Opened 6 weeks ago

Last modified 6 weeks ago

#18761 assigned defect

XMAS: color key deleted multiple times

Reported by: chimerax-bug-report@… Owned by: Richard Scheltema
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-14.7.7-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250709_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.194, step 1, values float32  
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32  
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.227, step 1, values float32  
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.227, step 1, values float32  
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.199, step 1, values float32  
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32  
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.199, step 1, values float32  
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.212, step 1, values float32  
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.24, step 1, values float32  
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32  
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32  
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32  
Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 4.58, step 1, values float32  
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32  
Opened cryosparc_P126_J4486_map_locres.mrc as #54, grid size 240,240,240,
pixel 2.38, shown at level 59.5, step 1, values float32  
Opened relion_locres_filtered.mrc as #55, grid size 292,292,292, pixel 1.71,
shown at level 0.005, step 1, values float32  
Log from Wed Jul 9 09:46:30 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"

Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.194, step 1, values float32  
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32  
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32  
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32  
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32  
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32  
Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 4.58, step 1, values float32  
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32  
Opened cryosparc_P126_J4486_map_locres.mrc as #54, grid size 240,240,240,
pixel 2.38, shown at level 59.5, step 1, values float32  
Opened relion_locres_filtered.mrc as #55, grid size 292,292,292, pixel 1.71,
shown at level 0.005, step 1, values float32  
Log from Tue Jul 8 14:43:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"

Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.194, step 1, values float32  
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32  
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32  
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32  
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32  
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32  
Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 4.58, step 1, values float32  
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32  
Opened cryosparc_P126_J4486_map_locres.mrc as #54, grid size 240,240,240,
pixel 2.38, shown at level 59.5, step 1, values float32  
Opened relion_locres_filtered.mrc as #55, grid size 292,292,292, pixel 1.71,
shown at level 0.005, step 1, values float32  
Log from Tue Jul 8 14:25:38 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.194, step 1, values float32  
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32  
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32  
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32  
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32  
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32  
Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 5.81, step 1, values float32  
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32  
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  
Log from Mon Jul 7 17:31:35 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32  
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32  
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32  
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32  
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32  
Log from Mon Jul 7 09:47:13 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250705_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Sat Jul 5 20:47:49 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Fri Jul 4 14:29:17 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Fri Jul 4 10:54:24 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Fri Jul 4 09:53:55 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250703_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Thu Jul 3 17:41:19 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Wed Jul 2 17:43:06 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Wed Jul 2 15:03:33 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.00608, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.00134, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000955, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000493, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.00616, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00152, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.000716, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.000812, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0066, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0013, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000798, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000426, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0064, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.00156, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.000666, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.000439, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.00725, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.00154, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.000864, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.000379, step 1, values float32  
Log from Tue Jul 1 15:42:09 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.00608, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.00134, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000955, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000493, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.00616, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00152, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.000716, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.000812, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0066, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0013, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000798, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000426, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0064, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.00156, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.000666, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.000439, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.00725, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.00154, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.000864, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.000379, step 1, values float32  
Log from Tue Jul 1 13:02:54 2025 Startup Messages  
---  
warning | No presets found in custom preset folder /Users/becca/Desktop/Postdoc/Computational_references/ChimeraX_presets  
note | available bundle cache has not been initialized yet  
  

> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true

Saved volume settings  

> graphics silhouettes true

> set silhouetteWidth 1.5

> ui mousemode right "translate selected models"

> alias t0 transparency 0

> alias t50 transparency 50

> alias t60 transparency 60

> alias t70 transparency 70

> alias t80 transparency 80

> alias t90 transparency 90

> alias fmap ui tool show "Fit in Map"

> alias delh select H; delete sel

> alias ls lighting soft

> alias 0 transp 0; lighting soft

> alias fit transp 50; lighting simple

> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1

> functionkey F1 mousemode right 'rotate selected models'

> functionkey F2 mousemode right 'translate selected models'

> functionkey F3 view sel

> functionkey F5 turn x 1 90

> functionkey F6 turn x -1 90

> functionkey F7 turn y 1 90

> functionkey F8 turn y -1 90

> functionkey F9 turn z 1 90

> functionkey F10 turn z -1 90

> cartoon smooth 1

> style stick

Changed 0 atom styles  

> size stickRadius 0.3

Changed 0 bond radii  

> set bgColor white

> alias bbh hide @C,N,O

> alias bb show @C,N,O

> cartoon all

> style stick

Changed 0 atom styles  

> color all byhetero

> hide atoms

> transparency 0

> lighting soft

> color name alphav1 #5786F5

Color 'alphav1' is opaque: rgb(34.1%, 52.5%, 96.1%) hex: #5786f5

  

> color name alphav2 #2A4B9B

Color 'alphav2' is opaque: rgb(16.5%, 29.4%, 60.8%) hex: #2a4b9b

  

> color name betapv1 #53EAF3

Color 'betapv1' is opaque: rgb(32.5%, 91.8%, 95.3%) hex: #53eaf3

  

> color name betapv2 #759ED9

Color 'betapv2' is opaque: rgb(45.9%, 62%, 85.1%) hex: #759ed9

  

> color name betav1 #37863D

Color 'betav1' is opaque: rgb(21.6%, 52.5%, 23.9%) hex: #37863d

  

> color name betav2 #207B35

Color 'betav2' is opaque: rgb(12.5%, 48.2%, 20.8%) hex: #207b35

  

> color name deltav1 #CE8041

Color 'deltav1' is opaque: rgb(80.8%, 50.2%, 25.5%) hex: #ce8041

  

> color name deltav2 #E97408

Color 'deltav2' is opaque: rgb(91.4%, 45.5%, 3.14%) hex: #e97408

  

> color name epsilonv1 #F06969

Color 'epsilonv1' is opaque: rgb(94.1%, 41.2%, 41.2%) hex: #f06969

  

> color name gammav1 #2AFF3C

Color 'gammav1' is opaque: rgb(16.5%, 100%, 23.5%) hex: #2aff3c

  

> color name gammav2 #61B230

Color 'gammav2' is opaque: rgb(38%, 69.8%, 18.8%) hex: #61b230

  

> color name zetav1 #E0C819

Color 'zetav1' is opaque: rgb(87.8%, 78.4%, 9.8%) hex: #e0c819

  

> color name zetav2 #EFE30C

Color 'zetav2' is opaque: rgb(93.7%, 89%, 4.71%) hex: #efe30c

  

> color name arf1v1 #FF76AF

Color 'arf1v1' is opaque: rgb(100%, 46.3%, 68.6%) hex: #ff76af

  

> color name arf1v2 #EB70A8

Color 'arf1v2' is opaque: rgb(92.2%, 43.9%, 65.9%) hex: #eb70a8

  

> color name label_red #E32723

Color 'label_red' is opaque: rgb(89%, 15.3%, 13.7%) hex: #e32723

  

> color name label_purple #6C4896

Color 'label_purple' is opaque: rgb(42.4%, 28.2%, 58.8%) hex: #6c4896

  

> color name alphav3 #57679E

Color 'alphav3' is opaque: rgb(34.1%, 40.4%, 62%) hex: #57679e

  

> color name betapv3 #7ACADA

Color 'betapv3' is opaque: rgb(47.8%, 79.2%, 85.5%) hex: #7acada

  

> color name betav3 #447A57

Color 'betav3' is opaque: rgb(26.7%, 47.8%, 34.1%) hex: #447a57

  

> color name gammav3 #ADE57C

Color 'gammav3' is opaque: rgb(67.8%, 89.8%, 48.6%) hex: #ade57c

  

> color name deltav3 #E5AF76

Color 'deltav3' is opaque: rgb(89.8%, 68.6%, 46.3%) hex: #e5af76

  

> color name epsilonv3 #EB8675

Color 'epsilonv3' is opaque: rgb(92.2%, 52.5%, 45.9%) hex: #eb8675

  

> color name zetav3 #F0E07B

Color 'zetav3' is opaque: rgb(94.1%, 87.8%, 48.2%) hex: #f0e07b

  

> color name arf1v3 #EB8BCA

Color 'arf1v3' is opaque: rgb(92.2%, 54.5%, 79.2%) hex: #eb8bca

  

> color name label_red_v3 #E51A16

Color 'label_red_v3' is opaque: rgb(89.8%, 10.2%, 8.63%) hex: #e51a16

  

> color name label_purple_v3 #691099

Color 'label_purple_v3' is opaque: rgb(41.2%, 6.27%, 60%) hex: #691099

  

