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#19010 closed defect (duplicate)

ffmpeg: Permission denied

Reported by:	sean@…	Owned by:	Zach Pearson
Priority:	normal	Milestone:
Component:	Build System	Version:
Keywords:		Cc:	Eric Pettersen
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-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Spin Movie

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat
> Collaboration/Resubmit to Science Retreats /Accepted
> Submission/IoR/20250101_chimera_for_figures.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.0066, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.124, step 1, values float32  
Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown
at level 0.36, step 1, values float32  
Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown
at level 0.3, step 1, values float32  
Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55,
shown at level 0.0057, step 1, values float32  
Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel
1.71, shown at level 0.0053, step 1, values float32  
Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel
1.71, shown at level 0.0054, step 1, values float32  
Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel
1.71, shown at level 0.0065, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292,
pixel 1.71, shown at level 0.0065, step 1, values float32  
Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size
292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32  
Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192,
pixel 2.55, shown at level 0.299, step 1, values float32  
Opened relion_locres_filtered_job073_lp15.mrc as #11, grid size 292,292,292,
pixel 1.71, shown at level 0.0047, step 1, values float32  
Opened relion_locres_filtered_job073_lp18.mrc as #10, grid size 292,292,292,
pixel 1.71, shown at level 0.00422, step 1, values float32  
Opened postprocess_job020_lp20.mrc as #13, grid size 192,192,192, pixel 2.55,
shown at level 0.289, step 1, values float32  
Opened postprocess_job020_lp25.mrc as #14, grid size 192,192,192, pixel 2.55,
shown at level 0.278, step 1, values float32  
Log from Thu Jan 9 16:57:06 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241218_chimera_for_figures.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.0066, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.124, step 1, values float32  
Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown
at level 0.36, step 1, values float32  
Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown
at level 0.3, step 1, values float32  
Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55,
shown at level 0.0057, step 1, values float32  
Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel
1.71, shown at level 0.0053, step 1, values float32  
Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel
1.71, shown at level 0.0054, step 1, values float32  
Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel
1.71, shown at level 0.0065, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292,
pixel 1.71, shown at level 0.0065, step 1, values float32  
Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size
292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32  
Opened relion_locres_filtered_job076.mrc gaussian 3.00 as #10, grid size
292,292,292, pixel 1.71, shown at level 0.00477, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc gaussian 3.50 as #11, grid size
292,292,292, pixel 1.71, shown at level 0.00468, step 1, values float32  
Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192,
pixel 2.55, shown at level 0.299, step 1, values float32  
Opened copi_triad_bin15_filt.mrc gaussian 1.5 as #13, grid size 236,236,236,
pixel 2.55, shown at level 0.00478, step 1, values float32  
Opened relion_locres_filtered_job073_coloredbymodel.mrc as #14, grid size
292,292,292, pixel 1.71, shown at level 0.006, step 1, values float32  
Log from Wed Dec 18 14:00:13 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241212_chimera_for_figures.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00851, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.179, step 1, values float32  
Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown
at level 0.36, step 1, values float32  
Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown
at level 0.3, step 1, values float32  
Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55,
shown at level 0.0057, step 1, values float32  
Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel
1.71, shown at level 0.0053, step 1, values float32  
Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel
1.71, shown at level 0.0049, step 1, values float32  
Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel
1.71, shown at level 0.0065, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292,
pixel 1.71, shown at level 0.0065, step 1, values float32  
Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size
292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32  
Opened relion_locres_filtered_job076.mrc gaussian 3.00 as #10, grid size
292,292,292, pixel 1.71, shown at level 0.00477, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc gaussian 3.50 as #11, grid size
292,292,292, pixel 1.71, shown at level 0.00468, step 1, values float32  
Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192,
pixel 2.55, shown at level 0.299, step 1, values float32  
Opened copi_triad_bin15_filt.mrc gaussian 1.5 as #13, grid size 236,236,236,
pixel 2.55, shown at level 0.00478, step 1, values float32  
Opened relion_locres_filtered_job073_coloredbymodel.mrc as #14, grid size
292,292,292, pixel 1.71, shown at level 0.006, step 1, values float32  
