id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14894 ISOLDE: ResidueStepper holding reference to closed structure chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-14.0-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > set bgColor transparent Log from Tue Apr 2 09:02:03 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/cryosparc/P6-P29/NU-refinement- > comparison-J891-J898/volume_aligned_rigid_body_docked_model-colored.cxs Opened cryosparc_P29_J810_class_02_00202_volume.mrc z flip as #4, grid size 128,128,128, pixel 3.51, shown at level 0.442, step 1, values float32 Opened cryosparc_P29_J891_004_volume_map.mrc as #1, grid size 270,270,270, pixel 1.67, shown at level 0.261, step 2, values float32 Opened cryosparc_P29_J892_003_volume_map.mrc as #2, grid size 270,270,270, pixel 1.67, shown at level 0.132, step 2, values float32 Opened cryosparc_P29_J898_004_volume_map.mrc as #6, grid size 270,270,270, pixel 1.67, shown at level 0.18, step 2, values float32 Opened cryosparc_P29_J894_003_volume_map.mrc z flip as #7, grid size 270,270,270, pixel 1.67, shown at level 0.269, step 1, values float32 Opened cryosparc_P29_J895_004_volume_map.mrc z flip as #3, grid size 270,270,270, pixel 1.67, shown at level 0.174, step 1, values float32 Log from Mon Apr 1 13:51:22 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/isolde/chimeraXsessions/Rigid-body- > docked-atomic-model-J810-low-res-density-full-complex.cxs format session Opened cryosparc_P29_J810_class_02_00202_volume.mrc z flip as #4, grid size 128,128,128, pixel 3.51, shown at level 0.442, step 1, values float32 Log from Tue Mar 26 12:11:35 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job009/chimera.session/10-class-3d-classification- > with-alignment.cxs Opened run_it016_class001.mrc as #1, grid size 336,336,336, pixel 1.07, shown at level 0.000912, step 2, values float32 Opened run_it016_class002.mrc as #2, grid size 336,336,336, pixel 1.07, shown at level 0.000912, step 2, values float32 Opened run_it016_class003.mrc as #3, grid size 336,336,336, pixel 1.07, shown at level 0.000912, step 2, values float32 Opened run_it016_class004.mrc as #4, grid size 336,336,336, pixel 1.07, shown at level 0.000912, step 2, values float32 Opened run_it016_class005.mrc as #5, grid size 336,336,336, pixel 1.07, shown at level 0.000912, step 2, values float32 Opened run_it016_class006.mrc as #6, grid size 336,336,336, pixel 1.07, shown at level 0.00185, step 2, values float32 Opened run_it016_class007.mrc as #7, grid size 336,336,336, pixel 1.07, shown at level 0.00202, step 2, values float32 Opened run_it016_class008.mrc as #8, grid size 336,336,336, pixel 1.07, shown at level 0.000912, step 2, values float32 Opened run_it016_class009.mrc as #9, grid size 336,336,336, pixel 1.07, shown at level 0.00177, step 2, values float32 Opened run_it016_class010.mrc as #10, grid size 336,336,336, pixel 1.07, shown at level 0.000912, step 2, values float32 Log from Thu Jan 18 21:16:39 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-apo/relion/g52h115_relion/Class3D/job009/run_it016_class001.mrc Opened run_it016_class001.mrc as #1, grid size 336,336,336, pixel 1.07, shown at level 0.00165, step 2, values float32 > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-apo/relion/g52h115_relion/Class3D/job009/run_it016_class002.mrc Opened run_it016_class002.mrc as #2, grid size 336,336,336, pixel 1.07, shown at level 0.00259, step 2, values float32 > volume #1 level 0.0008843 > volume #2 level 0.00105 > volume #2 level 0.002345 > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-apo/relion/g52h115_relion/Class3D/job009/run_it016_class003.mrc Opened run_it016_class003.mrc as #3, grid size 336,336,336, pixel 1.07, shown at level 0.00226, step 2, values float32 > hide #!2 models > hide #!1 models > show #!2 models > show #!1 models > hide #!2 models > hide #!3 models > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-apo/relion/g52h115_relion/Class3D/job009/run_it016_class004.mrc Opened run_it016_class004.mrc as #4, grid size 336,336,336, pixel 1.07, shown at level 0.0019, step 2, values float32 > hide #!1 models > hide #!2 models > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-apo/relion/g52h115_relion/Class3D/job009/run_it016_class005.mrc Opened run_it016_class005.mrc as #5, grid size 336,336,336, pixel 1.07, shown at level 0.000937, step 2, values float32 > hide #!4 models > volume #5 level 0.0005099 > volume #5 level 0.0001773 > volume #5 level 0.001056 > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-apo/relion/g52h115_relion/Class3D/job009/run_it016_class006.mrc Opened run_it016_class006.mrc as #6, grid size 336,336,336, pixel 1.07, shown at level 0.00185, step 2, values float32 > hide #!5 models > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-apo/relion/g52h115_relion/Class3D/job009/run_it016_class007.mrc Opened run_it016_class007.mrc as #7, grid size 336,336,336, pixel 1.07, shown at level 0.00202, step 2, values float32 > hide #!6 models > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-apo/relion/g52h115_relion/Class3D/job009/run_it016_class008.mrc Opened run_it016_class008.mrc as #8, grid size 336,336,336, pixel 1.07, shown at level 0.00185, step 2, values float32 > hide #!7 models > volume #8 level 0.0008233 > volume #8 level 0.00097 > volume #8 level 0.001133 > volume #8 level 0.001198 > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-apo/relion/g52h115_relion/Class3D/job009/run_it016_class009.mrc Opened run_it016_class009.mrc as #9, grid size 336,336,336, pixel 1.07, shown at level 0.00177, step 2, values float32 > hide #!8 models > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-apo/relion/g52h115_relion/Class3D/job009/run_it016_class010.mrc Opened run_it016_class010.mrc as #10, grid size 336,336,336, pixel 1.07, shown at level 0.00205, step 2, values float32 > hide #!9 models > show #!1 models > hide #!10 models > show #!10 models > show #!9 models > show #!8 models > show #!7 models > show #!6 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > tile 10 models tiled > volume #1 level 0.002459 [Repeated 1 time(s)] > volume #1 level 0.0009124 > volume #2 level 0.000912 > volume #3 level 0.000912 > volume #4 level 0.000912 > volume #5 level 0.000912 > volume #8 level 0.000912 > volume #10 level 0.000912 > ~tile > save /Users/whenriques/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job009/chimera.session/10-class-3d-classification- > with-alignment.cxs includeMaps true ——— End of log from Thu Jan 18 21:16:39 2024 ——— opened ChimeraX session > set bgColor white > tile 10 models tiled > lighting soft > graphics silhouettes true > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job009/chimera.session/10-class-3d-classification- > with-alignment.cxs includeMaps true > ~tile > tile 10 models tiled > lighting soft > save ""/Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job009/New > Folder/10-class-3d-classification-with-alignment.png"" width 899 height 804 > supersample 3 transparentBackground true Directory ""/Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- complex/cryoem/cas1-2-3-apo/relion/Class3D/job009/New Folder"" does not exist > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job009/png/10-class-3d-classification- > with-alignment.png width 899 height 804 supersample 3 transparentBackground > true > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/run_it020_class001.mrc Opened run_it020_class001.mrc as #1, grid size 336,336,336, pixel 1.07, shown at level 0.00328, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/run_it020_class002.mrc Opened run_it020_class002.mrc as #2, grid size 336,336,336, pixel 1.07, shown at level 0.00201, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/run_it020_class003.mrc Opened run_it020_class003.mrc as #3, grid size 336,336,336, pixel 1.07, shown at level 0.00145, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/run_it020_class004.mrc Opened run_it020_class004.mrc as #4, grid size 336,336,336, pixel 1.07, shown at level 0.0014, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/run_it020_class005.mrc Opened run_it020_class005.mrc as #5, grid size 336,336,336, pixel 1.07, shown at level 0.00214, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/run_it020_class006.mrc Opened run_it020_class006.mrc as #6, grid