> color name lable_purple_v4 #9057AD

Color 'lable_purple_v4' is opaque: rgb(56.5%, 34.1%, 67.8%) hex: #9057ad

  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3623_consensus_structure_sharp.mrc"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3623_consensus_structure.mrc"

Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc"

Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc"

Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc"

Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc"

Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc"

Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc"

Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc"

Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc"

Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc"

Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 0.729, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc"

Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 0.729, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4021_005_volume_map_bprime_local.mrc"

Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4021_005_volume_map_sharp_bprime_local.mrc"

Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_005_volume_map_bprime_local.mrc"

Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_005_volume_map_sharp_bprime_local.mrc"

Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4023_003_volume_map_bprime_local.mrc"

Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4023_003_volume_map_sharp_bprime_local.mrc"

Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4024_005_volume_map_bprime_local.mrc"

Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4024_005_volume_map_sharp_bprime_local.mrc"

Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4025_004_volume_map_bprime_local.mrc"

Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4025_004_volume_map_sharp_bprime_local.mrc"

Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4026_004_volume_map_gammazeta_local.mrc"

Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4026_004_volume_map_sharp_gammazeta_local.mrc"

Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4027_005_volume_map_gammazeta_local.mrc"

Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4027_005_volume_map_sharp_gammazeta_local.mrc"

Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4028_004_volume_map_gammazeta_local.mrc"

Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4028_004_volume_map_sharp_gammazeta_local.mrc"

Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  

> hide #!28 models

> hide #!27 models

> hide #!26 models

> hide #!25 models

> hide #!24 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!3 models

> show #!1 models

> select add #3

2 models selected  

> view matrix models #3,1,0,0,11.802,0,1,0,1.1649,0,0,1,22.807

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.42058,-0.90712,0.015978,332.41,-0.80828,0.38263,0.44752,138.26,-0.41207,0.1753,-0.89413,312.09

> fitmap #3 inMap #1

Fit map
W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138102 points  
correlation = 0.9343, correlation about mean = 0.6786, overlap = 2.406e+04  
steps = 156, shift = 6.42, angle = 18.1 degrees  
  
Position of
W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34036295 -0.91876592 -0.20005563 354.03277644  
-0.77656396 0.15469587 0.61075167 146.14319511  
-0.53019004 0.36323323 -0.76613324 277.46223631  
Axis -0.56713702 0.75643433 0.32582620  
Axis point 252.05264579 0.00000000 81.40495015  
Rotation angle (degrees) 167.39564073  
Shift along axis 0.16710354  
  

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!4 models

> select add #4

2 models selected  

> view matrix models
> #4,-0.16847,-0.98434,-0.051916,308.16,-0.77209,0.099036,0.62775,149.29,-0.61277,0.14584,-0.77668,305.19

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.16847,-0.98434,-0.051916,317.82,-0.77209,0.099036,0.62775,149.66,-0.61277,0.14584,-0.77668,323.39

> fitmap #4 inMap #1

Fit map
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
in map W20_J3623_consensus_structure_sharp.mrc using 138119 points  
correlation = 0.9535, correlation about mean = 0.7475, overlap = 3.27e+04  
steps = 128, shift = 2.65, angle = 13.7 degrees  
  
Position of
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
(#4) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34033481 -0.91878664 -0.20000833 354.04060287  
-0.77649015 0.15464973 0.61085719 146.12650484  
-0.53031619 0.36320047 -0.76606146 277.48080009  
Axis -0.56714143 0.75641504 0.32586328  
Axis point 252.06555110 0.00000000 81.39782971  
Rotation angle (degrees) 167.38858263  
Shift along axis 0.16199507  
  

> hide #!4 models

> select subtract #4

Nothing selected  

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> show #!9 models

> hide #!9 models

> select add #8

2 models selected  

> select add #7

4 models selected  

> select add #6

6 models selected  

> select add #5

8 models selected  

> view matrix models
> #5,1,0,0,10.109,0,1,0,2.5885,0,0,1,20.808,#6,1,0,0,10.109,0,1,0,2.5885,0,0,1,20.808,#7,1,0,0,10.109,0,1,0,2.5885,0,0,1,20.808,#8,1,0,0,10.109,0,1,0,2.5885,0,0,1,20.808

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.27105,-0.96135,0.048324,315.79,-0.78137,0.24907,0.5722,138.42,-0.56213,0.11734,-0.81869,331.41,#6,-0.27105,-0.96135,0.048324,315.79,-0.78137,0.24907,0.5722,138.42,-0.56213,0.11734,-0.81869,331.41,#7,-0.27105,-0.96135,0.048324,315.79,-0.78137,0.24907,0.5722,138.42,-0.56213,0.11734,-0.81869,331.41,#8,-0.27105,-0.96135,0.048324,315.79,-0.78137,0.24907,0.5722,138.42,-0.56213,0.11734,-0.81869,331.41

> fitmap #5 inMap #1

Fit map
W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138161 points  
correlation = 0.915, correlation about mean = 0.6261, overlap = 2.286e+04  
steps = 144, shift = 6.68, angle = 15.4 degrees  
  
Position of
W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc (#5)
relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33486423 -0.92026440 -0.20243362 353.69981178  
-0.77926293 0.14969047 0.60855734 147.51639631  
-0.52973128 0.36153311 -0.76725393 277.76199824  
Axis -0.56967931 0.75480327 0.32517303  
Axis point 252.70022071 0.00000000 81.39359448  
Rotation angle (degrees) 167.47826779  
Shift along axis 0.17110458  
  

> fitmap #6 inMap #1

Fit map
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
in map W20_J3623_consensus_structure_sharp.mrc using 138162 points  
correlation = 0.9385, correlation about mean = 0.703, overlap = 3.152e+04  
steps = 124, shift = 6.79, angle = 15.3 degrees  
  
Position of
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
(#6) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33341982 -0.92087059 -0.20206083 353.53923788  
-0.78000897 0.14906211 0.60775528 147.84755443  
-0.52954435 0.36024692 -0.76798759 277.99643882  
Axis -0.57030812 0.75458667 0.32457296  
Axis point 252.86314379 0.00000000 81.47103793  
Rotation angle (degrees) 167.46738658  
Shift along axis 0.16762333  
  

> fitmap #7 inMap #1

Fit map
W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138206 points  
correlation = 0.9279, correlation about mean = 0.6497, overlap = 2.411e+04  
steps = 136, shift = 6.69, angle = 15.3 degrees  
  
Position of
W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc (#7)
relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34035723 -0.91890040 -0.19944673 353.88927693  
-0.77660263 0.15512153 0.61059451 146.07614815  
-0.53013707 0.36271111 -0.76641721 277.57142341  
Axis -0.56711725 0.75656617 0.32555437  
Axis point 251.97967916 0.00000000 81.48001825  
Rotation angle (degrees) 167.37630205  
Shift along axis 0.18414629  
  

> fitmap #8 inMap #1

Fit map
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
in map W20_J3623_consensus_structure_sharp.mrc using 138103 points  
correlation = 0.9399, correlation about mean = 0.7087, overlap = 4.09e+04  
steps = 132, shift = 6.54, angle = 15.4 degrees  
  
Position of
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
(#8) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34016956 -0.91889502 -0.19979141 353.89977575  
-0.77635698 0.15454414 0.61105314 146.04451039  
-0.53061710 0.36297113 -0.76596178 277.53661238  
Axis -0.56719105 0.75636832 0.32588538  
Axis point 252.01132593 0.00000000 81.40408707  
Rotation angle (degrees) 167.36769172  
Shift along axis 0.17978067  
  

> select subtract #8

6 models selected  

> select subtract #7

4 models selected  

> select subtract #6

2 models selected  

> select subtract #5

Nothing selected  

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> show #!9 models

> show #!10 models

> show #!11 models

> hide #!11 models

> select add #10

2 models selected  

> select add #9

4 models selected  

> view matrix models
> #9,-0.20458,-0.9646,-0.16641,334.03,-0.77373,0.055221,0.6311,156.33,-0.59957,0.25787,-0.75764,298.39,#10,-0.20458,-0.9646,-0.16641,334.03,-0.77373,0.055221,0.6311,156.33,-0.59957,0.25787,-0.75764,298.39

> ui mousemode right "translate selected models"

> view matrix models
> #9,-0.20458,-0.9646,-0.16641,335.57,-0.77373,0.055221,0.6311,156.39,-0.59957,0.25787,-0.75764,301.3,#10,-0.20458,-0.9646,-0.16641,335.57,-0.77373,0.055221,0.6311,156.39,-0.59957,0.25787,-0.75764,301.3

