shown at level 3.29e-06, step
2, values float32
Opened F.mrc, grid size 360,360,360, pixel 1.09, shown at level 6.03e-06, step
2, values float32
Opened G.mrc, grid size 360,360,360, pixel 1.09, shown at level 2.1e-06, step
2, values float32
Opened H.mrc, grid size 360,360,360, pixel 1.09, shown at level 6.42e-07, step
2, values float32
Opened U.mrc, grid size 360,360,360, pixel 1.09, shown at level 9.96e-06, step
2, values float32
Opened V.mrc, grid size 360,360,360, pixel 1.09, shown at level 9.33e-06, step
2, values float32
> mousemode setting speed 0.1
> volume all step 1 level 0.02
> set bgColor white
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting soft
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> view
> view
> view orient
> set bgColor gray
> set bgColor white
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> hide #!10 models
> show #!10 models
> hide #!7 models
> hide #!8 models
> hide #!6 models
> hide #!5 models
> ui mousemode right zoom
> hide #!10 models
QFileSystemWatcher::removePaths: list is empty
QFileSystemWatcher::removePaths: list is empty
> save D:/RuvAB_figures/Sessions/Tests/1_Rings.cxs
opened ChimeraX session
> ui favorite true "Model Panel"
> view #!1-10 clip false
No displayed objects specified.
> select #1
2 models selected
> select #2
2 models selected
> select #3
2 models selected
> select #5
2 models selected
> ui mousemode right select
> select
20 models selected
Drag select of 1 A.mrc , 2 B.mrc , 3 C.mrc , 4 D.mrc , 9 U.mrc
Drag select of 1 A.mrc , 2 B.mrc , 3 C.mrc , 9 U.mrc
Drag select of 1 A.mrc , 2 B.mrc , 3 C.mrc , 4 D.mrc , 9 U.mrc
Drag select of 1 A.mrc , 2 B.mrc , 3 C.mrc , 4 D.mrc , 9 U.mrc
> select clear
> open
> D:/RuvAB_figures/Maps/RuvAB_HJ/Postprocessed_RuvAB_Refi912_job920/postprocess_masked.mrc
Opened postprocess_masked.mrc, grid size 360,360,360, pixel 1.09, shown at
level 0.0109, step 2, values float32
Drag select of 2 B.mrc , 3 C.mrc , 4 D.mrc , 11 postprocess_masked.mrc
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!10 models
> transparency sel 50
> hide #!11 models
> ui mousemode right select
Drag select of 1 A.mrc , 2 B.mrc , 3 C.mrc , 4 D.mrc , 5 E.mrc , 6 F.mrc , 7
G.mrc , 8 H.mrc , 9 U.mrc , 10 V.mrc
> ui mousemode right "translate selected models"
> show #!11 models
> volume #11 level 0.005168
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui tool show "Fit in Map"
> hide #!11 models
> ui mousemode right select
Drag select of 1 A.mrc , 2 B.mrc , 3 C.mrc , 4 D.mrc , 5 E.mrc , 6 F.mrc , 7
G.mrc , 8 H.mrc , 9 U.mrc , 10 V.mrc
Drag select of 1 A.mrc , 2 B.mrc , 3 C.mrc , 4 D.mrc , 5 E.mrc , 6 F.mrc , 7
G.mrc , 8 H.mrc , 9 U.mrc , 10 V.mrc
> volume sel style surface
> volume sel style surface
> volume sel style surface
> volume sel style surface
Drag select of 1 A.mrc , 2 B.mrc , 3 C.mrc , 4 D.mrc , 5 E.mrc , 6 F.mrc , 7
G.mrc , 8 H.mrc , 9 U.mrc , 10 V.mrc
Drag select of 1 A.mrc , 2 B.mrc , 3 C.mrc , 4 D.mrc , 5 E.mrc , 6 F.mrc , 7
G.mrc , 8 H.mrc , 9 U.mrc , 10 V.mrc
> transparency sel 0
> show #!11 models
> volume #11 level 0.007091
> open
> D:/RuvAB_figures/Maps/RuvA/Post_processed/First_D4_map_job591/postprocess_masked.mrc
Opened postprocess_masked.mrc, grid size 200,200,200, pixel 1.09, shown at
level 0.00818, step 1, values float32
> select #12
2 models selected
Drag select of 23 postprocess_masked.mrc
> ~select #12
2 models selected
> ~select #11
Nothing selected
> select #12
2 models selected
> hide #!12 models
> show #!12 models
> ui mousemode right translate
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> hide #!12 models
> show #!12 models
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui tool show "Fit in Map"
Fit map postprocess_masked.mrc in map postprocess_masked.mrc using 79960
points
correlation = 0.8091, correlation about mean = 0.04501, overlap = 16.45
steps = 72, shift = 2.31, angle = 3.87 degrees
Position of postprocess_masked.mrc (#12) relative to postprocess_masked.mrc
(#11) coordinates:
Matrix rotation and translation
0.88726783 0.00628740 -0.46121173 152.85941874
0.45564795 0.14348143 0.87852036 37.52583598
0.07169893 -0.98963304 0.12444162 281.51249321
Axis -0.93690152 -0.26726114 0.22535975
Axis point 0.00000000 171.01724889 151.33872863
Rotation angle (degrees) 85.54963527
Shift along axis -89.80183461
Fit map postprocess_masked.mrc in map postprocess_masked.mrc using 79960
points
correlation = 0.809, correlation about mean = 0.0449, overlap = 16.45
steps = 48, shift = 0.022, angle = 0.0169 degrees
Position of postprocess_masked.mrc (#12) relative to postprocess_masked.mrc
(#11) coordinates:
Matrix rotation and translation
0.88717433 0.00613810 -0.46139356 152.91107196
0.45583561 0.14363297 0.87839823 37.48085874
0.07166303 -0.98961199 0.12462952 281.49228487
Axis -0.93683872 -0.26733690 0.22553091
Axis point 0.00000000 171.00833915 151.37626148
Rotation angle (degrees) 85.54256781
Shift along axis -89.78781914
> hide #!11 models
> select #10
2 models selected
> select #9
2 models selected
> select #1
2 models selected
> select #2
2 models selected
> select #3
2 models selected
> select #4
2 models selected
> select #5
2 models selected
> ~select #5
Nothing selected
> open
> D:/RuvAB_figures/Maps/RuvB/Refinements/RuvB/run_class001_1a_before_post_processing.mrc
Opened run_class001_1a_before_post_processing.mrc, grid size 360,360,360,
pixel 1.09, shown at level 0.00436, step 2, values float32
> volume #13 step 1
> volume #13 level 0.0107
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> select #13
2 models selected
> mousemode setting speed 0.3
> mousemode setting speed 0.5
> mousemode setting speed 0.4
> mousemode setting speed 0.3
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> volume #12 level 0.01244
> volume #12 level 0.008606
> close #2-13
> open D:/RuvAB_figures/Maps/RuvB/Resampled_for_RuvAB-
> HJ/run_class001_5_before_post_processing_new_position_ring_1.mrc
> D:/RuvAB_figures/Maps/RuvB/Resampled_for_RuvAB-
> HJ/run_class001_5_before_post_processing_new_position_ring_2.mrc
Opened run_class001_5_before_post_processing_new_position_ring_1.mrc, grid
size 360,360,360, pixel 1.09, shown at level 0.00345, step 2, values float32
Opened run_class001_5_before_post_processing_new_position_ring_2.mrc, grid
size 360,360,360, pixel 1.09, shown at level 0.00346, step 2, values float32
> ui mousemode right zoom
> volume #2 step 1
> volume #3 step 1
> volume #2 level 0.0135
> volume #3 level 0.00998
> close #1
> open D:/RuvAB_figures/Maps/RuvA/Resampled_for_RuvAB-
> HJ/postprocess_masked_RuvA.mrc
Opened postprocess_masked_RuvA.mrc, grid size 360,360,360, pixel 1.09, shown
at level 2.77e-06, step 2, values float32
> volume #1 level 0.009137
> volume #1 step 1
> volume #3 level 0.01206
> volume #2 level 0.01541
> volume #1 level 0.01029
> lighting shadows true
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting full
> lighting shadows false
> lighting shadows true
> lighting full
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> save D:/RuvAB_figures/Sessions/Tests/RuvAB_HJ_composite.tif width 3132