size 336,336,336, pixel 1.07, shown at level 0.00199, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/run_it020_class007.mrc Opened run_it020_class007.mrc as #7, grid size 336,336,336, pixel 1.07, shown at level 0.00134, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/run_it020_class008.mrc Opened run_it020_class008.mrc as #8, grid size 336,336,336, pixel 1.07, shown at level 0.00198, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/run_it020_class009.mrc Opened run_it020_class009.mrc as #9, grid size 336,336,336, pixel 1.07, shown at level 0.00184, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/run_it020_class010.mrc Opened run_it020_class010.mrc as #10, grid size 336,336,336, pixel 1.07, shown at level 0.002, step 2, values float32 > lighting soft > set bgColor white > graphics silhouettes true > tile 10 models tiled > volume #1 level 0.001984 > volume #3 level 0.00201 > volume #4 level 0.00201 > volume #5 level 0.00201 > volume #6 level 0.00201 > volume #7 level 0.00201 > volume #8 level 0.00201 > volume #9 level 0.00201 > volume #10 level 0.00201 > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/chimerax.session/compare- > classes-threshold0-00201.cxs includeMaps true > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/png/spacer- > face.png width 899 height 804 supersample 3 transparentBackground true > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/png/side- > view.png width 899 height 804 supersample 3 transparentBackground true > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/jop010_T4_20its_alignment/png/repeat- > face.png width 899 height 804 supersample 3 transparentBackground true > lighting soft > volume #10 level 0.001783 > volume #2 level 0.00146 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/relion/PostProcess/job034/postprocess.mrc Opened postprocess.mrc as #11, grid size 270,270,270, pixel 1.67, shown at level 0.00829, step 2, values float32 > close #1-10 > ~tile > volume #11 level 0.00902 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/relion/Refine3D/job036/run_class001.mrc Opened run_class001.mrc as #1, grid size 270,270,270, pixel 1.67, shown at level 0.00344, step 2, values float32 > hide #!11 models > volume #1 level 0.005459 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/relion/PostProcess/job036/run_class001.mrc Opened run_class001.mrc as #2, grid size 270,270,270, pixel 1.67, shown at level 0.00344, step 2, values float32 > volume #2 level 0.001851 > volume #1 level 0.003873 > volume #11 level 0.0122 > hide #!2 models > hide #!11 models > hide #!1 models > show #!11 models > close #1 > close > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/relion/PostProcess/job037/postprocess_masked.mrc Opened postprocess_masked.mrc as #1, grid size 270,270,270, pixel 1.67, shown at level 0.00129, step 2, values float32 > volume #1 step 1 > volume #1 level 0.003481 > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/relion/PostProcess/job037/postprocess-threshold00348.png width 899 > height 804 supersample 3 transparentBackground true > volume #1 level 0.01151 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/relion/PostProcess/job037/postprocess.mrc Opened postprocess.mrc as #2, grid size 270,270,270, pixel 1.67, shown at level 0.0082, step 2, values float32 > volume #2 step 1 > volume #2 level 0.01641 > hide #!1 models > volume #2 level 0.01203 > close #1 > close > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J138/cryosparc_P29_cryosparc_P6_J138_class_00_00162_volume.mrc Opened cryosparc_P29_cryosparc_P6_J138_class_00_00162_volume.mrc as #1, grid size 128,128,128, pixel 3.51, shown at level 0.235, step 1, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J138/cryosparc_P29_cryosparc_P6_J138_class_01_00162_volume.mrc Opened cryosparc_P29_cryosparc_P6_J138_class_01_00162_volume.mrc as #2, grid size 128,128,128, pixel 3.51, shown at level 0.213, step 1, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J138/cryosparc_P29_cryosparc_P6_J138_class_02_00162_volume.mrc Opened cryosparc_P29_cryosparc_P6_J138_class_02_00162_volume.mrc as #3, grid size 128,128,128, pixel 3.51, shown at level 0.194, step 1, values float32 > tile 3 models tiled > volume #2 level 0.235 > volume #3 level 0.235 > volume #1 level 0.347 > volume #1 level 0.2525 > volume #2 level 0.252 > volume #3 level 0.252 > lighting soft > graphics silhouettes false > graphics silhouettes true > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J138/chimeraXsession/representative-3-class-abinitio- > het.cxs > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J138/pngs/representative-3class-abinitio-het.png > width 899 height 804 supersample 3 transparentBackground true > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/cryosparc_P29_J810_class_00_00202_volume.mrc Opened cryosparc_P29_J810_class_00_00202_volume.mrc as #4, grid size 128,128,128, pixel 3.51, shown at level 0.199, step 1, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/cryosparc_P29_J810_class_01_00202_volume.mrc Opened cryosparc_P29_J810_class_01_00202_volume.mrc as #5, grid size 128,128,128, pixel 3.51, shown at level 0.207, step 1, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/cryosparc_P29_J810_class_02_00202_volume.mrc Opened cryosparc_P29_J810_class_02_00202_volume.mrc as #6, grid size 128,128,128, pixel 3.51, shown at level 0.238, step 1, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/cryosparc_P29_J810_class_03_00202_volume.mrc Opened cryosparc_P29_J810_class_03_00202_volume.mrc as #7, grid size 128,128,128, pixel 3.51, shown at level 0.214, step 1, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/cryosparc_P29_J810_class_04_00202_volume.mrc Opened cryosparc_P29_J810_class_04_00202_volume.mrc as #8, grid size 128,128,128, pixel 3.51, shown at level 0.241, step 1, values float32 > undo [Repeated 1 time(s)] > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/cryosparc_P29_J810_class_00_00202_volume.mrc Opened cryosparc_P29_J810_class_00_00202_volume.mrc as #1, grid size 128,128,128, pixel 3.51, shown at level 0.199, step 1, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/cryosparc_P29_J810_class_01_00202_volume.mrc Opened cryosparc_P29_J810_class_01_00202_volume.mrc as #2, grid size 128,128,128, pixel 3.51, shown at level 0.207, step 1, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/cryosparc_P29_J810_class_02_00202_volume.mrc Opened cryosparc_P29_J810_class_02_00202_volume.mrc as #3, grid size 128,128,128, pixel 3.51, shown at level 0.238, step 1, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/cryosparc_P29_J810_class_03_00202_volume.mrc Opened cryosparc_P29_J810_class_03_00202_volume.mrc as #4, grid size 128,128,128, pixel 3.51, shown at level 0.214, step 1, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/cryosparc_P29_J810_class_04_00202_volume.mrc Opened cryosparc_P29_J810_class_04_00202_volume.mrc as #5, grid size 128,128,128, pixel 3.51, shown at level 0.241, step 1, values float32 > tile 5 models tiled > lighting soft > set bgColor white > lighting soft > graphics silhouettes true > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/chimerax.session/5-class-ab-inito-het- > refine-J810.cxs includeMaps true > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/cryosparc/P6-P29/J810/png/5-class- > ab-initio-het-refine-J810.png width 899 height 804 supersample 3 > transparentBackground true > close session > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-prespacer/relion/g52h115_relion/Class3D/job039/run_it040_class001.mrc Opened run_it040_class001.mrc as #1, grid size 270,270,270, pixel 1.67, shown at level 0.00699, step 2, values float32 > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-prespacer/relion/g52h115_relion/Class3D/job039/run_it040_class002.mrc Opened run_it040_class002.mrc as #2, grid size 270,270,270, pixel 1.67, shown at level 0.00775, step 2, values float32 > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-prespacer/relion/g52h115_relion/Class3D/job039/run_it040_class003.mrc Opened run_it040_class003.mrc as #3, grid size 270,270,270, pixel 1.67, shown at level 0.00765, step 2, values float32 > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-prespacer/relion/g52h115_relion/Class3D/job039/run_it040_class004.mrc Opened run_it040_class004.mrc as #4, grid size 270,270,270, pixel 