> fitmap #9 inMap #1

Fit map
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc in
map W20_J3623_consensus_structure_sharp.mrc using 138204 points  
correlation = 0.9071, correlation about mean = 0.5649, overlap = 2.482e+04  
steps = 92, shift = 0.476, angle = 8.65 degrees  
  
Position of
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc
(#9) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33561246 -0.92104503 -0.19758628 353.34320386  
-0.77965973 0.15387748 0.60700283 147.26083252  
-0.52867286 0.35776778 -0.76974491 278.24593808  
Axis -0.56920453 0.75613754 0.32289661  
Axis point 252.48560152 0.00000000 81.78647209  
Rotation angle (degrees) 167.35364255  
Shift along axis 0.06955954  
  

> fitmap #10 inMap #1

Fit map
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
in map W20_J3623_consensus_structure_sharp.mrc using 138104 points  
correlation = 0.9176, correlation about mean = 0.6072, overlap = 3.365e+04  
steps = 96, shift = 0.462, angle = 8.63 degrees  
  
Position of
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
(#10) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33524620 -0.92121016 -0.19743815 353.30178908  
-0.77963330 0.15360588 0.60710555 147.28662723  
-0.52894414 0.35745918 -0.76970191 278.32308895  
Axis -0.56934667 0.75603676 0.32288198  
Axis point 252.53350589 0.00000000 81.77924134  
Rotation angle (degrees) 167.33564064  
Shift along axis 0.06841760  
  

> select subtract #10

2 models selected  

> select subtract #9

Nothing selected  

> hide #!9 models

> hide #!10 models

> show #!11 models

> show #!12 models

> volume #11 level 1.414

> volume #12 level 1.511

> select add #11

2 models selected  

> select add #12

4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.12102,-0.028286,0.99225,32.717,0.99084,0.056881,0.12247,-30.578,-0.059904,0.99798,0.021144,3.463,#12,-0.12102,-0.028286,0.99225,32.717,0.99084,0.056881,0.12247,-30.578,-0.059904,0.99798,0.021144,3.463

> view matrix models
> #11,-0.047287,-0.19762,0.97914,47.757,0.3239,0.92424,0.20219,-66.044,-0.94491,0.3267,0.020305,232.25,#12,-0.047287,-0.19762,0.97914,47.757,0.3239,0.92424,0.20219,-66.044,-0.94491,0.3267,0.020305,232.25

[deleted to fit within ticket limits]

> key red-white-blue :3.0 :4.5 :6.5 showTool true

> color sample #1.1 map #48 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> key red-white-blue :3.0 :4.5 :6.0 showTool true

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4480_map_locres_J3623_v2.mrc"

Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4481_map_locres_J3623_v3.mrc"

Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32  

> hide #!52 models

> hide #!53 models

> color sample #1.1 map #52 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color single #1.1

> color sample #1.1 map #52 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #53 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color single #1.1

> color sample #1.1 map #53 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #53 palette 3,#ff0000:4.5,#ffffff:7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #53 palette 3,#ff0000:4.5,#ffffff:8,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color single #1.1

> color sample #1.1 map #53 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #53 palette 3,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> volume #1 level 0.1937

> view view5

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

——— End of log from Mon Jul 7 17:31:35 2025 ———

> view name session-start

opened ChimeraX session  

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments.cxs"

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2586_007_volume_map.mrc"

Opened cryosparc_P126_J2586_007_volume_map.mrc as #54, grid size 300,300,300,
pixel 1.24, shown at level 0.227, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J4482_map_locres.mrc"

Opened cryosparc_P126_J4482_map_locres.mrc as #55, grid size 400,400,400,
pixel 1.24, shown at level 39.3, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2954_map_locres_v3.mrc"

Opened cryosparc_P126_J2954_map_locres_v3.mrc as #56, grid size 300,300,300,
pixel 1.24, shown at level 6.45, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2953_map_locres_v2.mrc"

Opened cryosparc_P126_J2953_map_locres_v2.mrc as #57, grid size 300,300,300,
pixel 1.24, shown at level 6.45, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2952_map_locres_J2634_v1.mrc"

Opened cryosparc_P126_J2952_map_locres_J2634_v1.mrc as #58, grid size
400,400,400, pixel 1.24, shown at level 39.3, step 1, values float32  

> hide #!58 models

> hide #!57 models

> hide #!56 models

> hide #!55 models

> hide #!1 models

> show #!50 models

> hide #51 models

> hide #!50 models

> ui tool show "Surface Color"

> color sample #54.1 map #58 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.735, mean 6.524, maximum 41.56  

> color single #54.1

> color sample #54.1 map #58 palette 2.735,#ff0000:4,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.735, mean 6.524, maximum 41.56  

> color single #54.1

> color sample #54.1 map #58 palette 3.5,#ff0000:5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.735, mean 6.524, maximum 41.56  

> close #54

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2634_009_volume_map.mrc"

Opened cryosparc_P126_J2634_009_volume_map.mrc as #54, grid size 400,400,400,
pixel 1.24, shown at level 0.224, step 1, values float32  

> show #!58 models

> hide #!58 models

> color sample #54.1 map #58 palette 3.5,#ff0000:5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.735, mean 3.894, maximum 29.02  

> color single #54.1

> color sample #54.1 map #56 palette 3.5,#ff0000:5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 0.5331, maximum 17.84  

> close #54-58

> show #51 models

> show #!1 models

> view view9

Expected an objects specifier or a view name or a keyword  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4486_map_locres.mrc"

Opened cryosparc_P126_J4486_map_locres.mrc as #54, grid size 240,240,240,
pixel 2.38, shown at level 59.5, step 1, values float32  

> hide #!54 models

> color sample #1.1 map #54 palette 3,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color single #1.1

> color sample #1.1 map #54 palette 2,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color sample #1.1 map #54 palette 1,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color sample #1.1 map #54 palette 1,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color single #1.1

> color sample #1.1 map #54 palette 1,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color single #1.1

> color sample #1.1 map #54 palette 1,#ff0000:10,#ffffff:20,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color single #1.1

> color sample #1.1 map #54 palette 3,#ff0000:10,#ffffff:30,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color single #1.1

> color sample #1.1 map #54 palette 4,#ff0000:10,#ffffff:30,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color sample #1.1 map #54 palette 1,#ff0000:10,#ffffff:30,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color single #1.1

> color sample #1.1 map #54 palette 1,#ff0000:20,#ffffff:50,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> key red-white-blue :1 :20 :50 showTool true

> ui mousemode right "color key"

> color sample #1.1 map #54 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> key red-white-blue :7.5 :35.2 :62.8 showTool true

> ui mousemode right "color key"

> color single #1.1

> color sample #1.1 map #48 palette 7.493,#ff0000:35.17,#ffffff:62.84,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> key red-white-blue :2.58 :5.15 :7.72 showTool true

> ui mousemode right "color key"

> color sample #1.1 map #48 palette 3,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette 2.5,#ff0000:5.1,#ffffff:7.7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette 2.5,#ff0000:5.1,#ffffff:7.7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> key red-white-blue :2.5 :5.1 :7.7 showTool true

> ui mousemode right "color key"

> hide #51 models

> hide #!1 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2586_007_volume_map.mrc"

Opened cryosparc_P126_J2586_007_volume_map.mrc as #55, grid size 300,300,300,
pixel 1.24, shown at level 0.227, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J4484_map_locres_J2586.mrc"

Opened cryosparc_P126_J4484_map_locres_J2586.mrc as #56, grid size
300,300,300, pixel 2.48, shown at level 7.7, step 1, values float32  

> hide #!56 models

> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 0, mean 0.01555, maximum 9.579  

> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 0, mean 0.01555, maximum 9.579  

> color sample #55.1 map #56 palette 0,#ff0000:4.79,#ffffff:9.579,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 0.01555, maximum 9.579  

> color single #55.1

> close #56

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2953_map_locres_v2.mrc"

Opened cryosparc_P126_J2953_map_locres_v2.mrc as #56, grid size 300,300,300,
pixel 1.24, shown at level 6.45, step 1, values float32  

> color sample #55.1 map #56 palette 0,#ff0000:4.79,#ffffff:9.579,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> hide #!55 models

> show #!55 models

> hide #!56 models

> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color single #55.1

> color sample #55.1 map #56 palette 3,#ff0000:4,#ffffff:7.5,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette 3,#ff0000:4,#ffffff:7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color single #55.1