Log from Thu Dec 12 11:04:26 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241210_chimera_for_figures_v5.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00851, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.179, step 1, values float32  
Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown
at level 0.36, step 1, values float32  
Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown
at level 0.3, step 1, values float32  
Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55,
shown at level 0.0057, step 1, values float32  
Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel
1.71, shown at level 0.0055, step 1, values float32  
Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel
1.71, shown at level 0.0049, step 1, values float32  
Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel
1.71, shown at level 0.0065, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292,
pixel 1.71, shown at level 0.0065, step 1, values float32  
Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size
292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32  
Opened relion_locres_filtered_job076.mrc gaussian 3.00 as #10, grid size
292,292,292, pixel 1.71, shown at level 0.00477, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc gaussian 3.50 as #11, grid size
292,292,292, pixel 1.71, shown at level 0.00468, step 1, values float32  
Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192,
pixel 2.55, shown at level 0.299, step 1, values float32  
Opened copi_triad_bin15_filt.mrc gaussian 1.5 as #13, grid size 236,236,236,
pixel 2.55, shown at level 0.00478, step 1, values float32  
Opened relion_locres_filtered_job073_coloredbymodel.mrc as #14, grid size
292,292,292, pixel 1.71, shown at level 0.006, step 1, values float32  
Log from Tue Dec 10 13:42:08 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241207_chimera_for_figures.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.006, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.179, step 1, values float32  
Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown
at level 0.36, step 1, values float32  
Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown
at level 0.3, step 1, values float32  
Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55,
shown at level 0.0057, step 1, values float32  
Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel
1.71, shown at level 0.0055, step 1, values float32  
Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel
1.71, shown at level 0.0049, step 1, values float32  
Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel
1.71, shown at level 0.0065, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292,
pixel 1.71, shown at level 0.0065, step 1, values float32  
Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size
292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32  
Opened relion_locres_filtered_job076.mrc gaussian 3.00 as #10, grid size
292,292,292, pixel 1.71, shown at level 0.00477, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc gaussian 3.50 as #11, grid size
292,292,292, pixel 1.71, shown at level 0.00468, step 1, values float32  
Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192,
pixel 2.55, shown at level 0.323, step 1, values float32  
Opened copi_triad_bin15_filt.mrc gaussian 1.5 as #13, grid size 236,236,236,
pixel 2.55, shown at level 0.00472, step 1, values float32  
Log from Sat Dec 7 12:37:17 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241125_chimera_for_figures.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.005, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32  
Log from Tue Nov 26 17:24:46 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/20241122_chimera_for_figures.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32  
Log from Fri Nov 22 15:12:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure1/20241114_v2.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32  
Log from Thu Nov 14 15:28:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241017_COPI_leaf_all_AF3_results_aligned.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Log from Thu Oct 17 14:08:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241009_COPI_leaf_AF3_for_figs_v8.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size
292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Log from Wed Oct 9 16:21:15 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7_with_files.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size
292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Log from Wed Sep 25 22:56:27 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size
292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Log from Fri Aug 9 13:21:55 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #58, grid size 292,292,292,
pixel 1.71, shown at level 0.005, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc copy as #61, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Log from Tue Aug 6 15:17:45 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240715_leaf_fitting_AF3_only_v4.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00585, step 1, values float32  
Log from Wed Jul 24 16:40:43 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3
> /fold_20240711_copi_golph3/20240711_leaf_fitting_alphafold_withGolph3AF3_v2.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00736, step 1, values float32  
Log from Sat Jul 13 09:14:12 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v5.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00736, step 1, values float32  
Log from Fri Jul 12 14:16:12 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v4.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00465, step 1, values float32  