1.67, shown at level 0.00653, step 2, values float32 > tile 4 models tiled > lighting soft > graphics silhouettes true > set bgColor white > volume #1 level 0.007 > volume #2 level 0.007 > volume #3 level 0.007 > volume #4 level 0.007 > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/relion/Class3D/job039-4class- > noalign/chimerax.session/compare-4class.cxs includeMaps true > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/relion/Class3D/job039-4class- > noalign/png/4-class-compare.png width 899 height 804 supersample 3 > transparentBackground true > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/cryosparc_P29_J810_class_03_00202_volume.mrc Opened cryosparc_P29_J810_class_03_00202_volume.mrc as #1, grid size 128,128,128, pixel 3.51, shown at level 0.214, step 1, values float32 > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J810/cryosparc_P29_J810_class_02_00202_volume.mrc Opened cryosparc_P29_J810_class_02_00202_volume.mrc as #1, grid size 128,128,128, pixel 3.51, shown at level 0.238, step 1, values float32 > volume #1 level 0.3967 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/AlphaFold/Cas1-AF-Q02ML7-F1-model_v4.pdb Cas1-AF-Q02ML7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for crispr-associated endonuclease CAS1 (Q02ML7) [more info...] Chain information for Cas1-AF-Q02ML7-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | crispr-associated endonuclease CAS1 | CAS1_PSEAB 1-324 > select add #2 2549 atoms, 2602 bonds, 324 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,12.452,0,1,0,213.26,0,0,1,267.2 > view matrix models #2,1,0,0,205.61,0,1,0,245.67,0,0,1,255.32 > view matrix models #2,1,0,0,278.52,0,1,0,283.04,0,0,1,233.07 > view matrix models #2,1,0,0,270,0,1,0,291.16,0,0,1,256.7 > select subtract #1 340 atoms, 44 residues, 1 model selected > select add #2 2549 atoms, 2602 bonds, 324 residues, 1 model selected > select subtract #2 Nothing selected > select add #2 2549 atoms, 2602 bonds, 324 residues, 1 model selected > view matrix models #2,1,0,0,271.89,0,1,0,289.83,0,0,1,250.1 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.77164,-0.064513,-0.63278,269.29,-0.28733,0.8522,-0.43726,279.41,0.56747,0.51922,0.63905,273 > view matrix models > #2,0.61816,-0.70241,-0.35286,273.83,0.60255,0.7117,-0.36113,289.02,0.50479,0.010619,0.86318,277.17 > view matrix models > #2,0.37346,0.12879,-0.91866,263.4,0.51722,0.79319,0.32146,288.84,0.77008,-0.5952,0.22961,283.58 > view matrix models > #2,0.49054,0.11037,-0.8644,264.75,0.52589,0.75346,0.39464,289.4,0.69485,-0.64817,0.31156,283.49 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.49054,0.11037,-0.8644,219.58,0.52589,0.75346,0.39464,295.9,0.69485,-0.64817,0.31156,265.12 > view matrix models > #2,0.49054,0.11037,-0.8644,215.94,0.52589,0.75346,0.39464,290.89,0.69485,-0.64817,0.31156,256.54 > view matrix models > #2,0.48853,0.10606,-0.86607,215.15,0.54442,0.73862,0.39755,289.84,0.68187,-0.66572,0.3031,254.21 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.19042,-0.63302,0.75035,221.77,-0.33426,-0.76048,-0.55673,292.6,0.92305,-0.1448,-0.3564,250.75 > view matrix models > #2,-0.014916,-0.16189,0.9867,216.31,-0.30796,-0.93809,-0.15858,295.12,0.95128,-0.30622,-0.035864,253 > open 8flj Summary of feedback from opening 8flj fetched from pdb --- warnings | Atom H1 is not in the residue template for GLY /F:1 Atom H1 is not in the residue template for GLY /H:1 Atom H1 is not in the residue template for MET /M:1 Atom H1 is not in the residue template for MET /N:1 8flj title: Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA [more info...] Chain information for 8flj #3 --- Chain | Description | UniProt A B C D | CRISPR-associated endonuclease Cas1 | CAS1_PSEAB 1-324 E G | Integration host factor subunit alpha | IHFA_PSEAB 3-102 F H | Integration host factor subunit beta | IHFB_PSEAB 3-96 I | CRISPR leader, sense strand of DNA | J | CRISPR leader and repeat, anti-sense strand of DNA | K | CRISPR repeat and prespacer, sense strand of DNA | L | Prespacer, anti-sense strand of DNA | M N | CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST | CAS3_PSEAB 1-1076 > view matrix models > #2,-0.28288,0.16959,0.94404,210.92,-0.27995,-0.95599,0.087846,296.01,0.91739,-0.23944,0.31791,252.8 > view matrix models > #2,-0.11676,-0.68033,-0.72354,216.5,-0.94115,0.30847,-0.13817,278.67,0.31719,0.66483,-0.67631,237.62 > fitmap #3 inMap #1 Fit molecule 8flj (#3) to map cryosparc_P29_J810_class_02_00202_volume.mrc (#1) using 57091 atoms average map value = 0.6379, steps = 232 shifted from previous position = 35.3 rotated from previous position = 49.1 degrees atoms outside contour = 29814, contour level = 0.39667 Position of 8flj (#3) relative to cryosparc_P29_J810_class_02_00202_volume.mrc (#1) coordinates: Matrix rotation and translation 0.92972747 0.36795121 0.01479001 -53.45495800 -0.27356419 0.66323210 0.69662458 9.44224116 0.24651465 -0.65171703 0.71728338 157.77437844 Axis -0.89232267 -0.15335368 -0.42455023 Axis point 0.00000000 192.18185835 83.91575803 Rotation angle (degrees) 49.07113873 Shift along axis -20.73207995 > select subtract #2 Nothing selected > select add #3 57091 atoms, 58374 bonds, 431 pseudobonds, 3899 residues, 3 models selected > view matrix models > #3,-0.91967,-0.39247,0.012858,453.12,0.37622,-0.87127,0.3152,296.33,-0.1125,0.29472,0.94894,-26.179 > view matrix models > #3,-0.885,-0.36585,-0.28797,502.8,0.40441,-0.91052,-0.086087,381.98,-0.23071,-0.19264,0.95376,99.272 > view matrix models > #3,-0.97304,-0.22216,-0.06197,441.88,0.22996,-0.91381,-0.33478,466.15,0.017747,-0.34,0.94026,87.553 > fitmap #3 inMap #1 Fit molecule 8flj (#3) to map cryosparc_P29_J810_class_02_00202_volume.mrc (#1) using 57091 atoms average map value = 0.6435, steps = 176 shifted from previous position = 59.7 rotated from previous position = 23.9 degrees atoms outside contour = 27787, contour level = 0.39667 Position of 8flj (#3) relative to cryosparc_P29_J810_class_02_00202_volume.mrc (#1) coordinates: Matrix rotation and translation -0.94413765 -0.26363340 -0.19774107 519.99772405 0.32755005 -0.68467401 -0.65110096 428.87709776 0.03626380 -0.67949903 0.73277964 202.22948265 Axis -0.04461981 -0.36767475 0.92888339 Axis point 226.91898974 300.21401884 0.00000000 Rotation angle (degrees) 161.44452801 Shift along axis 6.95812960 > view matrix models > #3,-0.94628,-0.2612,-0.19059,518.4,0.28111,-0.95583,-0.085774,379.47,-0.15977,-0.13474,0.97792,71.405 > volume flip #1 Opened cryosparc_P29_J810_class_02_00202_volume.mrc z flip as #4, grid size 128,128,128, pixel 3.51, shown at step 1, values float32 > fitmap #3 inMap #4 Fit molecule 8flj (#3) to map cryosparc_P29_J810_class_02_00202_volume.mrc z flip (#4) using 57091 atoms average map value = 0.8723, steps = 92 shifted from previous position = 27.6 rotated from previous position = 8.05 degrees atoms outside contour = 18166, contour level = 0.39667 Position of 8flj (#3) relative to cryosparc_P29_J810_class_02_00202_volume.mrc z flip (#4) coordinates: Matrix rotation and translation -0.91185153 -0.37635412 -0.16396450 525.51517760 0.38123047 -0.92447815 0.00186367 323.35261375 -0.15228300 -0.06080888 0.98646448 27.60581454 Axis -0.08243543 -0.01536510 0.99647795 Axis point 231.89079576 213.79154199 0.00000000 Rotation angle (degrees) 157.65819422 Shift along axis -20.78082655 > delete #3/I > hide #!4 models > delete #3/IJ > delete #3/J > delete #3/E-F > delete #3/G-H > close #1 > show #!4 models > transparency 50 > mmaker #2 to #3/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8flj, chain A (#3) with Cas1-AF-Q02ML7-F1-model_v4.pdb, chain A (#2), sequence alignment score = 1506.6 RMSD between 207 pruned atom pairs is 0.644 angstroms; (across all 310 pairs: 10.133) > hide #!3 models > show #!3 models > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/AlphaFold/Cas1-AF-Q02ML7-F1-model_v4.pdb Cas1-AF-Q02ML7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for crispr-associated endonuclease CAS1 (Q02ML7) [more info...] Chain information for Cas1-AF-Q02ML7-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | crispr-associated endonuclease CAS1 | CAS1_PSEAB 1-324 > mmaker #1 to #3/B Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8flj, chain B (#3) with Cas1-AF-Q02ML7-F1-model_v4.pdb, chain A (#1), sequence alignment score = 1556.7 RMSD between 304 pruned atom