> color sample #55.1 map #56 palette 3,#ff0000:4,#ffffff:7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette 0,#ff0000:3.642,#ffffff:7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette 2,#ff0000:4,#ffffff:7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette 2.5,#ff0000:4,#ffffff:7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette 2,#ff0000:4,#ffffff:7.283,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> volume #55 level 0.1387

> volume #55 level 0.2647

> volume #56 level 5.608

> hide #!56 models

> volume #55 level 0.196

> color sample #55.1 map #56 palette 2,#ff0000:3,#ffffff:7.283,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19  

> color sample #55.1 map #56 palette 2,#ff0000:5,#ffffff:7.283,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19  

> color sample #55.1 map #56 palette 2,#ff0000:3.5,#ffffff:7.283,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19  

> key red-white-blue :2.00 :3.50 :7.28 showTool true

> ui mousemode right "color key"

> show #51 models

> color sample #55.1 map #56 palette 2,#ff0000:3.5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19  

> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19  

> color sample #55.1 map #56 palette 2,#ff0000:4,#ffffff:7.2,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19  

> close #55

> close #56

> hide #51 models

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Final maps and
> model/job073_local_res_filtered_map/relion_locres_filtered.mrc"

Opened relion_locres_filtered.mrc as #55, grid size 292,292,292, pixel 1.71,
shown at level 0.00473, step 1, values float32  

> select add #55

2 models selected  

> show #!1 models

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models #55,1,0,0,-49.466,0,1,0,19.546,0,0,1,-35.582

> view matrix models #55,1,0,0,-125.29,0,1,0,-27.177,0,0,1,-72.202

> view matrix models #55,1,0,0,-131.08,0,1,0,-78.985,0,0,1,-39.391

> ui mousemode right "rotate selected models"

> view matrix models
> #55,-0.38231,0.6929,0.61133,-29.962,0.21577,0.71024,-0.67007,84.421,-0.89849,-0.12426,-0.42104,593.37

> view matrix models
> #55,-0.86508,-0.091241,-0.49327,551.34,0.025332,-0.99001,0.1387,320.67,-0.501,0.10749,0.85875,116.81

> ui mousemode right "translate selected models"

> view matrix models
> #55,-0.86508,-0.091241,-0.49327,563.32,0.025332,-0.99001,0.1387,328.73,-0.501,0.10749,0.85875,49.963

> view matrix models
> #55,-0.86508,-0.091241,-0.49327,502.1,0.025332,-0.99001,0.1387,335.45,-0.501,0.10749,0.85875,10.384

> ui mousemode right "rotate selected models"

> view matrix models
> #55,-0.7625,0.17437,-0.62305,444.83,-0.32722,-0.93469,0.13888,425.79,-0.55814,0.30977,0.76975,3.7603

> ui mousemode right "translate selected models"

> view matrix models
> #55,-0.7625,0.17437,-0.62305,440.55,-0.32722,-0.93469,0.13888,403.93,-0.55814,0.30977,0.76975,-7.0818

> fitmap #55 inMap #1

Fit map relion_locres_filtered.mrc in map W20_J3623_consensus_structure.mrc
using 248012 points  
correlation = 0.446, correlation about mean = 0.2993, overlap = 121.7  
steps = 328, shift = 23.5, angle = 15 degrees  
  
Position of relion_locres_filtered.mrc (#55) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.64805723 0.29760230 -0.70103830 399.38555473  
-0.32266507 -0.94108474 -0.10122635 486.21101125  
-0.68986164 0.16060010 0.70590263 74.18713432  
Axis 0.38883752 -0.01659842 -0.92115682  
Axis point 261.23669220 207.73357377 0.00000000  
Rotation angle (degrees) 160.32536182  
Shift along axis 78.88777001  
  

> select subtract #55

Nothing selected  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Final maps and model/Model_files/COPI_GOLPH3_combined_model_v14.mmcif"

Summary of feedback from opening /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Final maps and
model/Model_files/COPI_GOLPH3_combined_model_v14.mmcif  
---  
warnings | Unknown polymer entity '1' on line 142  
Unknown polymer entity '2' on line 206  
Unknown polymer entity '3' on line 1183  
Unknown polymer entity '4' on line 3547  
Unknown polymer entity '5' on line 4479  
11 messages similar to the above omitted  
Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
Chain information for COPI_GOLPH3_combined_model_v14.mmcif #56  
---  
Chain | Description  
A | No description available  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
R S T | No description available  
  

> hide #!56 atoms

> show #!56 cartoons

> show #!24 models

> hide #!24 models

> select add #56

17013 atoms, 16995 bonds, 4 pseudobonds, 4252 residues, 2 models selected  

> view matrix models #56,1,0,0,-57.326,0,1,0,-94.635,0,0,1,-152.05

> view matrix models #56,1,0,0,-96.675,0,1,0,-128.13,0,0,1,-110.53

> hide #!1 models

> color #55 #929292ff models

> color #55 #92929240 models

> view matrix models #56,1,0,0,-87.633,0,1,0,-75.202,0,0,1,-105.19

> ui mousemode right "rotate selected models"

> view matrix models
> #56,-0.57627,0.2909,-0.76373,403.39,-0.3025,-0.94406,-0.13134,514.31,-0.75921,0.15534,0.63203,127.54

> ui mousemode right "translate selected models"

> view matrix models
> #56,-0.57627,0.2909,-0.76373,414.45,-0.3025,-0.94406,-0.13134,516.62,-0.75921,0.15534,0.63203,106.07

> view matrix models
> #56,-0.57627,0.2909,-0.76373,421.71,-0.3025,-0.94406,-0.13134,495.85,-0.75921,0.15534,0.63203,110.7

> fitmap #56 inMap #55

Fit molecule COPI_GOLPH3_combined_model_v14.mmcif (#56) to map
relion_locres_filtered.mrc (#55) using 17013 atoms  
average map value = 0.005565, steps = 148  
shifted from previous position = 12.3  
rotated from previous position = 7.06 degrees  
atoms outside contour = 9511, contour level = 0.0047295  
  
Position of COPI_GOLPH3_combined_model_v14.mmcif (#56) relative to
relion_locres_filtered.mrc (#55) coordinates:  
Matrix rotation and translation  
0.99861221 0.04491552 0.02749984 -28.06097041  
-0.04715481 0.99508491 0.08707710 -7.47857239  
-0.02345356 -0.08825301 0.99582194 24.76832483  
Axis -0.85742564 0.24917997 -0.45025617  
Axis point 0.00000000 330.55403154 136.14787847  
Rotation angle (degrees) 5.86829908  
Shift along axis 11.04459412  
  

> select subtract #56

Nothing selected  

> select add #56

17013 atoms, 16995 bonds, 4 pseudobonds, 4252 residues, 2 models selected  

> view matrix models
> #56,-0.64475,0.3289,-0.69002,379.8,-0.27547,-0.94202,-0.19162,491.22,-0.71303,0.066527,0.69797,103.59

> fitmap #56 inMap #55

Fit molecule COPI_GOLPH3_combined_model_v14.mmcif (#56) to map
relion_locres_filtered.mrc (#55) using 17013 atoms  
average map value = 0.005776, steps = 92  
shifted from previous position = 4.45  
rotated from previous position = 3.4 degrees  
atoms outside contour = 9140, contour level = 0.0047295  
  
Position of COPI_GOLPH3_combined_model_v14.mmcif (#56) relative to
relion_locres_filtered.mrc (#55) coordinates:  
Matrix rotation and translation  
0.99783486 0.06315960 -0.01834221 -2.15609454  
-0.06052615 0.99097184 0.11963015 -14.59510136  
0.02573241 -0.11826095 0.99264907 30.83542514  
Axis -0.87549404 -0.16220473 -0.45519206  
Axis point 0.00000000 213.68284829 151.38980884  
Rotation angle (degrees) 7.80841410  
Shift along axis -9.78099817  
  

> view matrix models
> #56,-0.68271,0.33689,-0.6484,381.54,-0.26761,-0.941,-0.20715,505.03,-0.67992,0.032098,0.73258,104.14

> fitmap #56 inMap #55

Fit molecule COPI_GOLPH3_combined_model_v14.mmcif (#56) to map
relion_locres_filtered.mrc (#55) using 17013 atoms  
average map value = 0.01255, steps = 84  
shifted from previous position = 7.68  
rotated from previous position = 7.81 degrees  
atoms outside contour = 1181, contour level = 0.0047295  
  
