Opened 20 months ago

Closed 19 months ago

#14894 closed defect (fixed)

ISOLDE: ResidueStepper holding reference to closed structure

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Greg Couch, Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x28de4eac0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x28d7bc100>
'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' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x28de4eac0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x28d7bc100>
'combination': Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x28de4eac0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x28d7bc100>
'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'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x28de4eac0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x28d7bc100>
'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>  
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' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x28de4eac0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x28d7bc100>
'combination': Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x28de4eac0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x28d7bc100>
'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'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x28de4eac0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x28d7bc100>
'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' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x28de4eac0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x28d7bc100>
'combination': Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x28de4eac0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x28d7bc100>
'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'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x28de4eac0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x28d7bc100>
'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>  
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' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x28de4eac0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x28d7bc100>
'combination': Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x28de4eac0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x28d7bc100>
'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
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    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
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    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
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    ChimeraX-Mole: 1.0
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    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
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    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
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    pexpect: 4.8.0
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Change History (7)

comment:1 by Eric Pettersen, 20 months ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: ResidueStepper holding reference to closed structure

comment:2 by Tristan Croll, 20 months ago 

So I've finally found the free time to track this down. The upshot is that
when I wrote the code I failed to understand the purpose of `StateManager`
and tried to make each `ResidueStepper` (one per structure, created when
the "isolde step" command is called on that structure) its own
`StateManager` instance. That actually worked mostly OK, but I messed up
the `init_state_manager()` logic so that each save_restore ended up
creating an extra entry in the `session._state_containers` map, only the
last of which would actually remove itself when the model was deleted. So
opening a model, stepping through it for a bit, saving and restoring the
session, then deleting the model and attempting to save the session would
trigger the traceback.

I've just committed a fix that should stop this in the future (created a
new `class ResidueStepperMgr(StateMgr)` to act as a session-level
singleton, maintaining a map of {structure: ResidueStepper(State)}` to
manage their save/restore (
https://github.com/tristanic/isolde/blob/820bce8a8427504cb9b5806bd20c28d27c9f64bd/isolde/src/navigate.py#L24).
I also tried an approach that used the `register_custom_attr` to make the
stepper a direct property of its model, but that approach failed on saving
due to circular references that looked pretty nasty to work around. Anyway,
this implementation still successfully opens old .cxs files dating from
before the change (with the warning: 'developer warning: container "isolde
residue stepper" snapshot methods are missing include_state method' - I
guess due to the change from `StateManager` to `State`), but the resulting
sessions will still have a bunch of spurious entries in
`session._state_containers` leading to tracebacks when attempting to
re-save. Any suggestions on the most future-proof way to clean those out?

On Wed, Apr 3, 2024 at 9:14 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>

comment:3 by Eric Pettersen, 19 months ago

Cc: Greg Couch Eric Pettersen added

comment:4 by Eric Pettersen, 19 months ago

Well, Greg's the main authority on session state containers Here's an approach that almost works, but will require an API enhancement:

(1) In your own ResidueStepperMgr restore_snapshot() routine register for the "end restore session" trigger in session.triggers
(2) In the handler call session.state_managers(ResidueStepper) to get all the ResidueStepper managers
(3) Remove all the problematic instances with session.remove_state_manager()

The difficulty is that remove_state_manager() takes a state managers 'tag' as its argument and state manager's tag isn't publicly accessible.

Greg, would it be better to enhance remove_state_manager to also accept an instance, or instead give StateManager a 'tag' property?

comment:5 by Tristan Croll, 19 months ago 

In this case I think the former approach is the only one that will work
(having remove_state_manager accept an instance) - after this fix, the
offending `ResidueStepper` entries after session restore aren't actually
`StateManager` instances any more - just `State`s.

On Tue, Apr 9, 2024 at 1:39 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>
>

comment:6 by Eric Pettersen, 19 months ago

Added session.state_managers_by_tag(class_obj) call, that returns tag→instance mapping for "state managers" of that class (so session.remove_state_manager(tag) could be called).

comment:7 by Tristan Croll, 19 months ago

Resolution: → fixed
Status: assigned → closed

A neat solution, and works beautifully. After ​https://github.com/tristanic/isolde/commit/6782c63ef07e293e25398f722e69decd1989b7d5 I can now open a problematic session file saved from ISOLDE 1.7, and re-save it without generating a traceback. Will go ahead and call this fixed.

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