pairs is 0.806 angstroms; (across all 317 pairs: 1.641) > hide #!3 models > show #!3 models > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/AlphaFold/Cas1-AF-Q02ML7-F1-model_v4.pdb Cas1-AF-Q02ML7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for crispr-associated endonuclease CAS1 (Q02ML7) [more info...] Chain information for Cas1-AF-Q02ML7-F1-model_v4.pdb #5 --- Chain | Description | UniProt A | crispr-associated endonuclease CAS1 | CAS1_PSEAB 1-324 > mmaker #5 to #3/C Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8flj, chain C (#3) with Cas1-AF-Q02ML7-F1-model_v4.pdb, chain A (#5), sequence alignment score = 1523.4 RMSD between 200 pruned atom pairs is 0.692 angstroms; (across all 303 pairs: 10.210) > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/AlphaFold/Cas1-AF-Q02ML7-F1-model_v4.pdb Cas1-AF-Q02ML7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for crispr-associated endonuclease CAS1 (Q02ML7) [more info...] Chain information for Cas1-AF-Q02ML7-F1-model_v4.pdb #6 --- Chain | Description | UniProt A | crispr-associated endonuclease CAS1 | CAS1_PSEAB 1-324 > mmaker #6 to #3/D Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8flj, chain D (#3) with Cas1-AF-Q02ML7-F1-model_v4.pdb, chain A (#6), sequence alignment score = 1608.9 RMSD between 303 pruned atom pairs is 0.869 angstroms; (across all 315 pairs: 1.647) > hide #!3 models > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/AlphaFold/Cas23_AF-Q02ML8-F1-model_v4(1).pdb Cas23_AF-Q02ML8-F1-model_v4(1).pdb title: Alphafold monomer V2.0 prediction for crispr-associated nuclease/helicase CAS3 subtype I-F/ypest (Q02ML8) [more info...] Chain information for Cas23_AF-Q02ML8-F1-model_v4(1).pdb #7 --- Chain | Description | UniProt A | crispr-associated nuclease/helicase CAS3 subtype I-F/ypest | CAS3_PSEAB 1-1076 > show #!3 models > mmaker #7 to #3/N Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8flj, chain N (#3) with Cas23_AF-Q02ML8-F1-model_v4(1).pdb, chain A (#7), sequence alignment score = 5189.9 RMSD between 809 pruned atom pairs is 0.920 angstroms; (across all 954 pairs: 13.926) > mmaker #7:1-100 to #3/N Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8flj, chain N (#3) with Cas23_AF-Q02ML8-F1-model_v4(1).pdb, chain A (#7), sequence alignment score = 501.5 RMSD between 85 pruned atom pairs is 0.681 angstroms; (across all 100 pairs: 3.160) > delete #7:95-1076 > hide #7 models > show #7 models > hide #!3 models > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/AlphaFold/Cas23_AF-Q02ML8-F1-model_v4(1).pdb Cas23_AF-Q02ML8-F1-model_v4(1).pdb title: Alphafold monomer V2.0 prediction for crispr-associated nuclease/helicase CAS3 subtype I-F/ypest (Q02ML8) [more info...] Chain information for Cas23_AF-Q02ML8-F1-model_v4(1).pdb #8 --- Chain | Description | UniProt A | crispr-associated nuclease/helicase CAS3 subtype I-F/ypest | CAS3_PSEAB 1-1076 > delete #:95-1076 Missing or invalid ""atoms"" argument: invalid atoms specifier > delete #8:95-1076 > show #!3 models > mmaker #8 to #3/M Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8flj, chain M (#3) with Cas23_AF-Q02ML8-F1-model_v4(1).pdb, chain A (#8), sequence alignment score = 4089.5 RMSD between 85 pruned atom pairs is 0.646 angstroms; (across all 94 pairs: 1.402) > hide #!3 models > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/AlphaFold/Cas23_AF-Q02ML8-F1-model_v4(1).pdb Cas23_AF-Q02ML8-F1-model_v4(1).pdb title: Alphafold monomer V2.0 prediction for crispr-associated nuclease/helicase CAS3 subtype I-F/ypest (Q02ML8) [more info...] Chain information for Cas23_AF-Q02ML8-F1-model_v4(1).pdb #9 --- Chain | Description | UniProt A | crispr-associated nuclease/helicase CAS3 subtype I-F/ypest | CAS3_PSEAB 1-1076 > delete #9:1-94 > mmaker #9 to #3/M Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8flj, chain M (#3) with Cas23_AF-Q02ML8-F1-model_v4(1).pdb, chain A (#9), sequence alignment score = 5094.5 RMSD between 813 pruned atom pairs is 1.015 angstroms; (across all 876 pairs: 1.299) > volume #4 level 1.29 > volume #4 level 0.3401 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/AlphaFold/Cas23_AF-Q02ML8-F1-model_v4(1).pdb Cas23_AF-Q02ML8-F1-model_v4(1).pdb title: Alphafold monomer V2.0 prediction for crispr-associated nuclease/helicase CAS3 subtype I-F/ypest (Q02ML8) [more info...] Chain information for Cas23_AF-Q02ML8-F1-model_v4(1).pdb #10 --- Chain | Description | UniProt A | crispr-associated nuclease/helicase CAS3 subtype I-F/ypest | CAS3_PSEAB 1-1076 > delete #10:1-94 > mmaker #10 to #3/N Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8flj, chain N (#3) with Cas23_AF-Q02ML8-F1-model_v4(1).pdb, chain A (#10), sequence alignment score = 5060.3 RMSD between 814 pruned atom pairs is 0.923 angstroms; (across all 860 pairs: 1.197) > volume #4 level 0.4985 > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/isolde/chimeraXsessions/Docking- > alphafold-into-preliminary-density-using-8flj-as-guide.cxs includeMaps true > combine #1 #2 #5 #6 #7 #8 #9 Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #2 to 'B' Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #5 to 'C' Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #6 to 'D' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #7 to 'E' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #8 to 'F' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #9 to 'G' > hide #10 models > hide #9 models > hide #8 models > show #10 models > show #8 models > show #9 models > hide #9 models > hide #10 models > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #!4 models > show #!4 models > combine #1 #2 #5 #6 #7 #8 #9 #10 Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #2 to 'B' Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #5 to 'C' Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #6 to 'D' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #7 to 'E' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #8 to 'F' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #9 to 'G' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #10 to 'H' > close #11 > hide #2 models > hide #1 models > show #!3 models > hide #!3 models > volume #4 level 0.8265 > volume #4 level 1.664 > show #!3 models > duplicate #3/K-L Unknown command: duplicate #3/K-L > copy #3/K-L Unknown command: copy #3/K-L > mcopy #3/K-L Unknown command: mcopy #3/K-L > combine #1 #2 #5 #6 #7 #8 #9 #10 #3/K:1-27 #3/L:1-27 Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #2 to 'B' Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #5 to 'C' Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #6 to 'D' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #7 to 'E' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #8 to 'F' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #9 to 'G' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #10 to 'H' Remapping chain ID 'A' in 8flj #3 to 'I' Remapping chain ID 'B' in 8flj #3 to 'J' Remapping chain ID 'C' in 8flj #3 to 'O' Remapping chain ID 'D' in 8flj #3 to 'P' > hide #!3 models > select subtract #3 Nothing selected > hide #!11 models > hide #12 models > show #12 models > hide #12 models > show #12 models > select add #12 27270 atoms, 27878 bonds, 3448 residues, 1 model selected > select subtract #12 Nothing selected > select add #12 27270 atoms, 27878 bonds, 3448 residues, 1 model selected > show sel atoms > hide sel atoms > combine #1 #2 #5 #6 #7 #8 #9 #10 #3/K #3/L Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #2 to 'B' Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #5 to 'C' Remapping chain ID 'A' in Cas1-AF-Q02ML7-F1-model_v4.pdb #6 to 'D' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #7 to 'E' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #8 to 'F' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #9 to 'G' Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #10 to 'H' Remapping chain ID 'A' in 8flj #3 to 'I' Remapping chain ID 'B' in 8flj #3 to 'J' Remapping chain ID 'C' in 8flj #3 to 'O' Remapping chain ID 'D' in 8flj #3 to 'P' > hide #12 models > select subtract #12 Nothing selected > hide #!13 atoms > select add #13 72505 atoms, 73683 bonds, 75 pseudobonds, 6680 residues, 3 models selected > show sel cartoons > delete ~#12 #13/K #13/L #4 $3 Expected a keyword > ~struts delete #12 #13/K #13/L #4 $3 > struts delete delete #12 #13/K #13/L #4 $3 Expected an atoms specifier or a keyword > delete #13/N > delete #13/P > delete #13/J > delete #13/I > delete #13/O > delete #13/G > undo Undo failed, probably because structures have been modified. > delete #13/M > show #10 models > hide #10 models > show #9 models > combine #13 #9 Remapping chain ID 'A' in Cas23_AF-Q02ML8-F1-model_v4(1).pdb #9 to 'G' > hide #!13 models > select subtract #13 Nothing selected > delete #4:24-36 > delete #14/K:24-36 > close #1 > close #2 > close #3 > close #5 > close #6 > close #7 > close #8 > close #9 > close #10 > close #11 > close #12 > close #13 > hide #!4 models > select #14/G #14/H 15558 atoms, 15932 bonds, 1964 residues, 1 model selected > color sel #94b8e0ff > select #14/A-D 10196 atoms, 10408 bonds, 1296 residues, 1 model selected > color sel #c2b096ff > select #14/E-F 1516 atoms, 1538 bonds, 188 residues, 1 model selected > color sel #ce9cc3ff > select #14/K-L 1589 atoms, 1713 bonds, 53 pseudobonds, 50 residues, 2 models selected > color (#!14 & sel) #ea983eff > show #!4 models > volume #4 level 0.4419 > ui tool show ""Color Zone"" > color zone #4 near #14 distance 21.09 > set bgColor white > lighting soft > graphics silhouettes true > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/isolde/chimeraXsessions/Rigid-body- > docked-atomic-model-J810-low-res-density-full-complex.cxs includeMaps true ——— End of log from Tue Mar 26 12:11:35 2024 ——— opened ChimeraX session > open /Users/whenriques/Downloads/cryosparc_P29_J898_004_volume_map.mrc Opened cryosparc_P29_J898_004_volume_map.mrc as #1, grid size 270,270,270, pixel 1.67, shown at level 0.0329, step 2, values float32 > close #1 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J891/cryosparc_P29_J891_004_volume_map.mrc Opened cryosparc_P29_J891_004_volume_map.mrc as #1, grid size 270,270,270, pixel 1.67, shown at level 0.0721, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J892/cryosparc_P29_J892_003_volume_map.mrc Opened cryosparc_P29_J892_003_volume_map.mrc as #2, grid size 270,270,270, pixel 1.67, shown at level 0.0336, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J894/cryosparc_P29_J894_003_volume_map.mrc Opened cryosparc_P29_J894_003_volume_map.mrc as #3, grid size 270,270,270, pixel 1.67, shown at level 0.0471, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J895/cryosparc_P29_J895_004_volume_map.mrc Opened cryosparc_P29_J895_004_volume_map.mrc as #5, grid size 270,270,270, pixel 1.67, shown at level 0.036, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J898/cryosparc_P29_J898_004_volume_map.mrc Opened cryosparc_P29_J898_004_volume_map.mrc as #6, grid size 270,270,270, pixel 1.67, shown at level 0.0329, step 2, values float32 > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!14 models > show #!14 models > hide #!2 models > show #!4 models > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.92438,0.37469,-0.071585,197.61,-0.17017,-0.23708,0.95647,202.83,0.34141,0.89633,0.28292,149.98 > undo > select add #14 28859 atoms, 29591 bonds, 53 pseudobonds, 3498 residues, 2 models selected > select subtract #14 Nothing selected > select add #1 2 models selected > view matrix models > #1,-0.68348,-0.7297,0.019783,537.19,-0.71742,0.67648,0.16638,193.57,-0.13479,0.099527,-0.98586,428.33 > volume #1 level 0.2614 > view matrix models > #1,-0.68348,-0.7297,0.019783,541.52,-0.71742,0.67648,0.16638,184.29,-0.13479,0.099527,-0.98586,423.2 > view matrix models > #1,-0.95875,-0.2803,-0.047271,513.67,-0.28024,0.9599,-0.0079352,60.99,0.0476,0.0056395,-0.99885,407.39 > fitmap #1 inMap #$ Invalid ""inMap"" argument: invalid density map specifier > fitmap #1 inMap #4 Fit map cryosparc_P29_J891_004_volume_map.mrc in map cryosparc_P29_J810_class_02_00202_volume.mrc z flip using 9971 points correlation = 0.6524, correlation about mean = 0.1128, overlap = 3787 steps = 96, shift = 11.9, angle = 19.4 degrees Position of cryosparc_P29_J891_004_volume_map.mrc (#1) relative to cryosparc_P29_J810_class_02_00202_volume.mrc z flip (#4) coordinates: Matrix rotation and translation -0.99475011 -0.05257462 -0.08779597 478.28484628 -0.07293539 0.96604009 0.24788499 -35.44736165 0.07178197 0.25298705 -0.96480304 345.56929047 Axis 0.03169919 -0.99145976 -0.12650176 Axis point 231.53500219 0.00000000 184.76308480 Rotation angle (degrees) 175.38405856 Shift along axis 6.59075014 > select subtract #1 Nothing selected > hide #!1 models > show #!2 models > volume #2 level 0.1317 > hide #!4 models > hide #!14 models > show #!1 models > hide #!2 models > show #!3 models > show #!4 models > hide #!3 models > show #!2 models > hide #!1 models > select add #2 2 models selected > view matrix models > #2,0.98673,0.14837,-0.065911,-11.383,-0.15551,0.74716,-0.6462,237.18,-0.046631,0.64788,0.76032,-114.42 > view matrix models > #2,0.98192,0.16064,-0.10017,-5.3856,-0.18724,0.74607,-0.639,243.09,-0.027912,0.64621,0.76265,-118.85 > view matrix models > #2,0.98192,0.16064,-0.10017,-8.0324,-0.18724,0.74607,-0.639,238.08,-0.027912,0.64621,0.76265,-112.63 > fitmap #2 inMap #4 Fit map cryosparc_P29_J892_003_volume_map.mrc in map cryosparc_P29_J810_class_02_00202_volume.mrc z flip using 15050 points correlation = 0.6801, correlation about mean = 0.2832, overlap = 3408 steps = 72, shift = 5.17, angle = 16.6 degrees Position of cryosparc_P29_J892_003_volume_map.mrc (#2) relative to cryosparc_P29_J810_class_02_00202_volume.mrc z flip (#4) coordinates: Matrix rotation and translation 0.99311201 -0.00960966 0.11677413 -23.96401132 0.07488915 0.81854597 -0.56953850 149.52354047 -0.09011192 0.57436064 0.81362749 -90.23359738 Axis 0.98144590 0.17750469 0.07249854 Axis point 0.00000000 219.51019597 193.69604833 Rotation angle (degrees) 35.64505672 Shift along axis -3.52005452 > select subtract #2 Nothing selected > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > select add #3 2 models selected > view matrix models > #3,-0.9992,-0.037714,-0.013263,460.68,-0.034434,0.98045,-0.19375,55.731,0.02031,-0.19314,-0.98096,484.62 > volume flip #3 Opened cryosparc_P29_J894_003_volume_map.mrc z flip as #7, grid size 270,270,270, pixel 1.67, shown at step 1, values float32 > select subtract #3 Nothing selected > select add #7 2 models selected > volume #7 level 0.2137 > view matrix models > #7,-0.96049,0.25241,0.11727,353.36,-0.2653,-0.95769,-0.11157,540.46,0.084147,-0.13828,0.98681,-8.5406 > view matrix models > #7,-0.96049,0.25241,0.11727,355.13,-0.2653,-0.95769,-0.11157,523.22,0.084147,-0.13828,0.98681,-1.3755 > view matrix models > #7,-0.97602,0.18865,0.10862,374.75,-0.20173,-0.97135,-0.12561,520.26,0.081812,-0.14451,0.98612,1.5271 > close #3 > fitmap #7 inMap #4 Fit map cryosparc_P29_J894_003_volume_map.mrc z flip in map cryosparc_P29_J810_class_02_00202_volume.mrc z flip using 67296 points correlation = 0.9227, correlation about mean = 0.5922, overlap = 5.515e+04 steps = 84, shift = 3.57, angle = 14.6 degrees Position of cryosparc_P29_J894_003_volume_map.mrc z flip (#7) relative to cryosparc_P29_J810_class_02_00202_volume.mrc z flip (#4) coordinates: Matrix rotation and translation -0.99379871 0.10940722 -0.01985426 429.59958319 -0.09691474 -0.93979377 -0.32771208 536.65426572 -0.05451298 -0.32375567 0.94456900 83.73146584 Axis 0.01890756 0.16563292 -0.98600621 Axis point 229.81420087 263.93960203 0.00000000 Rotation angle (degrees) 173.99443373 Shift along axis 14.45054931 > hide #!4 models > show #!4 models > hide #!4 models > volume #7 level 0.2693 > show #!5 models > select add #5 4 models selected > view matrix models > #5,0.9995,0.0024333,0.031367,-7.4262,-0.0088971,0.97817,0.20762,-39.518,-0.030177,-0.2078,0.97771,57.62,#7,-0.99525,0.096911,0.0089868,425.89,-0.097275,-0.98747,-0.12427,498.98,-0.0031686,-0.12455,0.99221,15.004 > undo [Repeated 1 time(s)] > select subtract #7 Nothing selected > select add #5 2 models selected > view matrix models > #5,-0.90756,-0.34941,0.23292,456.97,-0.4011,0.88551,-0.23448,168.4,-0.12432,-0.30623,-0.94381,529.56 > volume flip #5 Opened cryosparc_P29_J895_004_volume_map.mrc z flip as #3, grid size 270,270,270, pixel 1.67, shown at step 1, values float32 > select add #3 4 models selected > select subtract #5 2 models selected > select up 28859 atoms, 29591 bonds, 3498 residues, 15 models selected > select up 28859 atoms, 29591 bonds, 3498 residues, 15 models selected > select subtract #5 28859 atoms, 29591 bonds, 3498 residues, 13 models selected > select subtract #4 28859 atoms, 29591 bonds, 3498 residues, 11 models selected > select add #4 28859 atoms, 29591 bonds, 3498 residues, 13 models selected > select subtract #3 28859 atoms, 29591 bonds, 3498 residues, 11 models selected > select subtract #2 28859 atoms, 29591 bonds, 3498 residues, 9 models selected > select subtract #1 28859 atoms, 29591 bonds, 3498 residues, 7 models selected > select subtract #4 28859 atoms, 29591 bonds, 3498 residues, 5 models selected > select subtract #6 28859 atoms, 29591 bonds, 3498 residues, 3 models selected > select subtract #7 28859 atoms, 29591 bonds, 3498 residues, 1 model selected > select add #14 28859 atoms, 29591 bonds, 53 pseudobonds, 3498 residues, 2 models selected > select subtract #14 Nothing selected > fitmap #3 inMap #4 Fit map cryosparc_P29_J895_004_volume_map.mrc z flip in map cryosparc_P29_J810_class_02_00202_volume.mrc z flip using 196496 points correlation = 0.8085, correlation about mean = 0.607, overlap = 4.689e+04 steps = 172, shift = 28.5, angle = 21.1 degrees Position of cryosparc_P29_J895_004_volume_map.mrc z flip (#3) relative to cryosparc_P29_J810_class_02_00202_volume.mrc z flip (#4) coordinates: Matrix rotation and translation -0.98507603 -0.16750618 0.03958396 476.61624099 -0.16869186 0.98524871 -0.02877570 50.59852096 -0.03417994 -0.03502375 -0.99880182 433.98455861 Axis -0.08439024 0.99630408 -0.01601453 Axis point 244.48420812 0.00000000 212.96758049 Rotation angle (degrees) 177.87849618 Shift along axis 3.23969296 > volume #3 level 0.1743 > close #5 > show #!6 models > select add #6 2 models selected > view matrix models > #6,0.85237,0.52282,-0.010728,-47.798,0.4608,-0.76064,-0.45727,306.62,-0.24723,0.38482,-0.88926,360.78 > volume #6 level 0.18 > view matrix models > #6,0.45385,-0.76588,0.45545,226.47,-0.68771,-0.62609,-0.36752,529.67,0.56663,-0.14642,-0.81086,310.2 > view matrix models > #6,0.81894,-0.56619,0.093696,287.55,-0.48152,-0.76673,-0.42457,535.59,0.31222,0.30258,-0.90053,236.87 > view matrix models > #6,0.81894,-0.56619,0.093696,262.5,-0.48152,-0.76673,-0.42457,523.31,0.31222,0.30258,-0.90053,236.24 > view matrix models > #6,0.81894,-0.56619,0.093696,228.61,-0.48152,-0.76673,-0.42457,589.71,0.31222,0.30258,-0.90053,272.11 > view matrix models > #6,0.99401,0.010029,0.10879,47.713,0.074942,-0.78715,-0.61219,512.87,0.079493,0.61668,-0.78319,222.05 > view matrix models > #6,0.99401,0.010029,0.10879,-14.759,0.074942,-0.78715,-0.61219,519.26,0.079493,0.61668,-0.78319,202.89 > fitmap #6 inMap #4 Fit map cryosparc_P29_J898_004_volume_map.mrc in map cryosparc_P29_J810_class_02_00202_volume.mrc z flip using 11786 points correlation = 0.6429, correlation about mean = -0.09848, overlap = 3762 steps = 164, shift = 10, angle = 32 degrees Position of cryosparc_P29_J898_004_volume_map.mrc (#6) relative to cryosparc_P29_J810_class_02_00202_volume.mrc z flip (#4) coordinates: Matrix rotation and translation 0.99487505 -0.06615894 0.07646313 3.46146695 -0.05683209 -0.99134982 -0.11830317 479.36739466 0.08362852 0.11335131 -0.99002916 369.33079073 Axis 0.99871360 -0.03089159 0.04021013 Axis point 0.00000000 228.98282075 198.56270873 Rotation angle (degrees) 173.34005253 Shift along axis 3.49943011 > tile 3 models tiled > show #!1 models > show #!2 models > show #!4 models > show #!14 models > tile 7 models tiled > ~tile > view matrix models > #6,0.81894,-0.56619,0.093696,269.85,-0.48152,-0.76673,-0.42457,616.54,0.31222,0.30258,-0.90053,276.5 > select up 12 models selected > select up 12 models selected > fitmap #6 inMap #4 Fit map cryosparc_P29_J898_004_volume_map.mrc in map cryosparc_P29_J810_class_02_00202_volume.mrc z flip using 11786 points correlation = 0.05038, correlation about mean = -0.004565, overlap = 8.869 steps = 216, shift = 66.8, angle = 36.8 degrees Position of cryosparc_P29_J898_004_volume_map.mrc (#6) relative to cryosparc_P29_J810_class_02_00202_volume.mrc z flip (#4) coordinates: Matrix rotation and translation 0.79747689 -0.40186663 0.45003757 211.80725845 0.04165328 -0.70744899 -0.70553591 565.46089069 0.60190997 0.58139413 -0.54743516 80.01015123 Axis 0.93959929 -0.11088341 0.32381791 Axis point 0.00000000 289.43532921 126.50327949 Rotation angle (degrees) 136.77782465 Shift along axis 162.22243589 > show #!1 models > show #!2 models > show #!4 models > view matrix models > #4,1,0,0,5.3356,0,1,0,-0.2299,0,0,1,-0.92923,#1,-0.99475,-0.052575,-0.087796,483.62,-0.072935,0.96604,0.24788,-35.677,0.071782,0.25299,-0.9648,344.64,#2,0.99311,-0.0096097,0.11677,-18.628,0.074889,0.81855,-0.56954,149.29,-0.090112,0.57436,0.81363,-91.163,#6,0.79748,-0.40187,0.45004,217.14,0.041653,-0.70745,-0.70554,565.23,0.60191,0.58139,-0.54744,79.081,#7,-0.9938,0.10941,-0.019854,434.94,-0.096915,-0.93979,-0.32771,536.42,-0.054513,-0.32376,0.94457,82.802,#3,-0.98508,-0.16751,0.039584,481.95,-0.16869,0.98525,-0.028776,50.369,-0.03418,-0.035024,-0.9988,433.06 > select subtract #7 10 models selected > select subtract #6 8 models selected > select subtract #3 6 models selected > select subtract #2 4 models selected > select subtract #1 2 models selected > select add #6 4 models selected > select subtract #4 2 models selected > view matrix models > #6,0.79748,-0.40187,0.45004,83.066,0.041653,-0.70745,-0.70554,539.41,0.60191,0.58139,-0.54744,50.351 > view matrix models > #6,0.98566,-0.1173,-0.12128,105.91,-0.16712,-0.77771,-0.606,580.07,-0.023236,0.61758,-0.78617,238.45 > view matrix models > #6,0.98566,-0.1173,-0.12128,102.86,-0.16712,-0.77771,-0.606,563.51,-0.023236,0.61758,-0.78617,237.91 > view matrix models > #6,0.91529,-0.38125,-0.12999,183.93,-0.39285,-0.77365,-0.49713,588.03,0.088963,0.50608,-0.85789,256.03 > view matrix models > #6,0.91529,-0.38125,-0.12999,153.42,-0.39285,-0.77365,-0.49713,608.22,0.088963,0.50608,-0.85789,249.41 > view matrix models > #6,0.91529,-0.38125,-0.12999,154.24,-0.39285,-0.77365,-0.49713,597.14,0.088963,0.50608,-0.85789,257.86 > view matrix models > #6,0.91529,-0.38125,-0.12999,154.49,-0.39285,-0.77365,-0.49713,588.03,0.088963,0.50608,-0.85789,262.05 > view matrix models > #6,0.98354,-0.095178,-0.15361,76.155,-0.15294,-0.89121,-0.42703,545.68,-0.096256,0.44349,-0.89109,326.56 > fitmap #6 inMap #4 Fit map cryosparc_P29_J898_004_volume_map.mrc in map cryosparc_P29_J810_class_02_00202_volume.mrc z flip using 11786 points correlation = 0.6428, correlation about mean = -0.09886, overlap = 3763 steps = 108, shift = 18.7, angle = 23.1 degrees Position of cryosparc_P29_J898_004_volume_map.mrc (#6) relative to cryosparc_P29_J810_class_02_00202_volume.mrc z flip (#4) coordinates: Matrix rotation and translation 0.99439862 -0.07181479 0.07755006 4.65898262 -0.06238673 -0.99107401 -0.11781426 480.44581630 0.08531866 0.11231625 -0.99000292 369.16396085 Axis 0.99859399 -0.03370989 0.04091076 Axis point 0.00000000 229.62076300 198.39593188 Rotation angle (degrees) 173.38326634 Shift along axis 3.55943317 > show #!14 models > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/cryosparc/P6-P29/NU-refinement- > comparison-J891-J898/volume_aligned_rigid_body_docked_model.cxs includeMaps > true > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!7 models > hide #!14 models > show #!14 models > hide #!6 models > select subtract #6 Nothing selected > show #!1 models > ui tool show ""Color Zone"" > color zone #1 near #14 distance 10 > show #!2 models > hide #!1 models > color zone #2 near #14 distance 10 > hide #!2 models > show #!3 models > color zone #3 near #14 distance 10 > color zone #3 near #14 distance 2 > color zone #3 near #14 distance 20 > show #!2 models > hide #!3 models > color zone #2 near #14 distance 2 > color zone #2 near #14 distance 20 [Repeated 1 time(s)] > show #!3 models > hide #!3 models > hide #!2 models > show #!1 models > color zone #1 near #14 distance 2 > color zone #1 near #14 distance 20 [Repeated 1 time(s)] > hide #!1 models > show #!3 models > show #!4 models > show #!6 models > hide #!4 models > hide #!3 models > color zone #6 near #14 distance 20 > show #!4 models > hide #!6 models > show #!6 models > hide #!6 models > show #!7 models > hide #!4 models > color zone #7 near #14 distance 20 > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/cryosparc/P6-P29/NU-refinement- > comparison-J891-J898/volume_aligned_rigid_body_docked_model-colored.cxs > includeMaps true ——— End of log from Mon Apr 1 13:51:22 2024 ——— opened ChimeraX session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer- > bound/cryosparc/P6-P29/J893/cryosparc_P29_J893_007_volume_map.mrc Opened cryosparc_P29_J893_007_volume_map.mrc as #5, grid size 270,270,270, pixel 1.67, shown at level 0.0616, step 2, values float32 > select add #5 2 models selected > volume #7 region 0,0,0,269,269,269 [Repeated 4 time(s)] > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.8511,-0.49703,0.16909,490.72,0.51242,-0.71635,0.47357,163.82,-0.11425,0.4897,0.86438,-115.59 > view matrix models > #5,-0.82216,-0.56357,-0.080315,556.06,0.54511,-0.82006,0.17421,248.02,-0.16404,0.099449,0.98143,-44.074 > view matrix models > #5,-0.83878,-0.54193,0.052644,524.58,0.52606,-0.78167,0.33503,206.99,-0.14041,0.30871,0.94074,-86.779 > view matrix models > #5,-0.68155,0.64559,-0.34452,315.04,0.72987,0.63364,-0.2565,-19.429,0.052704,-0.42627,-0.90306,455.19 > view matrix models > #5,-0.96423,0.1405,-0.22476,463.54,0.22117,0.89381,-0.39011,66.474,0.14608,-0.42586,-0.89292,431.95 > view matrix models > #5,-0.92216,0.13978,-0.36067,480.62,0.2453,0.93227,-0.26588,19.978,0.29908,-0.33366,-0.89399,406.18 > view matrix models > #5,-0.92216,0.13978,-0.36067,479.46,0.2453,0.93227,-0.26588,18.788,0.29908,-0.33366,-0.89399,410.39 > volume #2 level 0.1778 > hide #!2 models > fitmap #5 inMap #4 Fit map cryosparc_P29_J893_007_volume_map.mrc in map cryosparc_P29_J810_class_02_00202_volume.mrc z flip using 24575 points correlation = 0.8863, correlation about mean = 0.7804, overlap = 9547 steps = 136, shift = 8.08, angle = 20.7 degrees Position of cryosparc_P29_J893_007_volume_map.mrc (#5) relative to cryosparc_P29_J810_class_02_00202_volume.mrc z flip (#4) coordinates: Matrix rotation and translation -0.99864064 -0.01155988 -0.05082545 461.63993262 0.00869688 0.92447426 -0.38114523 95.50468559 0.05139281 -0.38106914 -0.92311704 486.20656124 Axis 0.00073016 -0.98092378 0.19439135 Axis point 224.39776653 0.00000000 258.70075255 Rotation angle (degrees) 177.01336214 Shift along axis 1.16860463 > ui tool show ""Color Zone"" > color zone #7 near #14 distance 1.67 > color zone #5 near #14 distance 20 > select subtract #5 Nothing selected > hide #!5 models > color single #7 [Repeated 2 time(s)] > color zone #7 near #14 distance 20 > show #!5 models > volume #5 level 0.1015 > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/cryosparc/P6-P29/NU-refinement- > comparison-J891-J898/volume_aligned_rigid_body_docked_model-colored.cxs > includeMaps true > tile 3 models tiled > show #!6 models > show #!1 models > show #!2 models > show #!3 models > show #!4 models > hide #!14 models > hide #!4 models > tile 6 models tiled > volume #5 level 0.1365 > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/cryosparc/P6-P29/NU-refinement- > comparison-J891-J898/volume_aligned_rigid_body_docked_model-colored- > tiled.cxs includeMaps true > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/cryosparc/P6-P29/NU-refinement- > comparison-J891-J898/pngs/6-volumes-comparison.png width 800 height 670 > supersample 3 transparentBackground true > close session > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-apo/relion/g52h115_relion/PostProcess/job016/postprocess.mrc Opened postprocess.mrc as #1, grid size 336,336,336, pixel 1.07, shown at level 0.0002, step 2, values float32 > show surfaces > volume #1 level 0.1833 > volume #1 level -0.1578 > close session > open /Volumes/mcb-wiedenheft/EM-data/integration-complex-PA- > IF/cas123-apo/relion/g52h115_relion/Refine3D/job014/run_class001.mrc Opened run_class001.mrc as #1, grid size 336,336,336, pixel 1.07, shown at level 0.00161, step 2, values float32 > volume #1 step 1 > volume #1 level 0.002115 > volume #1 level 0.004358 > volume #1 level 0.002952 > volume #1 level 0.00178 > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job013/run_it025_class001.mrc Opened run_it025_class001.mrc as #1, grid size 336,336,336, pixel 1.07, shown at level 0.00193, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job013/run_it025_class002.mrc Opened run_it025_class002.mrc as #2, grid size 336,336,336, pixel 1.07, shown at level 0.00206, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job013/run_it025_class003.mrc Opened run_it025_class003.mrc as #3, grid size 336,336,336, pixel 1.07, shown at level 0.0021, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job013/run_it025_class004.mrc Opened run_it025_class004.mrc as #4, grid size 336,336,336, pixel 1.07, shown at level 0.0021, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job013/run_it025_class005.mrc Opened run_it025_class005.mrc as #5, grid size 336,336,336, pixel 1.07, shown at level 0.00215, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job013/run_it025_class006.mrc Opened run_it025_class006.mrc as #6, grid size 336,336,336, pixel 1.07, shown at level 0.00229, step 2, values float32 > tile 6 models tiled > set bgColor white > lighting soft > graphics silhouettes true > volume #1 level 0.003604 > tile 6 models tiled > volume #3 level 0.0036 > volume #4 level 0.0036 > volume #5 level 0.0036 > volume #6 level 0.0036 > lighting soft > graphics silhouettes false > graphics silhouettes true > volume #2 level 0.0036 > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Refine3D/job014/run_class001.mrc Opened run_class001.mrc as #1, grid size 336,336,336, pixel 1.07, shown at level 0.00161, step 2, values float32 > volume #1 level 0.0006596 > volume #1 level 0.001136 > volume #1 level 0.001 > volume #1 level 0.002 > volume #1 step 1 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/PostProcess/job019/postprocess.mrc Opened postprocess.mrc as #2, grid size 336,336,336, pixel 1.07, shown at level 0.00301, step 2, values float32 > hide #!1 models > volume #2 level 0.005096 > volume #2 step 1 > volume #2 color #475fff > set bgColor white > lighting soft > volume #2 level 0.008248 > volume #2 level 0.005011 > volume #2 level 0.004159 > volume #2 level 0.004671 > volume #2 level 0.007396 > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job013/run_it025_class001.mrc Opened run_it025_class001.mrc as #1, grid size 336,336,336, pixel 1.07, shown at level 0.00193, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job013/run_it025_class002.mrc Opened run_it025_class002.mrc as #2, grid size 336,336,336, pixel 1.07, shown at level 0.00206, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job013/run_it025_class003.mrc Opened run_it025_class003.mrc as #3, grid size 336,336,336, pixel 1.07, shown at level 0.0021, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job013/run_it025_class004.mrc Opened run_it025_class004.mrc as #4, grid size 336,336,336, pixel 1.07, shown at level 0.0021, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job013/run_it025_class005.mrc Opened run_it025_class005.mrc as #5, grid size 336,336,336, pixel 1.07, shown at level 0.00215, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job013/run_it025_class006.mrc Opened run_it025_class006.mrc as #6, grid size 336,336,336, pixel 1.07, shown at level 0.00229, step 2, values float32 > lighting soft > set bgColor white > tile 6 models tiled > lighting soft > graphics silhouettes true > volume #1 level 0.003 > volume #2 level 0.003 > volume #1 step 1 > volume #2 step 1 > volume #3 level 0.003 > volume #3 step 1 > volume #4 step 1 > volume #4 level 0.003 > volume #5 step 1 > volume #6 step 1 > volume #6 level 0.003 > volume #5 level 0.003 > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Refine3D/job014/run_class001.mrc format > mrc Opened run_class001.mrc as #1, grid size 336,336,336, pixel 1.07, shown at level 0.00161, step 2, values float32 > volume #1 level 0.0003737 > ui tool show ""Hide Dust"" > surface dust #1 size 6.41 > surface dust #1 size 10 > surface dust #1 size 109 > surface dust #1 size 10 [Repeated 1 time(s)] > surface dust #1 size 2 > surface dust #1 size 20 [Repeated 1 time(s)] > volume #1 level 0.001581 > ui tool show ""Segment Map"" Segmenting run_class001.mrc, density threshold 0.001581 Only showing 60 of 86 regions. Showing 60 of 86 region surfaces 1099 watershed regions, grouped to 86 regions Showing run_class001.seg - 86 regions, 60 surfaces > select add #2.58 1 model selected > select subtract #2.58 