Position of COPI_GOLPH3_combined_model_v14.mmcif (#56) relative to
relion_locres_filtered.mrc (#55) coordinates:  
Matrix rotation and translation  
0.99999995 0.00017955 -0.00021830 0.02553185  
-0.00017956 0.99999997 -0.00007215 0.05642662  
0.00021829 0.00007219 0.99999997 -0.06358059  
Axis 0.24739544 -0.74829798 -0.61550437  
Axis point 282.18300475 0.00000000 113.24807650  
Rotation angle (degrees) 0.01671451  
Shift along axis 0.00322666  
  

> select subtract #56

Nothing selected  

> color #56/a label_purple_v3

> color #56/b label_purple_v3

> color #56/d navy

> color #56/e navy

> color #56/f betapv3

> color #56/g betapv3

> color #56/h betav1

> color #56/i betav1

> color #56/j betav1

> color #56/k betav1

> color #56/l deltav1

> color #56/l deltav3

> color #56/m gammav3

> color #56/n gammav3

> color #56/o gammav3

> color #56/s arf1v3

> color #56/r arf1v3

> color #56/t arf1v3

> hide #!56 models

> hide #!55 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"

> show #!24 models

> select add #24.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select subtract #24.13

Nothing selected  

> select add #25.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select subtract #25.13

Nothing selected  

> hide #!24 models

> show #!26 models

> select add #26.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select add #26

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 15 models selected  

> select subtract #26

Nothing selected  

> show #!27 models

> select add #26.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> select add #26

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 15 models selected  

> select subtract #26

Nothing selected  

> select add #27.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select add #27

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 15 models selected  

> select subtract #27

Nothing selected  

> hide #!26 models

> hide #!27 models

> select add #28.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select subtract #28.13

Nothing selected  

> select add #29.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select add #29

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 15 models selected  

> select subtract #29

Nothing selected  

> select add #30.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select subtract #30.13

Nothing selected  

> select add #32.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select subtract #32.13

Nothing selected  

> show #!33.13 models

> select add #33.13

2744 atoms, 2786 bonds, 1 pseudobond, 354 residues, 2 models selected  

> color sel gammav3

> select subtract #33.13

Nothing selected  

> show #34.13 models

> select add #34.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select subtract #34.13

Nothing selected  

> hide #!33 models

> hide #!34 models

> show #!33 models

> hide #!33 models

> show #!35 models

> hide #!35 models

> show #!36 models

> hide #!36 models

> show #!37 models

> hide #!37 models

> show #!38 models

> hide #!38 models

> show #!39 models

> hide #!39 models

> show #!40 models

> hide #!40 models

> show #!41 models

> hide #!41 models

> show #!42 models

> hide #!42 models

> show #!43 models

> hide #!43 models

> show #!44 models

> hide #!44 models

> show #!45 models

> hide #!45 models

> show #!46 models

> hide #!46 models

> show #!47 models

> hide #!47 models

> show #!49 models

> show #!50 models

> hide #!50 models

> show #!50 models

> hide #!49 models

> hide #!50 models

> show #!50 models

> hide #!50 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"

> show #!55 models

> show #!56 models

> view view1

> view view2

> view view3

> view view4

> view view5

> view view6

Expected an objects specifier or a view name or a keyword  

> view view7

Expected an objects specifier or a view name or a keyword  

> view view8

Expected an objects specifier or a view name or a keyword  

> volume #55 level 0.0055

> volume #55 level 0.005

> color #55 darkgrey models

> color #55 #929292ff models

> color #55 #92929267 models

> ui tool show "Side View"

> view name view8

> hide #!56 models

> hide #!55 models

> show #!50 models

> show #!47 models

> color #47 #929292ff models

> color #47 #92929266 models

> ui mousemode right select

> select clear

[Repeated 2 time(s)]

> hide #!50 models

> show #!50 models

Drag select of 2 residues  

> select up

166 atoms, 167 bonds, 24 residues, 1 model selected  

> delete sel

Drag select of 7 residues  

> select up

149 atoms, 150 bonds, 18 residues, 1 model selected  

> delete sel

> select #50/L:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> select #50/L:2

9 atoms, 8 bonds, 1 residue, 1 model selected  

> delete sel

> select #50/L:3

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete sel

> select #50/L:4

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> select #47

3 models selected  

> select clear

> select #50/L:5

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> hide #!50 models

> show #!49 models

> hide #!47 models

> show #!46 models

> select #49/L:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> \

Unknown command: \  

> delete sel

> select #46

2 models selected  

> select clear

> select #46

2 models selected  

> hide #!46 models

> select subtract #46

Nothing selected  

> select #49/L:2

9 atoms, 8 bonds, 1 residue, 1 model selected  

> delete sel

> select #49/L:3

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete sel

> show #!46 models

> select #49/L:4

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> select #49/L:5

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

Drag select of 3 residues  

> select up

149 atoms, 150 bonds, 18 residues, 1 model selected  

> delete sel

> select clear

[Repeated 1 time(s)]Drag select of 4 residues  

> select up

166 atoms, 167 bonds, 24 residues, 1 model selected  

> delete sel

> hide #!49 models

> hide #!46 models

> color #46 #929292ff models

> color #46 #92929266 models

> show #!46 models

> show #!49 models

> view view8

> hide #!49 models

> hide #!46 models

> show #!55 models

> show #!56 models

> view name view8

> hide #!56 models

> hide #!55 models

> show #!50 models

> show #!47 models

> volume #47 level 4.58

> view view8

> hide #!50 models

> hide #!47 models

> show #!56 models

> show #!55 models

> hide #!56 models

> hide #!55 models

> show #!55 models

> show #!46 models

> hide #!46 models

> show #!46 models

> color #55 #d4fb79ff models

> select add #55

3 models selected  
Drag select of 46 composite_map_J4021_J4026.ccp4 , 55
relion_locres_filtered.mrc  

> select add #55

5 models selected  

> select subtract #55

2 models selected  

> ui mousemode right "translate selected models"

> select add #55

5 models selected  

> select subtract #55

2 models selected  

> select add #46

3 models selected  

> select subtract #46

Nothing selected  

> select add #55

3 models selected  

> view matrix models
> #55,-0.64806,0.2976,-0.70104,404.74,-0.32267,-0.94108,-0.10123,483.04,-0.68986,0.1606,0.7059,77.297

> ui mousemode right "rotate selected models"

> view matrix models
> #55,-0.73178,0.069047,-0.67804,474.38,-0.12094,-0.99222,0.029485,404.07,-0.67073,0.10358,0.73444,77.507

> fitmap #55 inMap #1

Fit map relion_locres_filtered.mrc in map W20_J3623_consensus_structure.mrc
using 191343 points  
correlation = 0.5091, correlation about mean = 0.3117, overlap = 135.7  
steps = 196, shift = 24.8, angle = 11.2 degrees  
  
Position of relion_locres_filtered.mrc (#55) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.75253459 0.06710395 -0.65512499 473.61243410  
0.00933094 -0.99360872 -0.11249292 428.86098374  
-0.65848662 -0.09076775 0.74709878 117.70957595  
Axis 0.35145885 0.05438278 -0.93462249  
Axis point 262.44867657 214.17046526 0.00000000  
Rotation angle (degrees) 178.22886921  
Shift along axis 79.76391490  
  

> select subtract #55

Nothing selected  

> color #55 #929292ff models

> color #55 #92929266 models

> hide #!46 models

> view view8

> show #!56 models

> hide #!56 models

> hide #!55 models

> show #!50 models

> show #!47 models

> hide #!50 models

> hide #!47 models

> show #!49 models

> show #!46 models

> view name view8a

> hide #!49 models

> hide #!46 models

> show #!46 models

> show #!49 models

> view name view9

> hide #!49 models

> hide #!46 models

> show #!47 models

> show #!50 models

> hide #!50 models

> view name view10

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"

——— End of log from Tue Jul 8 14:25:38 2025 ———

opened ChimeraX session  

> show #!1 models

> hide #!47 models

> view view1

> show #51 models

> ui tool show "Surface Color"

> color sample #1.1 map #48 palette 2.5,#ff0000:5.1,#ffffff:7.7,#0000ff

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> key red-white-blue :2.5 :5.1 :7.7 showTool true

> ui mousemode right "color key"

> ui mousemode right "translate selected models"

> key red-white-blue :2.5 :5.0 :7.0 showTool true

> ui mousemode right "color key"