> height 1927 supersample 4
> open
> D:/RuvAB_figures/Maps/RuvAB_HJ/RuvAB_refinement_job912_run_ct17_class001.mrc
Opened RuvAB_refinement_job912_run_ct17_class001.mrc, grid size 360,360,360,
pixel 1.09, shown at level 0.0103, step 2, values float32
> volume #4 color #485a6c
> volume #4 color #7996b4
> volume #4 color #8aacce
> volume #4 color #8caed0
> volume #4 color #8fb2d5
> volume #4 color #94b8dc
> volume #4 color #969bdc
> volume #4 color #a4aadc
> volume #4 color #b7c1dc
> volume #4 color #cbd3dc
> volume #4 color #dadbdc
> volume #4 color gainsboro
> volume #4 color #dfdfdf
> volume #4 color #dddddd
> volume #4 color #d1d1d1
> volume #4 color #c7c7c7
> volume #4 color #c3c3c3
> volume #4 color #b9b9b9
> volume #4 color #b0b0b0
> volume #4 color #ababab
> volume #4 color #a8a8a8
> volume #4 color #a3a3a3
> volume #4 color #9e9e9e
> volume #4 color #9a9a9a
> volume #4 color #989898
> transparency 50
> transparency 0
> volume #4 style image
> volume #4 style mesh
> volume #4 change image level -0.0005712,0 level 0.01028,0.8 level 0.02607,1
> volume #4 level 0.004928
> volume showOutlineBox true
> volume showOutlineBox false
> volume style mesh
> volume style mesh
> volume style mesh
> volume style mesh
> volume style surface
> volume #4 meshLighting
Missing "meshLighting" keyword's argument
> volume #4 style mesh
> volume #4 transparency
Missing "transparency" keyword's argument
> volume #4 transparency 1
> volume #2 level 0.01175
> save D:/RuvAB_figures/Sessions/Tests/RuvAB_HJ_composite_2.tif width 3132
> height 1927 supersample 3
> ui tool show "Side View"
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting flat
> lighting flat
> lighting soft
> view
> view orient
> view
> ui tool show "Side View"
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> view
> volume style image
> volume #4 level -0.0005712,0 level 0.0006416,0.2462 level 0.02607,1
> volume #4 level -0.0002141,0.4154 level 0.0006416,0.2462 level 0.02607,1
> volume #4 level -0.00188,0 level 0.0006416,0.2462 level 0.02607,1
> volume #4 level -0.00188,0 level 0.003796,0.3077 level 0.02607,1
> volume #4 level -0.00188,0 level 0.003796,0.3077 level 0.007141,1
> volume #4 level -0.00188,0 level 0.002784,0.5538 level 0.007141,1
> volume style surface
> volume style surface
> volume #4 step 1
> volume #4 level 0.004448
> select #4
3 models selected
> show #4.2 models
> hide #4.2 models
> show #4.2 models
> hide #4.2 models
> hide #4.1 models
> show #4.1 models
> close #4.2
> hide #4.1 models
> show #4.1 models
> volume sel style mesh
> volume sel style surface
> volume sel style surface
> volume sel style surface
> volume sel show
> volume sel hide
> volume sel show
> volume sel style surface
> volume #4 level 0.006008
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> volume sel style surface
> volume sel style surface
> volume sel style mesh
> transparency sel 0
> transparency sel 50
> volume sel hide
> volume sel show
> volume #1 change image level 2.836e-06,0 level 0.00686,0.8 level 0.06857,1
> volume sel style mesh
> volume sel style image
> volume sel hide
> volume sel show
> volume sel style image
> volume #3 change image level -0.00093,0 level 0.003448,0.8 level 0.06513,1
> volume #2 change image level -0.001113,0 level 0.003454,0.8 level 0.0691,1
> transparency #1.1#2.1#3.1 50
> transparency #1.1#2.1#3.1 50
> transparency #1.1#2.1#3.1 50
> volume sel style surface
> volume sel style surface
> select #1
3 models selected
> select #2
3 models selected
> select #3
3 models selected
> volume sel style surface
> volume sel style surface
> transparency sel 0
> transparency sel 50
> transparency sel 0
> select #2
3 models selected
> volume sel style surface
> transparency sel 0
> transparency sel 50
> transparency sel 0
> hide #!1 models
> show #!1 models
> select #1
3 models selected
> transparency sel 0
> transparency sel 50
> transparency sel 0
> volume transparency 0
> volume #4 transparency 1
> volume #4 transparency 0.5
> volume #4 transparency 0.2
> volume #4 transparency 0.8
> volume #4 transparency 0.9
> ~select #1
Nothing selected
> save D:/RuvAB_figures/Sessions/Tests/RuvAB_HJ_composite_3.tif width 3132
> height 1927 supersample 3
> open D:/RuvAB_figures/Maps/RuvA/Resampled_for_RuvAB-
> HJ/postprocess_masked_RuvA_ONLY_DNA.mrc
Opened postprocess_masked_RuvA_ONLY_DNA.mrc, grid size 360,360,360, pixel
1.09, shown at level 5.22e-06, step 2, values float32
> open D:/RuvAB_figures/Maps/RuvB/Resampled_for_RuvAB-
> HJ/run_class001_5_before_post_processing_new_position_ring_1_ONLY_DNA.mrc
> D:/RuvAB_figures/Maps/RuvB/Resampled_for_RuvAB-
> HJ/run_class001_5_before_post_processing_new_position_ring_2_ONLY_DNA.mrc
Opened run_class001_5_before_post_processing_new_position_ring_1_ONLY_DNA.mrc,
grid size 360,360,360, pixel 1.09, shown at level 4.41e-06, step 2, values
float32
Opened run_class001_5_before_post_processing_new_position_ring_2_ONLY_DNA.mrc,
grid size 360,360,360, pixel 1.09, shown at level 8.68e-07, step 2, values
float32
> volume #6 level 0.002269
> volume #7 level 0.002219
> volume #6 step 1
> volume #7 step 1
> volume #5 step 1
> volume #5 level 0.003033
> volume #7 level 0.004502
> volume #6 level 0.005332
> volume #5 level -0.00166
> volume #5 level 0.002579
> volume #5 level 0.00591
> volume #6 level 0.008169
> volume #6 level 0.005673
> volume #7 level 0.006267
> volume #5 color #2acc58
> volume #5 color #2acc50
> volume #5 color #2ccc47
> volume #5 color #2ecc48
> volume #5 color #2ecc41
> volume #5 color #33cc3d
> volume #5 color #35cc3f
> volume #5 color #3bcc3b
> volume #5 color #5acc51
> volume #5 color #63cc5b
> volume #5 color #64cc5d
> volume #5 color #66cc5f
> volume #5 color #6acc63
> volume #5 color #71cc6a
> volume #5 color #7ccc76
> volume #5 color #81cc7c
> volume #5 color #83cc7e
> volume #5 color #89cc84
> volume #5 color #90cc8d
> volume #5 color #92cc8f
> volume #5 color #94cc91
> volume #5 color #9bcc9b
> volume #5 color #9dcc9e
> volume #5 color #a1cca2
> volume #5 color #a5cca6
> volume #5 color #a7ccaa
> volume #5 color #a7cca9
> volume #5 color #a7cca7
> volume #5 color #a6cca6
> volume #5 color #a8cca6
> volume #6 color #aaff00
> volume #6 color lime
> volume #6 color #aaaa7f
> volume #6 color #aaffff
> volume #6 color cyan
> volume #6 color #55ff00
> volume #6 color #aaaaff
> volume #5 color #aaaaff
> volume #7 color #aaaaff
> volume #5 level 0.009089
> volume #5 level 0.008938
> volume #6 level 0.007828
> volume #7 level 0.007201
> volume #7 level 0.007823
> hide dust
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide
> show
> volume #5 level 0.008484
> volume #2 level 0.01286
> volume #3 level 0.01458
> volume #6 level 0.007601
> volume #7 level 0.006889
> hide #4.2 models
> show #4.2 models
> hide #4.2 models
> close #4.2
> close session
> open D:\RuvAB_figures\Maps\RuvA\Resampled_for_RuvAB-
> HJ\postprocess_masked_RuvA_ONLY_DNA.mrc format mrc
Opened postprocess_masked_RuvA_ONLY_DNA.mrc, grid size 360,360,360, pixel
1.09, shown at level 5.22e-06, step 2, values float32