Nothing selected > hide #!2 models > volume gaussian #1 sDev 2 Opened run_class001.mrc gaussian as #3, grid size 336,336,336, pixel 1.07, shown at step 1, values float32 > volume #3 level 0.001219 > volume copy #2 > volume copy #3 Opened run_class001.mrc gaussian copy as #4, grid size 336,336,336, pixel 1.07, shown at step 1, values float32 > volume copy #3 Opened run_class001.mrc gaussian copy as #5, grid size 336,336,336, pixel 1.07, shown at step 1, values float32 > hide #!4 models > ui mousemode right ""map eraser"" > select add #6 1 model selected > volume erase #5 center 150.65,204.79,217.67 radius 69.22 outside true > show #!4 models > hide #!5 models > volume erase #4 center 150.65,204.79,217.67 radius 69.149 > show #!5 models > hide #!4 models > show #!4 models > hide #6 models > select subtract #6 Nothing selected > hide #!4 models > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/LocalRefinementMasks/Cas1-Cas3-local- > refinement-mask.mrc models #4 > select add #5 2 models selected > select subtract #5 Nothing selected > show #!4 models > hide #!4 models > select add #4 2 models selected > show #!4 models > hide #!5 models > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/LocalRefinementMasks/chimeraX.sessions/cas1-cas3-local- > refinement.cxs includeMaps true ——— End of log from Tue Apr 2 09:02:03 2024 ——— opened ChimeraX session Showing run_class001.seg - 86 regions, 60 surfaces > hide #!2 models > show #!5 models > hide #!4 models > show #!2 models > hide #!2 models > volume #3 level 0.001641 > volume #4 level 0.003501 > volume #4 level 0.001384 > hide #!3 models > hide #!5 models > show #!5 models > hide #!4 models > volume #5 level 0.0008464 > volume #5 level 0.002503 > show #!1 models > show #!2 models > hide #!1 models > hide #!2 models > show #!3 models > volume copy #3 Opened run_class001.mrc gaussian copy as #6, grid size 336,336,336, pixel 1.07, shown at step 1, values float32 > volume #5 level 0.002987 > hide #!6 models > hide #7 models > volume #5 level 0.0004742 > volume #5 level 0.001665 > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/phenix/J411-alphafold/RealSpaceRefine_1/cas123-apo- > isolde-v0_real_space_refined_001.pdb format pdb Chain information for cas123-apo-isolde-v0_real_space_refined_001.pdb #1 --- Chain | Description A B | No description available C D E F | No description available > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/phenix/J411-alphafold/RealSpaceRefine_1/cas123-apo- > isolde-v0_real_space_refined_001.pdb format pdb Chain information for cas123-apo-isolde-v0_real_space_refined_001.pdb #1 --- Chain | Description A B | No description available C D E F | No description available > select #1/C:25 17 atoms, 17 bonds, 1 residue, 1 model selected > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job023/run_it035_class001.mrc Opened run_it035_class001.mrc as #1, grid size 336,336,336, pixel 1.07, shown at level 0.000427, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job023/run_it035_class002.mrc Opened run_it035_class002.mrc as #2, grid size 336,336,336, pixel 1.07, shown at level 0.000161, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job023/run_it035_class003.mrc Opened run_it035_class003.mrc as #3, grid size 336,336,336, pixel 1.07, shown at level 4.22e-05, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job023/run_it035_class004.mrc Opened run_it035_class004.mrc as #4, grid size 336,336,336, pixel 1.07, shown at level 0.000151, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job023/run_it035_class005.mrc Opened run_it035_class005.mrc as #5, grid size 336,336,336, pixel 1.07, shown at level 5.87e-05, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job023/run_it035_class006.mrc Opened run_it035_class006.mrc as #6, grid size 336,336,336, pixel 1.07, shown at level 0.000315, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job023/run_it035_class007.mrc Opened run_it035_class007.mrc as #7, grid size 336,336,336, pixel 1.07, shown at level 1.6e-05, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job023/run_it035_class008.mrc Opened run_it035_class008.mrc as #8, grid size 336,336,336, pixel 1.07, shown at level 0.000158, step 2, values float32 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job023/run_it035_class009.mrc Opened run_it035_class009.mrc as #9, grid size 336,336,336, pixel 1.07, shown at level 9.75e-05, step 2, values float32 > tile 9 models tiled > volume #1 level 0.001968 > volume #1 step 1 > volume #2 level 0.00197 > volume #2 step 1 > lighting soft > graphics silhouettes true > volume #3 step 1 > volume #3 level 0.00197 > volume #4 step 1 > volume #4 level 0.00197 > volume #5 step 1 > volume #5 level 0.00197 > volume #6 step 1 > volume #6 level 0.00197 > volume #8 level 0.000197 > volume #8 step 1 > volume #8 level 0.00197 > volume #7 step 1 > volume #7 level 0.00197 > volume #9 step 1 > volume #9 level 0.0197 > volume #9 level 0.00197 > set bgColor white > set bgColor #ffffff00 > lighting soft > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job023/pngs/9-class- > comparison.png width 864 height 823 supersample 3 transparentBackground true > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job023/chimeraX.session/9-class- > comparison.cxs includeMaps true Taking snapshot of stepper: combination Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 1392, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 208, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/models.py"", line 344, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'isolde residue stepper 0' -> -> 'combination' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'isolde residue stepper 0' -> -> 'combination': Error while saving session data for 'isolde residue stepper 0' -> -> 'combination' ValueError: error processing: 'isolde residue stepper 0' -> -> 'combination': Error while saving session data for 'isolde residue stepper 0' -> -> 'combination' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 1392, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 208, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/models.py"", line 344, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'isolde residue stepper 0' -> -> 'combination' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'isolde residue stepper 0' -> -> 'combination': Error while saving session data for 'isolde residue stepper 0' -> -> 'combination' ValueError: error processing: 'isolde residue stepper 0' -> -> 'combination': Error while saving session data for 'isolde residue stepper 0' -> -> 'combination' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/relion/Class3D/job023/chimeraX.session/9-class- > comparison.cxs includeMaps true Taking snapshot of stepper: combination Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 1392, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 208, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/models.py"", line 344, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'isolde residue stepper 0' -> -> 'combination' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'isolde residue stepper 0' -> -> 'combination': Error while saving session data for 'isolde residue stepper 0' -> -> 'combination' ValueError: error processing: 'isolde residue stepper 0' -> -> 'combination': Error while saving session data for 'isolde residue stepper 0' -> -> 'combination' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 1392, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 208, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/models.py"", line 344, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'isolde residue stepper 0' -> -> 'combination' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'isolde residue stepper 0' -> -> 'combination': Error while saving session data for 'isolde residue stepper 0' -> -> 'combination' ValueError: error processing: 'isolde residue stepper 0' -> -> 'combination': Error while saving session data for 'isolde residue stepper 0' -> -> 'combination' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MJ123LL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 35 days, 1 hour, 50 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal BenQ GW2760HS: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Third Party fixed Greg Couch Eric Pettersen all ChimeraX