Log from Wed Jul 10 18:08:13 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v2.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00465, step 1, values float32  
Log from Wed Jul 10 17:31:38 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00404, step 1, values float32  
Log from Wed Jul 10 16:36:09 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00404, step 1, values float32  
Log from Wed Jul 10 16:07:37 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240709_leaf_fitting_v39_labelled.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00473, step 1, values float32  
Log from Tue Jul 9 17:02:08 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240708_leaf_fitting_v36_labelled.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.12, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00463, step 1, values float32  
Log from Mon Jul 8 16:31:05 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240522_leaf_fitting_v32_labelled.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.12, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00733, step 1, values float32  
Log from Mon Jun 3 13:56:09 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera
> sessions/20240521_leaf_fitting_v31_mutations_interactions_labeled.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.12, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00733, step 1, values float32  
Log from Tue May 21 23:56:29 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v25.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32  
Log from Mon Apr 15 16:36:47 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v21.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32  
Log from Mon Apr 15 15:35:58 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240328_leaf_fitting_v17.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32  
Opened cryosparc_P126_J1413_005_volume_map.mrc as #35, grid size 480,480,480,
pixel 0.953, shown at level 0.136, step 1, values float32  
Opened cryosparc_P126_J1449_008_volume_map_sharp.mrc as #36, grid size
480,480,480, pixel 0.953, shown at level 0.227, step 1, values float32  
Log from Fri Mar 29 15:25:34 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240326_leaf_fitting_v13.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00747, step 1, values float32  
Log from Tue Mar 26 13:48:19 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v10.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Log from Thu Feb 15 12:14:52 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v2.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00338, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Log from Mon Feb 12 10:40:16 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240126_linkage_3_fitting_v1.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00369, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened postprocess_20231221.mrc as #24, grid size 156,156,156, pixel 2.55,
shown at level 0.00376, step 1, values float32  
Opened postprocess_20231221.mrc as #36, grid size 156,156,156, pixel 2.55,
shown at level 0.00396, step 1, values float32  
Opened emd_3720_2017_leaf.map as #37, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32  
Opened postprocess_20231221.mrc as #48, grid size 156,156,156, pixel 2.55,
shown at level 0.00387, step 1, values float32  
Opened emd_3720_2017_leaf.map as #49, grid size 128,128,128, pixel 1.78, shown
at level 0.226, step 1, values float32  
Log from Fri Jan 26 14:05:24 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240125_linkage_3_fitting.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00369, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened postprocess_20231221.mrc as #24, grid size 156,156,156, pixel 2.55,
shown at level 0.0033, step 1, values float32  
Opened postprocess_20231221.mrc as #36, grid size 156,156,156, pixel 2.55,
shown at level 0.00303, step 1, values float32  
Opened emd_3720_2017_leaf.map as #37, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32  
Log from Thu Jan 25 18:04:25 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240125_linkage_1_fitting.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00369, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.606, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 3.38, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened postprocess_20231221.mrc as #24, grid size 156,156,156, pixel 2.55,
shown at level 0.0033, step 1, values float32  
Opened postprocess_20231221.mrc as #36, grid size 156,156,156, pixel 2.55,
shown at level 0.00453, step 1, values float32  
Opened emd_3720_2017_leaf.map as #37, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32  
Log from Thu Jan 25 16:06:42 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240124_Golph3_fitting.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #15, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #16, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #17, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #18, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #19, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #20, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.606, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #22, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #23, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #24, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32  
Opened emd_3720_2017_leaf.map as #26, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32  
Opened postprocess_20231221.mrc as #27, grid size 156,156,156, pixel 2.55,
shown at level 0.00356, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00402, step 1, values float32  
Log from Wed Jan 24 14:57:19 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/All_Linkages_fitting_Golph_AF_RT.cxs"