> key red-white-blue :2.5 :5.0 :7.0

> ui mousemode right "translate selected models"

> color sample #1.1 map #48 palette 2.5,#ff0000:5,#ffffff:7,#0000ff

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> view view1

> view view2

> view view3

> view view4

> view view5

> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette 3,#ff0000:5,#ffffff:8,#0000ff

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette 3,#ff0000:5,#ffffff:8,#0000ff

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> key red-white-blue :3 :5 :8 showTool true

> ui mousemode right "color key"

> ui mousemode right "translate selected models"

> save
> /Users/becca/Desktop/Postdoc/Figures/20250707_Poster/chimerax_images/J3623_consensus_view5_locales_color_v2.png
> width 866 height 597 supersample 3 transparentBackground true

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from
> csparc/J3740_betaprime_3Dclass/J3740_betaprime_3Dclass_aligned.py"

Failed opening file /Users/becca/Desktop/Postdoc/COPI notebooks and
resources/Processing/Files from
csparc/J3740_betaprime_3Dclass/J3740_betaprime_3Dclass_aligned.py:  
ChimeraX cannot open a regular Chimera session. An exporter from Chimera to  
ChimeraX is available in the latest Chimera release. Use its File->Export
Scene  
menu item, and change the resulting dialog's "File Type" to ChimeraX.  

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"

——— End of log from Tue Jul 8 14:43:14 2025 ———

> view name session-start

opened ChimeraX session  

> hide #!1 models

> hide #51 models

> show #!6 models

> volume #6 level 0.198

> color #6 darkgrey models

> color #6 #929292ff models

> color #6 darkgrey models

> volume #6 level 0.2274

> hide #!6 models

> show #!8 models

> color #8 #929292ff models

> color #8 darkgrey models

> volume #8 level 0.2266

> show #!6 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4021_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!6 models

> show #!8 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4022_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> color #8 #797979ff models

> show #!6 models

> color #6 #d6d6d6ff models

> color #6 silver models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4021_J4022_betaprime_focused_superimposed_lightgrey_darkgrey.png"
> width 866 height 597 supersample 3 transparentBackground true

> color #6 darkgrey models

> color #8 darkgrey models

> hide #!8 models

> hide #!6 models

> show #!10 models

> color #10 #929292ff models

> color #10 darkgrey models

> volume #10 level 0.1989

> hide #!10 models

> color #11 darkgrey models

> color #11 #929292ff models

> color #11 darkgrey models

> show #!12 models

> color #12 #929292ff models

> color #12 darkgrey models

> volume #12 level 0.1985

> hide #!12 models

> show #!14 models

> color #14 #929292ff models

> color #14 darkgrey models

> volume #14 level 0.1912

> volume #14 level 0.2118

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!10 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4023_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!10 models

> show #!12 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4024_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!12 models

> show #!14 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4025_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!14 models

> show #!12 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4024_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> show #!14 models

> show #!16 models

> hide #!16 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> color #12 #d6d6d6ff models

> color #10 #797979ff models

> color #14 #797979ff models

> color #10 darkgrey models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4023_J4024_J4025_betaprime_focused_superimposed_lightgrey_darkgrey.png"
> width 866 height 597 supersample 3 transparentBackground true

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> color #12 darkgrey models

> color #14 darkgrey models

> show #!16 models

> hide #!14 models

> show #!18 models

> show #!20 models

> hide #!20 models

> hide #!16 models

> hide #!18 models

> show #!16 models

> hide #!16 models

> hide #!10 models

> hide #!12 models

> show #!16 models

> color #16 #929292ff models

> color #16 darkgrey models

> volume #16 level 0.2403

> hide #!16 models

> show #!18 models

> color #18 #797979ff models

> color #18 darkgrey models

> hide #!18 models

> show #!20 models

> color #20 darkgrey models

[Repeated 1 time(s)]

> hide #!20 models

> show #!22 models

> color #22 #929292ff models

> color #22 darkgrey models

> hide #!22 models

> show #!22 models

> hide #!22 models

> show #!16 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4026_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!16 models

> show #!18 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4027_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!18 models

> show #!20 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4028_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!20 models

> show #!22 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J3988_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!22 models

> show #!20 models

> show #!18 models

> show #!16 models

> show #!22 models

> hide #!22 models

> hide #!20 models

> color #16 silver models

> color #16 #919191ff models

> color #18 #d6d6d6ff models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4027_J4026_gammazeta_focused_superimposed_lightgrey_darkgrey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!18 models

> hide #!16 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250709_W20_COPI_cyto_alignments.cxs"

——— End of log from Wed Jul 9 09:46:30 2025 ———

opened ChimeraX session  

> ui tool show XMAS

> show #!56 models

  
Peptide pair mapping of XlinkX evidence file:
/Users/becca/Desktop/Postdoc/Data/Mass spec data/KDELR budding reaction
xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample04_Crosslinks.txt  
Unique peptide pairs: 257 out of 257  
Unique peptide pairs with pseudobonds: 118  
Pseudobonds are stored in /Users/becca/Desktop/Postdoc/Data/Mass spec
data/KDELR budding reaction xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample04_Crosslinks_56.pb  
Mapping information is stored in /Users/becca/Desktop/Postdoc/Data/Mass spec
data/KDELR budding reaction xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample04_Crosslinks_56.tsv  
  
Peptide pair mapping of XlinkX evidence file:
/Users/becca/Desktop/Postdoc/Data/Mass spec data/KDELR budding reaction
xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample03_Crosslinks.txt  
Unique peptide pairs: 395 out of 395  
Unique peptide pairs with pseudobonds: 157  
Pseudobonds are stored in /Users/becca/Desktop/Postdoc/Data/Mass spec
data/KDELR budding reaction xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample03_Crosslinks_56.pb  
Mapping information is stored in /Users/becca/Desktop/Postdoc/Data/Mass spec
data/KDELR budding reaction xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample03_Crosslinks_56.tsv  
  
Peptide pair mapping of XlinkX evidence file:
/Users/becca/Desktop/Postdoc/Data/Mass spec data/KDELR budding reaction
xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample02_Crosslinks.txt  
Unique peptide pairs: 405 out of 405  
Unique peptide pairs with pseudobonds: 166  
Pseudobonds are stored in /Users/becca/Desktop/Postdoc/Data/Mass spec
data/KDELR budding reaction xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample02_Crosslinks_56.pb  
Mapping information is stored in /Users/becca/Desktop/Postdoc/Data/Mass spec
data/KDELR budding reaction xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample02_Crosslinks_56.tsv  
  
Peptide pair mapping of XlinkX evidence file:
/Users/becca/Desktop/Postdoc/Data/Mass spec data/KDELR budding reaction
xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample01_Crosslinks.txt  
Unique peptide pairs: 384 out of 384  
Unique peptide pairs with pseudobonds: 159  
Pseudobonds are stored in /Users/becca/Desktop/Postdoc/Data/Mass spec
data/KDELR budding reaction xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample01_Crosslinks_56.pb  
Mapping information is stored in /Users/becca/Desktop/Postdoc/Data/Mass spec
data/KDELR budding reaction xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample01_Crosslinks_56.tsv  

> hide #57 models

> hide #58 models

> hide #59 models

Please select pseudobonds  
Please select pseudobonds  

> hide #60 models

> show #59 models

Please select pseudobonds  

> hide #59 models

> show #60 models

> select subtract #60

Nothing selected  

> hide #60 models

/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py:1116: UserWarning: Tight layout not applied.
The left and right margins cannot be made large enough to accommodate all Axes
decorations.  
plt.tight_layout()  
Venn diagrams can only be plotted for two or three groups  
Please select pseudobonds  
Please select pseudobonds  

> view matrix models #61,1,0,0,0,0,1,0,0,0,0,1,0

> select subtract #61

Nothing selected  

> close #57

> close #58

> close #59

> close #60

> close #61

> close #62

  
Peptide pair mapping of XlinkX evidence file:
/Users/becca/Desktop/Postdoc/Data/Mass spec data/KDELR budding reaction
xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample04_Crosslinks.txt  
Unique peptide pairs: 257 out of 257  
Unique peptide pairs with pseudobonds: 118  
Pseudobonds are stored in /Users/becca/Desktop/Postdoc/Data/Mass spec
data/KDELR budding reaction xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample04_Crosslinks_56.pb  
Mapping information is stored in /Users/becca/Desktop/Postdoc/Data/Mass spec
data/KDELR budding reaction xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample04_Crosslinks_56.tsv  
Traceback (most recent call last):  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 1739, in <lambda>  
gradient_group.buttonToggled.connect(lambda button,
checked:self.uncheck(button, checked, gradient_group, pbs))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 1990, in uncheck  
self.color_gradient(checked, pbs, button.policy)  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 2013, in color_gradient  
color_key.delete()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_key/model.py", line 104, in delete  
self.session.main_view.remove_overlays([self], delete = False)  
^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'main_view'  
  