> open D:/RuvAB_figures/Maps/RuvB/Resampled_for_RuvAB-
> HJ/run_class001_5_before_post_processing_new_position_ring_1.mrc
> D:/RuvAB_figures/Maps/RuvB/Resampled_for_RuvAB-
> HJ/run_class001_5_before_post_processing_new_position_ring_1_ONLY_DNA.mrc
> D:/RuvAB_figures/Maps/RuvB/Resampled_for_RuvAB-
> HJ/run_class001_5_before_post_processing_new_position_ring_2.mrc
> D:/RuvAB_figures/Maps/RuvB/Resampled_for_RuvAB-
> HJ/run_class001_5_before_post_processing_new_position_ring_2_ONLY_DNA.mrc
Opened run_class001_5_before_post_processing_new_position_ring_1.mrc, grid
size 360,360,360, pixel 1.09, shown at level 0.00345, step 2, values float32
Opened run_class001_5_before_post_processing_new_position_ring_1_ONLY_DNA.mrc,
grid size 360,360,360, pixel 1.09, shown at level 4.41e-06, step 2, values
float32
Opened run_class001_5_before_post_processing_new_position_ring_2.mrc, grid
size 360,360,360, pixel 1.09, shown at level 0.00346, step 2, values float32
Opened run_class001_5_before_post_processing_new_position_ring_2_ONLY_DNA.mrc,
grid size 360,360,360, pixel 1.09, shown at level 8.68e-07, step 2, values
float32
> volume #5 level 0.006269
> volume #4 level 0.00719
> volume #3 level 0.007518
> volume #2 level 0.008279
> volume #1 level 0.006447
> volume #1 step 1
> volume #2 step 1
> volume #3 step 1
> volume #4 step 1
> volume #5 step 1
> open D:/RuvAB_figures/Maps/RuvA/Resampled_for_RuvAB-
> HJ/postprocess_masked_RuvA_ONLY_DNA.mrc
Opened postprocess_masked_RuvA_ONLY_DNA.mrc, grid size 360,360,360, pixel
1.09, shown at level 5.22e-06, step 2, values float32
> volume #6 level 0.004486
> volume #6 step 1
> open D:/RuvAB_figures/Maps/RuvA/Resampled_for_RuvAB-
> HJ/postprocess_masked_RuvA.mrc
Opened postprocess_masked_RuvA.mrc, grid size 360,360,360, pixel 1.09, shown
at level 2.77e-06, step 2, values float32
> volume #7 level 0.004205
> volume #6 level 0.006757
> open
> D:/RuvAB_figures/Maps/RuvAB_HJ/Postprocessed_RuvAB_Refi912_job920/postprocess_masked.mrc
Opened postprocess_masked.mrc, grid size 360,360,360, pixel 1.09, shown at
level 0.0109, step 2, values float32
> volume #7 step 1
> volume #8 step 1
> volume #8 level 0.008818
> show #!1 models
> hide #!1 models
> hide #!8 models
> show #!8 models
> select #8
2 models selected
> transparency sel 50
> volume #8 transparency 0.9
> volume #8 transparency 0.8
> ~select #8
Nothing selected
> volume #8 level 0.00819
> volume #8 level 0.008112
> show #!7 models
> volume #7 level 0.007848
> volume #5 level 0.006166
> volume #5 level 0.006788
> volume #1 level 0.004024
> volume #2 level 0.01211
> show #!4 models
> volume #4 level 0.009562
> volume #4 level 0.01105
> volume #5 color #d7fffc
> volume #5 color #d9fffc
> volume #5 color #d9fff9
> volume #5 color #d9fff6
> volume #5 color #d9fff4
> volume #5 color #d5ffee
> volume #5 color #d5ffec
> volume #5 color #d4ffeb
> volume #5 color #d4ffe1
> volume #5 color #d4ffde
> volume #5 color #d5ffdf
> volume #5 color #d7ffde
> volume #5 color #d7ffdf
> volume #5 color #d9ffe5
> volume #5 color #dcffea
> volume #5 color #dcfff2
> volume #5 color #dcfff4
> volume #5 color #dcfff8
> volume #5 color #dbfffc
> volume #5 color #d8ffff
> volume #5 color #d5faff
> volume #5 color #d5f6ff
> volume #5 color #d4f6ff
> volume #5 color #d2f6ff
> volume #5 color #d2f7ff
> volume #5 color #cff7ff
> volume #5 color #cdf7ff
> volume #5 color #c5faff
> volume #5 color #c2ffff
> volume #5 color #c2fffb
> volume #5 color #c4fffc
> volume #5 color #c4fffe
> volume #5 color #c4ffff
> volume #5 color white
> volume #5 color #aaaaff
> volume #6 color #aaaaff
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!7 models
> show #!7 models
> volume #7 level 0.01015
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!1 models
> show #!6 models
> close #6
> hide #!5 models
> show #!5 models
> select #8
2 models selected
> transparency sel 0
> transparency sel 50
> volume sel style mesh
> volume sel style surface
> volume #8 transparency 0.8
> lighting soft
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting full
> lighting soft
> view sel
> ~select #8
Nothing selected
> select #8
2 models selected
> ~select #8
Nothing selected
> hide #!8 models
> show #!8 models
> show #!8 target m
> hide #!5 models
> hide #!4 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> hide #!7 models
> show #!1 models
> show #!3 models
> show #!5 models
> select #8
2 models selected
> volume #8 transparency 0.7
> ~select #8
Nothing selected
QFileSystemWatcher::removePaths: list is empty
> save
> D:/RuvAB_figures/Sessions/Composite_model_maps/Composite_trial_1_Figure_1.cxs
QFileSystemWatcher::removePaths: list is empty
> save D:/RuvAB_figures/Sessions/Figure_1/Composite_DNA.tif width 3132 height
> 1927 supersample 3
> show #!7 models
> show #!2 models
> show #!4 models
> hide #!8 models
> save D:/RuvAB_figures/Sessions/Figure_1/Composite_All.tif width 3132 height
> 1927 supersample 3
> show #!8 models
> volume #8 level 0.007876
> volume #7 level 0.01379
> volume #4 level 0.01327
> volume #2 level 0.01418
> save D:/RuvAB_figures/Sessions/Figure_1/Composite_All_overlay_RuvAB.tif
> width 3132 height 1927 supersample 3
> open D:/RuvAB_figures/Maps/RuvB/Resampled_for_RuvAB-
> HJ/run_class001_5_before_post_processing_new_position_ring_1_ONLY_RuvA.mrc
> D:/RuvAB_figures/Maps/RuvB/Resampled_for_RuvAB-
> HJ/run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc
Opened
run_class001_5_before_post_processing_new_position_ring_1_ONLY_RuvA.mrc, grid
size 360,360,360, pixel 1.09, shown at level 8.5e-07, step 2, values float32
Opened
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc, grid
size 360,360,360, pixel 1.09, shown at level 6.61e-07, step 2, values float32
> volume #6 level 0.001376
> volume #9 level 0.002013
> volume #7 color #b6ffb2
> volume #7 color #baffb2
> volume #7 color #b7ffaf
> volume #7 color #bbffaf
> volume #7 color #c2ffaf
> volume #7 color #c7ffaf
> volume #7 color #cfffaf
> volume #7 color #ddffaf
> volume #7 color #deffac
> volume #7 color #e7ffac
> volume #7 color #f4ffac
> volume #7 color #feffaa
> volume #7 color #fffaaa
> volume #7 color #fff6aa
> volume #7 color #ffedaa
> volume #7 color #ffeeaa
> volume #7 color #fff3aa
> volume #7 color #feffab
> volume #7 color #edffab
> volume #7 color #c5ffaa
> volume #7 color #b7ffaa
> volume #7 color #b0ffaa
> volume #7 color #acffaa
> volume #7 color #aaffad
> volume #7 color #aaffb1
> volume #7 color #aaffb7
> volume #7 color #9effad
> volume #7 color #9cffab
> volume #7 color #99ffa8
> volume #7 color #94ff9b
> volume #7 color #8fff89
> volume #7 color #8fff83
> volume #7 color #94ff81
> volume #7 color #91ff7e
> volume #7 color #84ff6e
> volume #7 color #85ff6f
> volume #7 color #8eff74
> volume #7 color #95ff7d
> volume #7 color #a3ff87
> volume #7 color #adff8a
> volume #7 color #afff8c
> volume #7 color #aeff8b
> volume #7 color #adff89
> volume #7 color #aaff86
> volume #7 color #a8ff83
> volume #7 color #a4ff83
> volume #7 color #a1ff87
> volume #7 color #a8ff98
> volume #7 color #aaff9d
> volume #7 color #a4ff9d
> volume #7 color #a7ffa1