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.01, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #15, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #16, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #17, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #18, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #19, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #20, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.606, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #22, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #23, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #24, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32  
Opened emd_3720_2017_leaf.map as #26, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32  
Log from Tue Dec 5 16:56:09 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/Linkage_1_fitting_Golph_AF_RT.cxs" format
> session

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00761, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.193, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #15, grid size 128,128,128,
pixel 3.4, shown at level 0.372, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #16, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #17, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Log from Tue Dec 5 14:45:54 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI-GOLPH
> dataset/Chimera_COPI_golph/alphafold_copi_colored_RT_4.cxs"

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00761, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.109, step 1, values float32  
Log from Tue Nov 7 12:35:14 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open alphafold_copi_colored_RT_2.cxs

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00761, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.109, step 1, values float32  
Log from Tue Nov 7 08:56:24 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/alphafold_copi_colored_RT.cxs
> format session

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00761, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.109, step 1, values float32  
Log from Mon Nov 6 14:26:30 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open alphafold_copi_gt_colored.cxs

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00914, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.155, step 1, values float32  
Log from Sun Nov 5 21:56:53 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open alphafold_copi_gt.cxs

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.012, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.155, step 1, values float32  
Log from Sun Nov 5 03:35:04 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/warpV1_erase/relion/PostProcess/job062/postprocess.mrc

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00604, step 1, values float32  

> open 5nzr

Summary of feedback from opening 5nzr fetched from pdb  
---  
note | Fetching compressed mmCIF 5nzr from http://files.rcsb.org/download/5nzr.cif  
  
5nzr title:  
The structure of the COPI coat leaf [more info...]  
  
Chain information for 5nzr #2  
---  
Chain | Description | UniProt  
A | Coatomer subunit alpha | COPA_MOUSE 1-1224  
B | Coatomer subunit beta | COPB_MOUSE 16-968  
C | Coatomer subunit beta' | COPB2_MOUSE 1-905  
D | Coatomer subunit delta | COPD_MOUSE 1-511  
F M R | ADP-ribosylation factor 1 | ARF1_YEAST 1-181  
G K | Coatomer subunit gamma-1 | COPG1_MOUSE 1-874  
L Z | Coatomer subunit zeta-1 | COPZ1_MOUSE 1-177  
  

> select add #2

18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select add #2

18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected  

> volume #1 level 0.0087

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models #2,1,0,0,-37.882,0,1,0,64.414,0,0,1,202.79

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.52562,-0.43202,0.73286,-19.37,-0.17024,0.79062,0.58817,39.912,-0.83351,-0.43392,0.34202,421.68

> view matrix models
> #2,0.7,0.68406,-0.20508,-62.275,0.0068065,0.28077,0.95975,37.92,0.71411,-0.67322,0.19188,297.56

> view matrix models
> #2,0.28224,0.88452,-0.37142,-20.952,-0.65525,0.46053,0.5988,130.99,0.7007,0.074371,0.70957,150.66

> view matrix models
> #2,0.49213,0.75481,-0.43366,-21.427,-0.82839,0.25296,-0.49979,301.54,-0.26755,0.6052,0.74977,189.39

> view matrix models
> #2,0.36057,0.92393,-0.12783,-62.367,-0.57964,0.11459,-0.80677,326.12,-0.73076,0.365,0.57687,288.65

> view matrix models
> #2,-0.61475,0.27359,-0.73975,192.39,-0.35757,-0.93266,-0.047782,338.05,-0.70301,0.23514,0.67118,290.08

> view matrix models
> #2,-0.91301,0.40193,0.069771,116.36,-0.4071,-0.9087,-0.092394,345.81,0.026265,-0.11276,0.99328,214.04

> view matrix models
> #2,-0.88167,0.40879,0.2357,92.928,-0.40453,-0.91196,0.068457,327.32,0.24293,-0.034992,0.96941,183.81

> view matrix models
> #2,-0.5303,0.84267,0.093238,19.456,-0.82612,-0.53832,0.16656,317.99,0.19054,0.011299,0.98161,182.67

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.5303,0.84267,0.093238,263.37,-0.82612,-0.53832,0.16656,455.06,0.19054,0.011299,0.98161,199.63

> fitmap #1 #2

Missing required "in_map" argument  

> fitmap #2 inMap #1

Fit molecule 5nzr (#2) to map postprocess.mrc (#1) using 18970 atoms  
average map value = 0.01091, steps = 116  
shifted from previous position = 7.15  
rotated from previous position = 12 degrees  
atoms outside contour = 7834, contour level = 0.0087005  
  
Position of 5nzr (#2) relative to postprocess.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.53470562 0.84443643 -0.03189051 278.17154273  
-0.84484986 -0.53500265 -0.00093313 482.55400590  
-0.01784948 0.02644375 0.99949093 224.67222139  
Axis 0.01620349 -0.00831044 -0.99983418  
Axis point 273.19248819 162.79104531 0.00000000  
Rotation angle (degrees) 122.35128157  
Shift along axis -224.13785000  
  