AttributeError: 'NoneType' object has no attribute 'main_view'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_key/model.py", line 104, in delete  
self.session.main_view.remove_overlays([self], delete = False)  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2485, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 821, in close_request  
tool_window._destroy()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2367, in _destroy  
self.cleanup()  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 1882, in visualize_dialog_close_function  
self.reset_style(pbs, reset_values, visualize_dialog.apply,
visualize_dialog.color_keys)  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 1966, in reset_style  
setattr(pbs, attribute, value)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 221, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 159 does not match objects array length 0  
  
ValueError: Values array length 159 does not match objects array length 0  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 221, in set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  

> close #58

> close #57

  
Peptide pair mapping of XlinkX evidence file:
/Users/becca/Desktop/Postdoc/Data/Mass spec data/KDELR budding reaction
xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample01_Crosslinks.txt  
Unique peptide pairs: 384 out of 384  
Unique peptide pairs with pseudobonds: 159  
Pseudobonds are stored in /Users/becca/Desktop/Postdoc/Data/Mass spec
data/KDELR budding reaction xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample01_Crosslinks_56.pb  
Mapping information is stored in /Users/becca/Desktop/Postdoc/Data/Mass spec
data/KDELR budding reaction xlinking MS/crosslink
files/20250901_EXPL6_BaSt_SA_30SPD_PepSep_Orbi5816__F-45-55_Sample01_Crosslinks_56.tsv  
Please select pseudobonds  

> select subtract #57

Nothing selected  

> hide #57 models

Please select pseudobonds  

> select subtract #58

Nothing selected  

> select add #58

159 pseudobonds, 1 model selected  

> select subtract #58

Nothing selected  
Please select pseudobonds  
Please select pseudobonds  

> close #57

> close #58

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2485, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 814, in close_request  
tool_instance.delete()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tools.py", line 172, in delete  
self.session.ui.remove_tool(self)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 417, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 946, in remove_tool  
tw._mw_set_shown(False)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2419, in _mw_set_shown  
self.__toolkit.shown = shown  
^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2701, in shown  
self.dock_widget.hide()  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2701, in shown  
self.dock_widget.hide()  
  
See log for complete Python traceback.  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2634_009_volume_map.mrc"

Opened cryosparc_P126_J2634_009_volume_map.mrc as #57, grid size 400,400,400,
pixel 1.24, shown at level 0.224, step 1, values float32  

> hide #!56 models

> show #!55 models

> select add #57

2 models selected  

> view matrix models #57,1,0,0,-156.14,0,1,0,-94.053,0,0,1,-176.88

> ui mousemode right "rotate selected models"

> view matrix models
> #57,0.090465,-0.97645,0.19586,276.57,0.8255,-0.03649,-0.56322,89.049,0.5571,0.21263,0.80276,-326.48

> fitmap #57 inMap #55

Fit map cryosparc_P126_J2634_009_volume_map.mrc in map
relion_locres_filtered.mrc using 638719 points  
correlation = 0.7166, correlation about mean = 0.147, overlap = 737.8  
steps = 348, shift = 27, angle = 35.8 degrees  
  
Position of cryosparc_P126_J2634_009_volume_map.mrc (#57) relative to
relion_locres_filtered.mrc (#55) coordinates:  
Matrix rotation and translation  
-0.68786957 0.69883465 -0.19612646 334.50874133  
-0.70973517 -0.59099802 0.38340230 476.10985714  
0.15202446 0.40292863 0.90251708 -152.70997519  
Axis 0.01345633 -0.23992389 -0.97069844  
Axis point 273.64081418 182.98952152 0.00000000  
Rotation angle (degrees) 133.48583733  
Shift along axis 38.50646224  
  

> ui mousemode right "translate selected models"

> view matrix models
> #57,0.12799,-0.91124,-0.3915,437.9,0.87448,0.2899,-0.38889,-67.466,0.46787,-0.29259,0.83396,-151.48

> ui mousemode right "rotate selected models"

> view matrix models
> #57,0.78611,-0.33971,-0.51636,154.35,0.1896,0.92768,-0.32167,-64.729,0.58829,0.15496,0.79366,-284.71

> ui mousemode right "translate selected models"

> view matrix models
> #57,0.78611,-0.33971,-0.51636,124.88,0.1896,0.92768,-0.32167,-73.701,0.58829,0.15496,0.79366,-307.91

> view matrix models
> #57,0.78611,-0.33971,-0.51636,103.93,0.1896,0.92768,-0.32167,-32.433,0.58829,0.15496,0.79366,-301.66

> fitmap #57 inMap #55

Fit map cryosparc_P126_J2634_009_volume_map.mrc in map
relion_locres_filtered.mrc using 638719 points  
correlation = 0.7836, correlation about mean = 0.2722, overlap = 1322  
steps = 380, shift = 24.8, angle = 17.8 degrees  
  
Position of cryosparc_P126_J2634_009_volume_map.mrc (#57) relative to
relion_locres_filtered.mrc (#55) coordinates:  
Matrix rotation and translation  
-0.99766912 -0.05748329 -0.03676950 585.35075599  
0.05752002 -0.99834434 0.00005894 467.64350457  
-0.03671201 -0.00205619 0.99932377 10.94386608  
Axis -0.01838871 -0.00049979 0.99983079  
Axis point 286.04560310 242.24895212 0.00000000  
Rotation angle (degrees) 176.70302123  
Shift along axis -0.05555743  
  

> view matrix models
> #57,0.6894,-0.25842,-0.67672,159.47,0.2715,0.95828,-0.089349,-149.47,0.67158,-0.12213,0.7308,-233.84

> view matrix models
> #57,0.6894,-0.25842,-0.67672,161.05,0.2715,0.95828,-0.089349,-140.44,0.67158,-0.12213,0.7308,-238.55

> fitmap #57 inMap #55

Fit map cryosparc_P126_J2634_009_volume_map.mrc in map
relion_locres_filtered.mrc using 638719 points  
correlation = 0.7835, correlation about mean = 0.2717, overlap = 1322  
steps = 140, shift = 13, angle = 0.00411 degrees  
  
Position of cryosparc_P126_J2634_009_volume_map.mrc (#57) relative to
relion_locres_filtered.mrc (#55) coordinates:  
Matrix rotation and translation  
-0.99766660 -0.05754684 -0.03673831 585.33595905  
0.05758304 -0.99834071 0.00007287 467.63374453  
-0.03668155 -0.00204281 0.99932491 10.92763767  
Axis -0.01837331 -0.00049296 0.99983107  
Axis point 286.03069540 242.25309971 0.00000000  
Rotation angle (degrees) 176.69938925  
Shift along axis -0.05929284  
  

> hide #!55 models

> select subtract #57

Nothing selected  

> combine #56

[Repeated 1 time(s)]

> hide #!59 models

> select add #58

17013 atoms, 16995 bonds, 4 pseudobonds, 4252 residues, 2 models selected  

> view matrix models
> #58,-0.64826,0.29744,-0.70092,284.17,-0.32252,-0.94115,-0.10109,534.51,-0.68974,0.16053,0.70604,-9.6503

> ui mousemode right "rotate selected models"

> view matrix models
> #58,0.46689,0.57973,-0.66778,-56.984,-0.85271,0.49521,-0.16627,317.21,0.2343,0.64705,0.72555,-353.37

> ui mousemode right "translate selected models"

> view matrix models
> #58,0.46689,0.57973,-0.66778,-43.532,-0.85271,0.49521,-0.16627,320.57,0.2343,0.64705,0.72555,-341.27

> fitmap #58 inMap #57

Fit molecule copy of COPI_GOLPH3_combined_model_v14.mmcif (#58) to map
cryosparc_P126_J2634_009_volume_map.mrc (#57) using 17013 atoms  
average map value = 0.2917, steps = 180  
shifted from previous position = 15.2  
rotated from previous position = 19.3 degrees  
atoms outside contour = 5889, contour level = 0.2244  
  