> volume #7 color #a3ffa1
> volume #7 color #a4ffa7
> volume #7 color #a6ffa9
> volume #7 color #a6ffb4
> volume #7 color #a6ffb1
> volume #7 color #a5ffab
> volume #7 color #a5ffa5
> volume #7 color #aaffa5
> volume #7 color #aeffa5
> volume #7 color white
> volume #7 color #fffaf9
> volume #7 color #fff8f7
> volume #7 color #fff6f4
> volume #7 color #fff0eb
> volume #7 color #ffecdc
> volume #7 color #ffedce
> volume #7 color #ffecc9
> volume #7 color #fff0c0
> volume #7 color #f7ffaa
> volume #7 color #efff9e
> volume #7 color #e4ff97
> volume #7 color #ddff92
> volume #7 color #caff8c
> volume #7 color #b6ff89
> volume #7 color #a0ff86
> volume #7 color #94ff83
> volume #7 color #8bff83
> volume #7 color #85ff83
> volume #7 color #83ff87
> volume #7 color #85ff89
> volume #7 color #8aff8e
> volume #7 color #93ff97
> volume #7 color #a0ffa3
> volume #7 color #a6ffa9
> volume #6 color #a6ffa9
> volume #9 color #a6ffa9
> volume #9 step 1
> volume #6 step 1
> volume #9 level 0.00706
> volume #6 level 0.007868
> volume #9 level 0.01097
> volume #6 level 0.01075
> save
> D:/RuvAB_figures/Sessions/Session_Composite_model_maps/Composite_trial_1_Figure_1.cxs
> hide #!8 models
> view
> save D:/RuvAB_figures/Sessions/Figure_1/Composite_All.tif width 3132 height
> 1927 supersample 3
> show #!8 models
> hide #!8 models
> show #!8 models
> view
> save D:/RuvAB_figures/Sessions/Figure_1/Composite_All_overlay_RuvAB.tif
> width 3132 height 1927 supersample 3
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> open D:/RuvAB_figures/Maps/RuvA/Maps_zoned/A.mrc
> D:/RuvAB_figures/Maps/RuvA/Maps_zoned/B.mrc
> D:/RuvAB_figures/Maps/RuvA/Maps_zoned/C.mrc
> D:/RuvAB_figures/Maps/RuvA/Maps_zoned/D.mrc
> D:/RuvAB_figures/Maps/RuvA/Maps_zoned/E.mrc
> D:/RuvAB_figures/Maps/RuvA/Maps_zoned/F.mrc
> D:/RuvAB_figures/Maps/RuvA/Maps_zoned/G.mrc
> D:/RuvAB_figures/Maps/RuvA/Maps_zoned/H.mrc
Opened A.mrc, grid size 200,200,200, pixel 1.09, shown at level 1.01e-06, step
1, values float32
Opened B.mrc, grid size 200,200,200, pixel 1.09, shown at level 1.01e-06, step
1, values float32
Opened C.mrc, grid size 200,200,200, pixel 1.09, shown at level 1.01e-06, step
1, values float32
Opened D.mrc, grid size 200,200,200, pixel 1.09, shown at level 1.01e-06, step
1, values float32
Opened E.mrc, grid size 200,200,200, pixel 1.09, shown at level 1.01e-06, step
1, values float32
Opened F.mrc, grid size 200,200,200, pixel 1.09, shown at level 1.01e-06, step
1, values float32
Opened G.mrc, grid size 200,200,200, pixel 1.09, shown at level 1.01e-06, step
1, values float32
Opened H.mrc, grid size 200,200,200, pixel 1.09, shown at level 1.01e-06, step
1, values float32
> volume #15 level 0.005752
> volume #14 level 0.005752
> volume #13 level 0.005113
> volume #12 level 0.004474
> volume #11 level 0.004474
> volume #10 level 0.005326
> volume #16 level 0.007669
> volume #17 level 0.008095
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!9 models
> hide #!9 models
> show #!7 models
Drag select of 10 A.mrc , 11 B.mrc , 12 C.mrc , 13 D.mrc , 14 E.mrc , 15 F.mrc
, 16 G.mrc , 17 H.mrc
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected models"
Drag select of 10 A.mrc , 11 B.mrc , 12 C.mrc , 13 D.mrc , 14 E.mrc , 15 F.mrc
, 16 G.mrc , 17 H.mrc
> select clear
Drag select of 10 A.mrc , 11 B.mrc , 12 C.mrc , 13 D.mrc , 14 E.mrc , 15 F.mrc
, 16 G.mrc , 17 H.mrc
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui tool show "Fit in Map"
Fit map A.mrc in map
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc using
8134 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of A.mrc (#10) relative to
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc (#9)
coordinates:
Matrix rotation and translation
0.85338285 -0.07329404 0.51610627 57.45091615
-0.50455547 0.13267193 0.85312480 146.56939812
-0.13100178 -0.98844632 0.07623904 307.59034283
Axis -0.92123253 0.32371109 -0.21573539
Axis point 0.00000000 246.92918680 51.97900398
Rotation angle (degrees) 88.21512460
Shift along axis -71.83763630
Fit map A.mrc in map
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc using
8134 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of A.mrc (#10) relative to
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc (#9)
coordinates:
Matrix rotation and translation
0.85338285 -0.07329404 0.51610627 57.45091615
-0.50455547 0.13267193 0.85312480 146.56939812
-0.13100178 -0.98844632 0.07623904 307.59034283
Axis -0.92123253 0.32371109 -0.21573539
Axis point 0.00000000 246.92918680 51.97900398
Rotation angle (degrees) 88.21512460
Shift along axis -71.83763630
Fit map B.mrc in map
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc using
8500 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of B.mrc (#11) relative to
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc (#9)
coordinates:
Matrix rotation and translation
0.85338285 -0.07329404 0.51610627 57.45091615
-0.50455547 0.13267193 0.85312480 146.56939812
-0.13100178 -0.98844632 0.07623904 307.59034283
Axis -0.92123253 0.32371109 -0.21573539
Axis point 0.00000000 246.92918680 51.97900398
Rotation angle (degrees) 88.21512460
Shift along axis -71.83763630
Fit map B.mrc in map
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc using
8500 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of B.mrc (#11) relative to
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc (#9)
coordinates:
Matrix rotation and translation
0.85338285 -0.07329404 0.51610627 57.45091615
-0.50455547 0.13267193 0.85312480 146.56939812
-0.13100178 -0.98844632 0.07623904 307.59034283
Axis -0.92123253 0.32371109 -0.21573539
Axis point 0.00000000 246.92918680 51.97900398
Rotation angle (degrees) 88.21512460
Shift along axis -71.83763630
Fit map C.mrc in map
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc using
8505 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of C.mrc (#12) relative to
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc (#9)
coordinates:
Matrix rotation and translation
0.85338285 -0.07329404 0.51610627 57.45091615
-0.50455547 0.13267193 0.85312480 146.56939812
-0.13100178 -0.98844632 0.07623904 307.59034283
Axis -0.92123253 0.32371109 -0.21573539
Axis point 0.00000000 246.92918680 51.97900398
Rotation angle (degrees) 88.21512460
Shift along axis -71.83763630
Fit map D.mrc in map
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc using
8235 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of D.mrc (#13) relative to
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc (#9)
coordinates:
Matrix rotation and translation
0.85338285 -0.07329404 0.51610627 57.45091615
-0.50455547 0.13267193 0.85312480 146.56939812
-0.13100178 -0.98844632 0.07623904 307.59034283
Axis -0.92123253 0.32371109 -0.21573539
Axis point 0.00000000 246.92918680 51.97900398
Rotation angle (degrees) 88.21512460
Shift along axis -71.83763630
Fit map E.mrc in map
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc using
7978 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of E.mrc (#14) relative to
