Opened 20 months ago

Closed 19 months ago

#14828 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:
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.  

> 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/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/cryosparc/P6-P29/J820/cryosparc_P29_J820_008_volume_map.mrc

Opened cryosparc_P29_J820_008_volume_map.mrc as #1, grid size 270,270,270,
pixel 1.67, shown at level 0.0405, step 2, values float32  

> select add #14

28859 atoms, 29591 bonds, 53 pseudobonds, 3498 residues, 2 models selected  

> select add #1

28859 atoms, 29591 bonds, 53 pseudobonds, 3498 residues, 4 models selected  

> select subtract #14

2 models selected  

> view matrix models
> #1,-0.96421,-0.065835,-0.25685,513.41,0.016534,-0.98173,0.18957,403.7,-0.26464,0.17853,0.94768,30.598

> view matrix models
> #1,-0.95342,0.23654,-0.18719,426.85,-0.097476,-0.82886,-0.5509,559.7,-0.28547,-0.50699,0.81331,220.79

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.95342,0.23654,-0.18719,440.12,-0.097476,-0.82886,-0.5509,545.85,-0.28547,-0.50699,0.81331,164.62

> fitmap #1 inMap #4

Fit map cryosparc_P29_J820_008_volume_map.mrc in map
cryosparc_P29_J810_class_02_00202_volume.mrc z flip using 24583 points  
correlation = 0.9588, correlation about mean = 0.907, overlap = 8394  
steps = 196, shift = 28.1, angle = 34.7 degrees  
  
Position of cryosparc_P29_J820_008_volume_map.mrc (#1) relative to
cryosparc_P29_J810_class_02_00202_volume.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
-0.99931410 -0.02026069 -0.03099757 462.78372385  
0.02153771 -0.99890910 -0.04143368 455.04091595  
-0.03012428 -0.04207288 0.99866031 -22.41211490  
Axis -0.01528726 -0.02088592 0.99966498  
Axis point 228.84540054 229.70305213 0.00000000  
Rotation angle (degrees) 178.80207559  
Shift along axis -38.98325080  
  

> hide #!4 models

> volume #1 level 0.06576

> ui tool show "Hide Dust"

> surface dust #1 size 10

> volume #1 level -0.005464

> volume #1 level 0.007486

> volume #1 level 0.03986

> ui tool show "Color Zone"

> color zone #1 near #14 distance 10

> color zone #1 near #14 distance 2

> color zone #1 near #14 distance 20

[Repeated 1 time(s)]

> close #4

> select subtract #1

Nothing selected  

> volume #1 level 0.2642

> volume #1 level 0.08093

> hide #!14 models

> save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-
> bound/cryosparc/P6-P29/J820/colored_by_subunit_rigid_body_model.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 0x2b3b4c190> ->
<chimerax.atomic.structure.AtomicStructure object at 0x2e7ab9220>
'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 0x2b3b4c190> ->
<chimerax.atomic.structure.AtomicStructure object at 0x2e7ab9220>
'combination': Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x2b3b4c190> ->
<chimerax.atomic.structure.AtomicStructure object at 0x2e7ab9220>
'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 0x2b3b4c190> ->
<chimerax.atomic.structure.AtomicStructure object at 0x2e7ab9220>
'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 0x2b3b4c190> ->
<chimerax.atomic.structure.AtomicStructure object at 0x2e7ab9220>
'combination': Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x2b3b4c190> ->
<chimerax.atomic.structure.AtomicStructure object at 0x2e7ab9220>
'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-prespacer-
> bound/cryosparc/P6-P29/J820/chimeraX.session/colored-by-subunit-rigid-body-
> dock.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 0x2b3b4c190> ->
<chimerax.atomic.structure.AtomicStructure object at 0x2e7ab9220>
'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 0x2b3b4c190> ->
<chimerax.atomic.structure.AtomicStructure object at 0x2e7ab9220>
'combination': Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x2b3b4c190> ->
<chimerax.atomic.structure.AtomicStructure object at 0x2e7ab9220>
'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 0x2b3b4c190> ->
<chimerax.atomic.structure.AtomicStructure object at 0x2e7ab9220>
'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 0x2b3b4c190> ->
<chimerax.atomic.structure.AtomicStructure object at 0x2e7ab9220>
'combination': Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x2b3b4c190> ->
<chimerax.atomic.structure.AtomicStructure object at 0x2e7ab9220>
'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: 27 days, 3 hours, 14 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        BenQ GW2760HS:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

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

probably long ago fixed

comment:2 by Tristan Croll, 19 months ago

Resolution: → fixed
Status: assigned → closed

See #14894.

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