> select subtract #2

Nothing selected  

> close #2

> open 3720

Fetching url http://files.rcsb.org/download/3720.cif failed:  
HTTP Error 404: Not Found  

> open emdb3720

'emdb3720' has no suffix  

> open 3720 fromDatabase emdb

Summary of feedback from opening 3720 fetched from emdb  
---  
note | Fetching compressed map 3720 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-3720/map/emd_3720.map.gz  
  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.226, step 1, values float32  

> volume #2 level 0.09618

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,223.78,0,1,0,-35.337,0,0,1,158.95

> view matrix models #2,1,0,0,225.18,0,1,0,9.8187,0,0,1,170.58

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.76316,0.27646,-0.58409,288.27,-0.32541,0.94531,0.022268,51.04,0.5583,0.17307,0.81138,108.15

> view matrix models
> #2,0.95657,0.056083,-0.28607,257.23,-0.28053,-0.089841,-0.95563,285,-0.079296,0.99438,-0.070206,187.24

> view matrix models
> #2,-0.25273,0.83078,0.49592,211.05,-0.38627,0.3833,-0.83897,226.83,-0.88708,-0.4036,0.22403,412.13

> view matrix models
> #2,-0.051655,0.96539,0.25564,200.28,-0.9833,-0.093889,0.15587,234.85,0.17448,-0.24332,0.95412,185.06

> view matrix models
> #2,0.02585,0.7816,-0.62325,317.1,-0.70553,-0.42742,-0.56528,327.98,-0.70821,0.45433,0.54039,251.79

> view matrix models
> #2,-0.58335,0.28587,0.76025,282.85,-0.81203,-0.1846,-0.55366,309.81,-0.017932,-0.94032,0.33982,362.91

> view matrix models
> #2,-0.98042,-0.17156,0.096691,461.36,-0.048228,-0.26686,-0.96253,280.32,0.19094,-0.94834,0.25336,350.12

> view matrix models
> #2,-0.92285,0.28368,-0.26051,442.55,-0.18618,-0.92069,-0.34304,301.1,-0.33716,-0.26807,0.90248,252.78

> view matrix models
> #2,-0.93117,0.30503,-0.1997,433.78,-0.29572,-0.95227,-0.07566,285.87,-0.21324,-0.011399,0.97693,199.12

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.93117,0.30503,-0.1997,397.2,-0.29572,-0.95227,-0.07566,498.67,-0.21324,-0.011399,0.97693,255.17

> fitmap #2 inMap #1

Fit map emdb 3720 in map postprocess.mrc using 114393 points  
correlation = 0.6691, correlation about mean = 0.05303, overlap = 91.28  
steps = 100, shift = 27.4, angle = 14.2 degrees  
  
Position of emdb 3720 (#2) relative to postprocess.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.90384624 0.23353058 -0.35850446 426.60125938  
-0.28809092 -0.95167357 0.10640039 474.89273455  
-0.31633147 0.19945147 0.92744462 222.06398803  
Axis 0.17506212 -0.07934236 -0.98135521  
Axis point 264.85851560 196.87446978 0.00000000  
Rotation angle (degrees) 164.58753247  
Shift along axis -180.92104267  
  

> volume #2 level 0.136

> select clear

> ui mousemode right "translate selected models"

> select #2

2 models selected  

> view matrix models
> #2,-0.90385,0.23353,-0.3585,425.99,-0.28809,-0.95167,0.1064,430.09,-0.31633,0.19945,0.92744,249.04

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.93137,0.093427,-0.35189,445.01,-0.15388,-0.97696,0.14789,412.92,-0.32997,0.19189,0.92428,251.87

> view matrix models
> #2,-0.3246,0.87931,-0.3485,282.32,-0.83775,-0.43832,-0.32566,483.27,-0.43911,0.18625,0.87892,270.36

> view matrix models
> #2,-0.71374,0.63847,-0.28798,347.66,-0.6764,-0.73504,0.046791,455.31,-0.18181,0.22819,0.95649,226.9