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc (#9)
coordinates:
Matrix rotation and translation
0.85338285 -0.07329404 0.51610627 57.45091615
-0.50455547 0.13267193 0.85312480 146.56939812
-0.13100178 -0.98844632 0.07623904 307.59034283
Axis -0.92123253 0.32371109 -0.21573539
Axis point 0.00000000 246.92918680 51.97900398
Rotation angle (degrees) 88.21512460
Shift along axis -71.83763630
Fit map E.mrc in map
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc using
7978 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of E.mrc (#14) relative to
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc (#9)
coordinates:
Matrix rotation and translation
0.85338285 -0.07329404 0.51610627 57.45091615
-0.50455547 0.13267193 0.85312480 146.56939812
-0.13100178 -0.98844632 0.07623904 307.59034283
Axis -0.92123253 0.32371109 -0.21573539
Axis point 0.00000000 246.92918680 51.97900398
Rotation angle (degrees) 88.21512460
Shift along axis -71.83763630
Fit map F.mrc in map
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc using
7978 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of F.mrc (#15) relative to
run_class001_5_before_post_processing_new_position_ring_2_ONLY_RuvA.mrc (#9)
coordinates:
Matrix rotation and translation
0.85338285 -0.07329404 0.51610627 57.45091615
-0.50455547 0.13267193 0.85312480 146.56939812
-0.13100178 -0.98844632 0.07623904 307.59034283
Axis -0.92123253 0.32371109 -0.21573539
Axis point 0.00000000 246.92918680 51.97900398
Rotation angle (degrees) 88.21512460
Shift along axis -71.83763630
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!9 models
Fit map F.mrc in map postprocess_masked_RuvA.mrc using 7978 points
correlation = 0.9942, correlation about mean = 0.9774, overlap = 4.162
steps = 88, shift = 4.74, angle = 5.54 degrees
Position of F.mrc (#15) relative to postprocess_masked_RuvA.mrc (#7)
coordinates:
Matrix rotation and translation
0.84605704 0.02153039 0.53265740 47.68449887
-0.53022026 0.13756568 0.83662545 150.02718786
-0.05526251 -0.99025861 0.12780427 296.49958446
Axis -0.91486300 0.29441725 -0.27630448
Axis point 0.00000000 241.03289197 40.50636810
Rotation angle (degrees) 86.80619819
Shift along axis -81.37835687
Fit map H.mrc in map postprocess_masked_RuvA.mrc using 7026 points
correlation = 0.9946, correlation about mean = 0.9743, overlap = 4.118
steps = 68, shift = 4.75, angle = 5.5 degrees
Position of H.mrc (#17) relative to postprocess_masked_RuvA.mrc (#7)
coordinates:
Matrix rotation and translation
0.84556728 0.02072066 0.53346659 47.72423655
-0.53091202 0.13765896 0.83617129 150.12405142
-0.05611043 -0.99026292 0.12740076 296.59548991
Axis -0.91461736 0.29524052 -0.27623925
Axis point 0.00000000 241.16793681 40.48727473
Rotation angle (degrees) 86.82915158
Shift along axis -81.25802918
Fit map G.mrc in map postprocess_masked_RuvA.mrc using 7194 points
correlation = 0.9945, correlation about mean = 0.9747, overlap = 4.134
steps = 72, shift = 6.02, angle = 5.51 degrees
Position of G.mrc (#16) relative to postprocess_masked_RuvA.mrc (#7)
coordinates:
Matrix rotation and translation
0.84560305 0.02092252 0.53340202 47.72336387
-0.53088151 0.13752338 0.83621297 150.14827189
-0.05585956 -0.99027751 0.12739757 296.62947452
Axis -0.91464292 0.29508171 -0.27632427
Axis point 0.00000000 241.17032326 40.49503569
Rotation angle (degrees) 86.83210705
Shift along axis -81.30975113
Fit map F.mrc in map postprocess_masked_RuvA.mrc using 7978 points
correlation = 0.9942, correlation about mean = 0.9774, overlap = 4.162
steps = 44, shift = 0.00221, angle = 0.00642 degrees
Position of F.mrc (#15) relative to postprocess_masked_RuvA.mrc (#7)
coordinates:
Matrix rotation and translation
0.84607124 0.02150934 0.53263570 47.68679023
-0.53019016 0.13767222 0.83662700 150.01198055
-0.05533385 -0.99024426 0.12788455 296.49551353
Axis -0.91486174 0.29444376 -0.27628042
Axis point 0.00000000 241.04223622 40.50284315
Rotation angle (degrees) 86.80043051
Shift along axis -81.37263324
Fit map E.mrc in map postprocess_masked_RuvA.mrc using 7978 points
correlation = 0.9941, correlation about mean = 0.977, overlap = 4.165
steps = 72, shift = 2.44, angle = 5.5 degrees
Position of E.mrc (#14) relative to postprocess_masked_RuvA.mrc (#7)
coordinates:
Matrix rotation and translation
0.84614314 0.02082219 0.53254879 47.76816130
-0.53004383 0.13718838 0.83679918 150.01863961
-0.05563551 -0.99032609 0.12711768 296.61359459
Axis -0.91495891 0.29454164 -0.27585398
Axis point 0.00000000 241.04323274 40.62849317
Rotation angle (degrees) 86.83425299
Shift along axis -81.34120970
Fit map D.mrc in map postprocess_masked_RuvA.mrc using 8235 points
correlation = 0.994, correlation about mean = 0.9778, overlap = 4.175
steps = 56, shift = 0.908, angle = 5.55 degrees
Position of D.mrc (#13) relative to postprocess_masked_RuvA.mrc (#7)
coordinates:
Matrix rotation and translation
0.84597117 0.02174037 0.53278524 47.63282481
-0.53043141 0.13651923 0.83666302 150.10234555
-0.05454607 -0.99039883 0.12702311 296.51735408
Axis -0.91490354 0.29410690 -0.27650072
Axis point 0.00000000 240.88914394 40.58318265
Rotation angle (degrees) 86.86109900
Shift along axis -81.42056662
Fit map C.mrc in map postprocess_masked_RuvA.mrc using 8505 points
correlation = 0.9939, correlation about mean = 0.9787, overlap = 4.175
steps = 76, shift = 3.17, angle = 5.57 degrees
Position of C.mrc (#12) relative to postprocess_masked_RuvA.mrc (#7)
coordinates:
Matrix rotation and translation
0.84588794 0.02204244 0.53290498 47.61158713
-0.53054430 0.13731592 0.83646104 150.06119441
-0.05473870 -0.99028201 0.12784837 296.44376898
Axis -0.91478282 0.29427584 -0.27672029
Axis point 0.00000000 240.95970930 40.46685336
Rotation angle (degrees) 86.81695083
Shift along axis -81.42688293
Fit map B.mrc in map postprocess_masked_RuvA.mrc using 8500 points
correlation = 0.9939, correlation about mean = 0.9789, overlap = 4.179
steps = 80, shift = 3.83, angle = 5.57 degrees
Position of B.mrc (#11) relative to postprocess_masked_RuvA.mrc (#7)
coordinates:
Matrix rotation and translation
0.84566344 0.02202048 0.53326207 47.57678881
-0.53090032 0.13721280 0.83625205 150.12771182
-0.05475571 -0.99029679 0.12772653 296.45222779
Axis -0.91467414 0.29445950 -0.27688412
Axis point 0.00000000 240.97868082 40.44053447
Rotation angle (degrees) 86.82984706
Shift along axis -81.39364067
Fit map A.mrc in map postprocess_masked_RuvA.mrc using 8134 points
correlation = 0.9941, correlation about mean = 0.9777, overlap = 4.166
steps = 72, shift = 2.45, angle = 5.54 degrees
Position of A.mrc (#10) relative to postprocess_masked_RuvA.mrc (#7)
coordinates:
Matrix rotation and translation
0.84576633 0.02145896 0.53312176 47.64653768
-0.53073005 0.13649241 0.83647799 150.16522594
-0.05481712 -0.99040866 0.12682960 296.56795682
Axis -0.91480515 0.29440771 -0.27650613
Axis point 0.00000000 240.95010376 40.57251378
Rotation angle (degrees) 86.87329771
Shift along axis -81.38035411
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right zoom
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
Drag select of
