id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3605 wrapped C/C++ object of type SideViewCanvas has been deleted chimerax-bug-report@… Greg Couch "{{{ 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 }}} " defect assigned normal Graphics 1.0 Tom Goddard all ChimeraX