Position of copy of COPI_GOLPH3_combined_model_v14.mmcif (#58) relative to
cryosparc_P126_J2634_009_volume_map.mrc (#57) coordinates:  
Matrix rotation and translation  
0.54960376 0.83460906 0.03692430 -129.73175672  
-0.83271305 0.55084269 -0.05622527 394.90286975  
-0.06726560 0.00015427 0.99773508 18.05374051  
Axis 0.03372939 0.06233223 -0.99748535  
Axis point 302.21009536 318.61779184 0.00000000  
Rotation angle (degrees) 56.69534136  
Shift along axis 2.23106001  
  

> select subtract #58

Nothing selected  

> show #!59 models

> select add #59

17013 atoms, 16995 bonds, 4 pseudobonds, 4252 residues, 2 models selected  

> view matrix models
> #59,-0.64826,0.29744,-0.70092,288.09,-0.32252,-0.94115,-0.10109,385.62,-0.68974,0.16053,0.70604,-44.769

> ui mousemode right "rotate selected models"

> view matrix models
> #59,0.86324,-0.49258,0.11042,-75.153,0.5047,0.84648,-0.16955,-237.84,-0.0099558,0.20209,0.97932,-284.05

> view matrix models
> #59,0.16208,-0.8199,-0.54909,337.99,0.82865,0.41522,-0.37541,-154.44,0.53579,-0.39415,0.74671,-204.9

> ui mousemode right "translate selected models"

> view matrix models
> #59,0.16208,-0.8199,-0.54909,379.39,0.82865,0.41522,-0.37541,-126.9,0.53579,-0.39415,0.74671,-163.23

> fitmap #59 inMap #57

Fit molecule copy of COPI_GOLPH3_combined_model_v14.mmcif (#59) to map
cryosparc_P126_J2634_009_volume_map.mrc (#57) using 17013 atoms  
average map value = 0.2918, steps = 228  
shifted from previous position = 14.2  
rotated from previous position = 27.4 degrees  
atoms outside contour = 5940, contour level = 0.2244  
  
Position of copy of COPI_GOLPH3_combined_model_v14.mmcif (#59) relative to
cryosparc_P126_J2634_009_volume_map.mrc (#57) coordinates:  
Matrix rotation and translation  
0.44607693 -0.89445838 0.03097708 309.19604848  
0.89244857 0.44715029 0.05993484 -152.54155037  
-0.06746064 0.00090991 0.99772153 17.92949613  
Axis -0.03296397 0.05497504 0.99794345  
Axis point 278.25838488 173.33361718 0.00000000  
Rotation angle (degrees) 63.54630730  
Shift along axis -0.68568332  
  

> select subtract #59

Nothing selected  

> color #57 #b2b2b2aa models

> show #!56 models

> hide #!57 models

> hide #!59 models

> hide #!58 models

> hide #!56 models

> show #!49 models

> show #!58 models

> hide #!58 models

> show #!56 models

> hide #!56 models

> show #!56 models

> hide #!56 models

> combine #56

> ui tool show Matchmaker

> hide #!49 models

> show #!49 models

> matchmaker #!60 to #49/M pairing bs

Parameters  
---  
Chain pairing | bs  
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 Model_for_composite_J4021_J4026, chain M (#49) with copy of
COPI_GOLPH3_combined_model_v14.mmcif, chain O (#60), sequence alignment score
= 1473.2  
RMSD between 282 pruned atom pairs is 0.377 angstroms; (across all 283 pairs:
0.400)  
  

> hide #!49 models

> show #!49 models

> hide #!49 models

> split #60 chains

Split copy of COPI_GOLPH3_combined_model_v14.mmcif (#60) into 18 models  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif A #60.1  
---  
Chain | Description  
A | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif B #60.2  
---  
Chain | Description  
B | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif D #60.3  
---  
Chain | Description  
D | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif E #60.4  
---  
Chain | Description  
E | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif F #60.5  
---  
Chain | Description  
F | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif G #60.6  
---  
Chain | Description  
G | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif H #60.7  
---  
Chain | Description  
H | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif I #60.8  
---  
Chain | Description  
I | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif J #60.9  
---  
Chain | Description  
J | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif K #60.10  
---  
Chain | Description  
K | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif L #60.11  
---  
Chain | Description  
L | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif M #60.12  
---  
Chain | Description  
M | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif N #60.13  
---  
Chain | Description  
N | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif O #60.14  
---  
Chain | Description  
O | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif P #60.15  
---  
Chain | Description  
P | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif R #60.16  
---  
Chain | Description  
R | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif S #60.17  
---  
Chain | Description  
S | No description available  
  
Chain information for copy of COPI_GOLPH3_combined_model_v14.mmcif T #60.18  
---  
Chain | Description  
T | No description available  
  

> hide #60.1 models

> hide #60.2 models

> hide #60.3 models

> hide #60.4 models

> hide #60.5 models

> hide #60.6 models

> hide #60.7 models

> hide #!60.8 models

> hide #60.9 models

> hide #60.10 models

> hide #!60.11 models

> hide #60.12 models

> hide #60.13 models

> hide #60.14 models

> hide #60.15 models

> hide #60.16 models

> hide #60.17 models

> show #!49 models

> combine #49 #60.18

> rename #61 Soluble-COPI_modeled_gamma_Arf1

> hide #!61 models

> close #60

> hide #!49 models

> show #!61 models

> hide #!61 models

> combine #46

No structures specified  

> combine #56

> ui tool show Matchmaker

> matchmaker #!60 to #49/H pairing bs

Parameters  
---  
Chain pairing | bs  
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 Model_for_composite_J4021_J4026, chain H (#49) with copy of
COPI_GOLPH3_combined_model_v14.mmcif, chain G (#60), sequence alignment score
= 267.6  
RMSD between 52 pruned atom pairs is 0.219 angstroms; (across all 52 pairs:
0.219)  
  

> show #!49 models

> hide #!60 models

> show #!60 models

> hide #!60 models

> show #!60 models

> hide #!60 models

> ui tool show Matchmaker

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 786, in changeEvent  
self.hide_floating_tools = self.isMinimized()  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 885, in hide_floating_tools  
if not tw.floating:  
^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _get_floating  
return self.__toolkit.dock_widget.isFloating()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  

Window position QRect(386,-727 600x300) outside any known screen, using
primary screen  

RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _get_floating  
return self.__toolkit.dock_widget.isFloating()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 786, in changeEvent  
self.hide_floating_tools = self.isMinimized()  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 885, in hide_floating_tools  
if not tw.floating:  
^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _get_floating  
return self.__toolkit.dock_widget.isFloating()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _get_floating  
return self.__toolkit.dock_widget.isFloating()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 786, in changeEvent  
self.hide_floating_tools = self.isMinimized()  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 885, in hide_floating_tools  
if not tw.floating:  
^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _get_floating  
return self.__toolkit.dock_widget.isFloating()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _get_floating  
return self.__toolkit.dock_widget.isFloating()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16S000N6D/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7.7 (23H723)
      Kernel Version: Darwin 23.6.0
      Time since boot: 8 days, 2 hours, 13 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      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


Installed Packages:
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    biopython: 1.85
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.6.0
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-locscalesurfer: 0.1.1
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.3.9
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 2.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RIBFIND: 0.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    einops: 0.3.2
    et_xmlfile: 2.0.0
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    fsspec: 2025.5.1
    funcparserlib: 2.0.0a0
    geomdl: 5.3.1
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    mpmath: 1.3.0
    mrcfile: 1.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.24.4
    numpy: 1.26.4
    openpyxl: 3.1.5
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    pandas: 2.2.3
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pyarrow: 19.0.1
    pycollada: 0.8
    pydantic: 2.11.1
    pydantic_core: 2.33.0
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    QtRangeSlider: 0.1.5
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    ribfind: 2.0.2
    scipy: 1.10.1
    scipy: 1.14.0
    seaborn: 0.13.2
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    starfile: 0.5.12
    superqt: 0.6.3
    sympy: 1.14.0
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    timm: 0.4.12
    tinyarray: 1.2.4
    tomli: 2.0.1
    torch: 2.2.2
    torchvision: 0.17.2
    tornado: 6.4.2
    tqdm: 4.66.6
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing-inspection: 0.4.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (1)

comment:1 by Eric Pettersen, 6 weeks ago

Component: Unassigned → Third Party
Description: modified (diff)
Owner: set to Richard Scheltema
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → XMAS: color key deleted multiple times
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