> surface dust
Missing or invalid "surfaces" argument: empty atom specifier
> surface dust 0
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #1
> surface dust #1 0
Expected a keyword
> surface undust #1
> surface dust #1
> volume #3 level 0.009129
> volume #1 level 0.009554
> surface dust #1
> surface dust #1 size 40
> surface dust #1 size 80
> surface dust #1 size 800
> surface dust #1 size 80
> volume #1 level 0.01478
> surface dust #1 size 30
> volume #1 level 0.01124
> volume #14 level 0.01078
> volume #15 level 0.0112
> volume #16 level 0.01165
> volume #17 level 0.01229
> view
> save D:/RuvAB_figures/Sessions/Figure_1/Figure_1_whole_session.cxs
> save D:/RuvAB_figures/Sessions/Figure_1/RuvA_tetramer_HJ.tif width 3123
> height 1927 supersample 3
> show #!12 models
> show #!11 models
> show #!13 models
> show #!10 models
> volume #13 level 0.009932
> volume #12 level 0.009293
> volume #11 level 0.009293
> volume #10 level 0.01517
> view
> save D:/RuvAB_figures/Sessions/Figure_1/RuvA_octamer_sideview_HJ.tif width
> 3123 height 1927 supersample 3
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting full
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> save D:/RuvAB_figures/Sessions/Figure_1/RuvA_octamer_sideview_HJ.tif width
> 3123 height 1927 supersample 3
> show #!2 models
> show #!4 models
> select #13
2 models selected
> save D:/RuvAB_figures/Sessions/Figure_1/Figure_1_whole_session.cxs
> select clear
> hide #!1 models
> hide #!2 models
> hide #!4 models
> hide #!10 models
> show #!10 models
> show #!2 models
> hide #!2 models
> show #!1 models
> fetch 1bdx
Unknown command: fetch 1bdx
> open 1bdx
Summary of feedback from opening 1bdx fetched from pdb
---
note | Fetching compressed mmCIF 1bdx from
http://files.rcsb.org/download/1bdx.cif
1bdx title:
E. Coli DNA helicase ruva with bound DNA holliday junction, α carbons and
phosphate atoms ONLY [more info...]
Chain information for 1bdx #18
---
Chain | Description
A B C D | holliday junction DNA helicase ruva
J K L M | DNA (5'-D(P*GP*CP*ap*TP*GP*CP*ap*TP*ap*TP*GP*CP*ap*TP*GP*C)-3')
> select #18
824 atoms, 816 pseudobonds, 2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "rotate selected models"
> ~select #18
Nothing selected
> select #18
824 atoms, 816 pseudobonds, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected models"
> view sel
> ui mousemode right "rotate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!14 models
> show #!14 models
> fitmap #18 inMap #14
Fit molecule 1bdx (#18) to map E.mrc (#14) using 824 atoms
average map value = 0.001451, steps = 280
shifted from previous position = 1.88
rotated from previous position = 12 degrees
atoms outside contour = 776, contour level = 0.01078
Position of 1bdx (#18) relative to E.mrc (#14) coordinates:
Matrix rotation and translation
0.95228751 -0.11337875 -0.28336156 80.86168374
0.16231297 0.97439252 0.15560759 106.04728248
0.25846279 -0.19417642 0.94630466 111.21623316
Axis -0.49871106 -0.77251615 0.39307262
Axis point -501.61702623 0.00000000 231.61014516
Rotation angle (degrees) 20.52940416
Shift along axis -78.53379846
> hide sel atoms
> show sel cartoons
> select #14
2 models selected
> select up
824 atoms, 35 models selected
> select down
2 models selected
> select /B:11
1 atom, 1 model selected
> select up
190 atoms, 1 model selected
> fitmap sel inMap #14
Fit molecule 1bdx (#18) to map E.mrc (#14) using 190 atoms
average map value = 0.005563, steps = 44
shifted from previous position = 0.224
rotated from previous position = 0.678 degrees
atoms outside contour = 151, contour level = 0.01078
Position of 1bdx (#18) relative to E.mrc (#14) coordinates:
Matrix rotation and translation
0.95236546 -0.12417098 -0.27853476 80.52125681
0.17150297 0.97330891 0.15250083 106.13075628
0.25216419 -0.19300606 0.94824147 111.29041743
Axis -0.49436913 -0.75935149 0.42306558
Axis point -513.68380933 0.00000000 246.81251681
Rotation angle (degrees) 20.45320278
Shift along axis -73.31462617
> hide #!14 models
> show #!14 models
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> fitmap sel inMap #14
Fit molecule 1bdx (#18) to map E.mrc (#14) using 190 atoms
average map value = 0.02185, steps = 152
shifted from previous position = 3.55
rotated from previous position = 21.2 degrees
atoms outside contour = 75, contour level = 0.01078
Position of 1bdx (#18) relative to E.mrc (#14) coordinates:
Matrix rotation and translation
0.99585338 -0.09078532 0.00583765 71.47088395
0.09097256 0.99394981 -0.06154484 106.93884431
-0.00021496 0.06182070 0.99808725 104.80968352
Axis 0.56138137 0.02754270 0.82709876
Axis point -1133.78269159 36.67756138 0.00000000
Rotation angle (degrees) 6.30821203
Shift along axis 129.75576644
> ui mousemode right rotate
> ui mousemode right translate
> select up
816 pseudobonds, 1 model selected
> select #1
2 models selected
> select clear
> select /B:197
1 atom, 1 model selected
> select up
190 atoms, 1 model selected
> select down
1 atom, 1 model selected
> select up
190 atoms, 1 model selected
> select down
1 atom, 1 model selected
> select up
190 atoms, 1 model selected
> select down
1 atom, 1 model selected
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> select clear
> select clear
> select /B:158
1 atom, 1 model selected
> select down
1 atom, 1 model selected
> select clear
> select /B:157
1 atom, 1 model selected
> select #1
2 models selected
> select /B:156
1 atom, 1 model selected
> select clear
> select clear
> select /B:158
1 atom, 1 model selected
> select up
190 atoms, 1 model selected
> select down
1 atom, 1 model selected
> select up
190 atoms, 1 model selected
> select down
1 atom, 1 model selected
> select up
190 atoms, 1 model selected
> select up
824 atoms, 1 model selected
> select down
190 atoms, 1 model selected
> select down
1 atom, 1 model selected
> select up
190 atoms, 1 model selected
> select down
1 atom, 1 model selected
> select up
190 atoms, 1 model selected
> select #18:153-203
192 atoms, 188 pseudobonds, 2 models selected
> surface sel
> transparency #sel 20
Missing or invalid "percent" argument: Expected a number
> transparency sel 20
> transparency sel 80
> transparency sel 70
> select #18
824 atoms, 816 pseudobonds, 2 models selected
> ~select #18
4 models selected
> hide #!18 models
> hide #18.1 models
> hide #18.2 models
> hide #18.3 models
> hide #18.4 models
> hide #18.5 models
> show #18.5 models
> hide #18.5 models
> show #18.5 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #18.5 models
> show #18.5 models
> select #18
824 atoms, 816 pseudobonds, 2 models selected
> hide sel atoms
> hide sel cartoons
> show #18.4 models
> show #18.3 models
> show #18.2 models
> select clear
> select /A:190@CA
1 atom, 1 model selected
> select up
190 atoms, 2 models selected
> transparency sel 70
> transparency sel 75
> select up
760 atoms, 5 models selected
> transparency sel 75
> hide #!15 models
> show #!15 models
> hide #!10 models
> hide #!12 models
> hide #!11 models
> hide #!13 models
> hide #!14 models
> show #!14 models
> hide #!1 models
> transparency sel 75
> show #!1 models
> transparency sel 75
> hide #!1 models
> volume #1 orthoplanes xyz positionPlanes 180,180,180 style image region all
> mousemode rightMode "move planes"
> volume #2 orthoplanes xyz positionPlanes 180,180,180 style image region all
> mousemode rightMode "move planes"
> volume #3 orthoplanes xyz positionPlanes 180,180,180 style image region all
> mousemode rightMode "move planes"
> volume #4 orthoplanes xyz positionPlanes 180,180,180 style image region all
> mousemode rightMode "move planes"
> volume #5 orthoplanes xyz positionPlanes 180,180,180 style image region all
> mousemode rightMode "move planes"
> volume #7 orthoplanes xyz positionPlanes 180,180,180 style image region all
> mousemode rightMode "move planes"
> volume #8 orthoplanes xyz positionPlanes 180,180,180 style image region all
> mousemode rightMode "move planes"
> volume #6 orthoplanes xyz positionPlanes 180,180,180 style image region all
> mousemode rightMode "move planes"
> volume #9 orthoplanes xyz positionPlanes 180,180,180 style image region all
> mousemode rightMode "move planes"
> volume #10 orthoplanes xyz positionPlanes 100,100,100 style image region all
> mousemode rightMode "move planes"
> volume #11 orthoplanes xyz positionPlanes 100,100,100 style image region all
> mousemode rightMode "move planes"
> volume #12 orthoplanes xyz positionPlanes 100,100,100 style image region all
> mousemode rightMode "move planes"
> volume #13 orthoplanes xyz positionPlanes 100,100,100 style image region all
> mousemode rightMode "move planes"
> volume #14 orthoplanes xyz positionPlanes 100,100,100 style image region all
> mousemode rightMode "move planes"
> volume #15 orthoplanes xyz positionPlanes 100,100,100 style image region all
> mousemode rightMode "move planes"
> volume #16 orthoplanes xyz positionPlanes 100,100,100 style image region all
> mousemode rightMode "move planes"
> volume #17 orthoplanes xyz positionPlanes 100,100,100 style image region all
> mousemode rightMode "move planes"
> volume #!14-17 region all imageMode "full region"
> mousemode rightMode "crop volume"
> volume #!14-17 region all imageMode "full region"
> mousemode rightMode "crop volume"
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> volume #!1,10-14,16-17 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> volume #!1,10-14,16-17 region all imageMode "full region"
> mousemode rightMode "crop volume"
> show #!3 models
> hide #!3 models
> show #!2 models
> volume #!1-2,10-14,16-17 style surface
> show #!4 models
> show #!3 models
> volume #!1-4,10-14,16-17 style surface
> volume #1 region 0,0,0,359,359,359
> show #18.1 models
> hide #18.1 models
> show #!15 models
> volume #!1-4,10-17 style surface
> volume #1 region 0,0,0,359,359,359
> view sel
> volume #1 region 0,0,0,359,359,359
> ui mousemode right zoom
> ui tool show "Side View"
> ui mousemode right translate
> ui mousemode right rotate
> show #18.1 models
> hide #18.1 models
> select #18
824 atoms, 816 pseudobonds, 2 models selected
> show #17.2 models
> hide #17.2 models
> show #17.2 models
> hide #17.2 models
> show #4.2 models
> hide #4.2 models
> show #4.2 models
> hide #4.2 models
> close #4.2
> close #1.2
> close #2.2
> close #3.2
> close #10.2
> close #11.2#12.2
> close #17.2
> close #13.2#14.2#15.2#16.2
> view sel
> ui tool show "Side View"
> volume #!1-4,10-17 showOutlineBox false
> hide #!1 models
> hide #1.1 models
> hide #!2 models
> hide #1-2,4-18#!3 target m
> show #18.5 models
> hide #18.5 models
> show #18.4 models
> show #18.5 models
> show #18.3 models
> show #18.2 models
> show #!17 models
> hide #!17 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> show #17.1 models
> show #16.1 models
> show #15.1 models
> show #14.1 models
> ui mousemode right rotate
> show #!1 models
> hide #!1 models
> show #1.1 models
> select clear
> hide #!1 models
> view
> save D:/RuvAB_figures/Sessions/Figure_1/Figure_1_Flexible_N_terminal.cxs
> save D:/RuvAB_figures/Sessions/Figure_1/RuvA_flexible_N_terminal.tif width
> 3123 height 1906 supersample 3
> lighting full
> lighting soft
> lighting soft
> lighting flat
> view
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting flat
> select /D:160@CA
1 atom, 1 model selected
> select /D:190@CA
1 atom, 1 model selected
> select up
760 atoms, 5 models selected
> select #18
824 atoms, 816 pseudobonds, 2 models selected
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> volume #!14-17 style mesh
> volume #!14-17 style surface
> volume #!14-17 style mesh
> volume #!14-17 style mesh
> volume #!14-17 style surface
> volume #!14-17 style surface
> volume #!14-17 style surface
> select #17
2 models selected
> select #16
2 models selected
> select #15
2 models selected
> select #14
2 models selected
> select #15
2 models selected
> volume sel style surface
> volume sel style surface
> lighting soft
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting soft
> lighting flat
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> select /B:191@CA
1 atom, 1 model selected
> select up
760 atoms, 5 models selected
> molmap sel 4
> hide #19.1 models
> show #19.1 models
> hide #19.1 models
> show #19.1 models
> hide #19.1 models
> hide #!18 models
> hide #17.1 models
> hide #!17 models
> show #17.1 models
> show #18.1 models
> hide #18.1 models
> hide #!18 models
> show #19.1 models
> hide #19.1 models
> close #19
> select #18:153-203
192 atoms, 188 pseudobonds, 2 models selected
> molmap sel 4
> select #19
2 models selected
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting flat
> select #17
2 models selected
> volume sel style surface
> volume sel style surface
> select #19
2 models selected
> hide #19.1 models
> show #19.1 models
> transparency #14.1#15.1#16.1#17.1#19.1 50
> volume #!14-17,19 style mesh
> hide #!14 models
> hide #14.1 models
> hide #!15 models
> hide #!16 models
> hide #17.1 models
> hide #!17 models
> hide #16.1 models
> hide #15.1 models
> hide #18.2 models
> hide #18.3 models
> hide #18.4 models
> hide #18.5 models
> hide #!19 models
> show #!19 models
> select #19
2 models selected
> volume sel style surface
> show #14.1 models
> hide #14.1 models
> show #14.1 models
> show #15.1 models
> show #!16 models
> show #16.1 models
> show #17.1 models
> volume sel style mesh
> volume sel style surface
> select #15
2 models selected
> volume sel style surface
> lighting soft
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting soft
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes true
> volume sel style surface
> transparency sel 0
> lighting soft
> lighting flat
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> hide #14-17 target m
> select #19
2 models selected
> lighting soft
> lighting soft
> volume sel style mesh
> graphics silhouettes false
> volume sel style surface
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> show #!17 models
> hide #!17 models
> show #!17 models
> show #17.1 models
> show #16.1 models
> show #15.1 models
> show #14.1 models
> select #17
2 models selected
> lighting soft
> hide #!19 models
> show #!19 models
> hide #19.1 models
> show #19.1 models
> select #19
2 models selected
> molmap sel 8
No atoms specified
> select #18:153-203
192 atoms, 188 pseudobonds, 2 models selected
> molmap sel 8
> molmap sel 6
> molmap sel 4
> molmap sel 4
> view sel
> save D:/RuvAB_figures/Sessions/Figure_1/RuvA_flexible_N_terminal.tif width
> 3123 height 1906 supersample 3
> save D:/RuvAB_figures/Sessions/Figure_1/Figure_1_Flexible_N_terminal.cxs
> hide #19.1 models
> hide #!19 models
> hide #17.1 models
> hide #!17 models
> hide #16.1 models
> hide #!16 models
> hide #15.1 models
> show #!2 models
> hide #!2 models
> hide #1.1 models
> show #!3 models
> show #!6 models
> close #6.2
> volume #!3,6,14-15 showOutlineBox false
> volume #!3,6,14-15 showOutlineBox true
> volume #!3,6,14-15 showOutlineBox false
> volume #!3,6,14-15 showOutlineBox true
> volume #!3,6,14-15 showOutlineBox false
> volume #!3,6,14-15 showOutlineBox true
> volume #2 change image level -0.001113,0 level 0.003454,0.8 level 0.0691,1
> view sel
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #2.1 models
> hide #!3 models
> hide #!6 models
> hide #3.1 models
> hide #!15 models
> hide #!14 models
> hide #14.1 models
> select #18
824 atoms, 816 pseudobonds, 2 models selected
> ~select #18.1
824 atoms, 5 models selected
> ~select #18.2
634 atoms, 5 models selected
> ~select #18.3
444 atoms, 4 models selected
> ~select #18.4
254 atoms, 3 models selected
> ~select #18.5
64 atoms, 2 models selected
> select #18
824 atoms, 816 pseudobonds, 2 models selected
> ~select #18
4 models selected
> show #1.1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #2.1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> volume #!1-3 showOutlineBox false
> show #6.1 models
> show #5.1 models
> close #5.2
> hide #!5 models
> hide #5.1 models
> hide #!6 models
> show #4.1 models
> hide #4.1 models
> show #5.1 models
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> show #!6 models
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\sideview\tool.py", line 112, in _redraw
self.render()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\sideview\tool.py", line 142, in render
mvwin = self.view.render.use_shared_context(self)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 476, in use_shared_context
self.make_current()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 431, in make_current
return self._opengl_context.make_current()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 135, in make_current
raise OpenGLError("Could not make graphics context current")
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current
Error processing trigger "frame drawn":
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 135, in make_current
raise OpenGLError("Could not make graphics context current")
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\ui\graphics.py", line 123, in resizeEvent
v.resize(w, h)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\view.py", line 498, in resize
r.set_default_framebuffer_size(width, height)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 516, in
set_default_framebuffer_size
s = self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\view.py", line 140, in draw
if not self._use_opengl():
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\view.py", line 105, in _use_opengl
if not self._render.make_current():
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 431, in make_current
return self._opengl_context.make_current()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 134, in make_current
if not qc.makeCurrent(w):
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\ui\graphics.py", line 56, in event
self._check_opengl()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\ui\graphics.py", line 64, in _check_opengl
mc = r.make_current()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 431, in make_current
return self._opengl_context.make_current()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 134, in make_current
if not qc.makeCurrent(w):
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 134, in make_current
if not qc.makeCurrent(w):
See log for complete Python traceback.
> show #5.1 models
> hide #!1 models
> show #!1 models
> view
> hide #6.1 models
> lighting soft
> volume #!1-6 style surface
> volume #1 step 4
> volume #1 step 1
> volume #1 change image level 3.382e-06,0 level 0.005289,0.8 level 0.05286,1
> volume #1 level 0.006175
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\ui\graphics.py", line 123, in resizeEvent
v.resize(w, h)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\view.py", line 498, in resize
r.set_default_framebuffer_size(width, height)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 516, in
set_default_framebuffer_size
s = self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 730, in moveEvent
if not hasattr(self, '_last_pixel_scale') or r.pixel_scale() !=
self._last_pixel_scale:
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1068, in pixel_scale
return self._opengl_context.pixel_scale()
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
RuntimeError: wrapped C/C++ object of type SideViewCanvas has been deleted
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 237, in pixel_scale
return self.window.devicePixelRatio()
See log for complete Python traceback.
OpenGL version: unknown
Could not make opengl context current
Manufacturer: Alienware
Model: Alienware 13 R3
OS: Microsoft Windows 10 Pro (Build 18362)
Memory: 34,186,350,592
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
Change History (3)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → wrapped C/C++ object of type SideViewCanvas has been deleted |
| Version: | → 1.0 |
comment:2 by , 5 years ago
follow-up: 3 comment:3 by , 5 years ago
One possibility is that the QWindow becomes unusable before the Qt closeEvent() method is called. In this case the side view render code would need to check if the window has been deleted so it does not try to render because it would not be guaranteed to have been notified before the QWindow became unusable.
Note:
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Somehow Side View seems to have tried to render after its canvas window had been destroyed. That is probably why make_current() failed (the first error). That make_current() failure in Render.use_shared_context() left the OpenGLContext.window set to the deleted window which caused all the subsequent errors. I have fixed the use_shared_context() code so if make_current() fails it does not set OpenGLContext.window. But the underlying problem is that Side View was somehow closed and later tried to render. Specifically a "frame drawn" trigger fired and side view tried to redraw itself in response, but make current on the side view canvas window failed suggesting the window had been deleted (as later errors say the window was deleted). The SideViewUI ToolWindow close method removes the "frame drawn" trigger so it seems the SideViewUI.close() had not been called yet.