> view matrix models
> #2,-0.30923,0.92464,-0.22232,259.88,-0.94209,-0.32976,-0.06112,450.03,-0.12982,0.19054,0.97306,223.52

> view matrix models
> #2,-0.79733,0.57614,-0.1798,351.42,-0.59927,-0.79112,0.1225,444.11,-0.071665,0.20542,0.97605,214.81

> view matrix models
> #2,-0.58975,0.77816,-0.21604,308.27,-0.80056,-0.59852,0.029561,455.12,-0.1063,0.19039,0.97594,220.53

> view matrix models
> #2,-0.86768,0.45921,-0.1904,374.6,-0.48592,-0.8643,0.12984,439.16,-0.10494,0.20518,0.97308,218.96

> view matrix models
> #2,-0.74473,0.62297,-0.23933,347.11,-0.64295,-0.76587,0.0071296,460.02,-0.17885,0.15918,0.97091,233.05

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.74473,0.62297,-0.23933,342.91,-0.64295,-0.76587,0.0071296,479.3,-0.17885,0.15918,0.97091,239.3

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.79959,0.57272,-0.1807,347.99,-0.59537,-0.79538,0.11357,464.54,-0.078687,0.19839,0.97696,222.58

> view matrix models
> #2,-0.67006,0.71251,-0.20821,320.02,-0.73726,-0.67144,0.074925,470.46,-0.086418,0.20371,0.97521,223.03

> view matrix models
> #2,-0.91364,0.36722,-0.17437,384.62,-0.37083,-0.92862,-0.012671,470.39,-0.16657,0.053082,0.9846,248.92

> view matrix models
> #2,-0.75132,0.63901,-0.16488,332.72,-0.64038,-0.76631,-0.051852,486.21,-0.15948,0.066629,0.98495,246.46

> view matrix models
> #2,-0.77803,0.62815,-0.010172,318.27,-0.62601,-0.77654,-0.071466,488.18,-0.052791,-0.049235,0.99739,246.73

> view matrix models
> #2,-0.65763,0.75315,0.017269,286.44,-0.75149,-0.65422,-0.085182,489.42,-0.052856,-0.068995,0.99622,249.24

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.65763,0.75315,0.017269,300.45,-0.75149,-0.65422,-0.085182,488.98,-0.052856,-0.068995,0.99622,232.81

> view matrix models
> #2,-0.65763,0.75315,0.017269,297.73,-0.75149,-0.65422,-0.085182,497.05,-0.052856,-0.068995,0.99622,233.9

> fitmap #2 inMap #1

Fit map emdb 3720 in map postprocess.mrc using 73589 points  
correlation = 0.8646, correlation about mean = 0.3064, overlap = 147.1  
steps = 96, shift = 6.01, angle = 10.4 degrees  
  
Position of emdb 3720 (#2) relative to postprocess.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.53666347 0.84316340 -0.03267727 278.66671757  
-0.84365691 -0.53687633 0.00261266 482.08926923  
-0.01534075 0.02897052 0.99946254 223.65484556  
Axis 0.01562303 -0.01027584 -0.99982515  
Axis point 272.76166410 162.45158774 0.00000000  
Rotation angle (degrees) 122.48227196  
Shift along axis -224.21599001  
  

> select clear

> volume #2 level 0.1256

> volume #1 level 0.007442

> volume #2 level 0.07023

> volume #2 level 0.1775

> volume #1 level 0.005345

> volume #1 level 0.009819

> ui tool show AlphaFold

> alphafold match
> MLTKFETKSARVKGLSFHPKRPWILTSLHNGVIQLWDYRMCTLIDKFDEHDGPVRGIDFHKQQPLFVSGGDDYKIKVWNYKLRRCLFTLLGHLDYIRTTFFHHEYPWILSASDDQTIRVWNWQSRTCVCVLTGHNHYVMCAQFHPSEDLVVSASLDQTVRVWDISGLRKKNLSPGAVESDVRGITGVDLFGTTDAVVKHVLEGHDRGVNWAAFHPTMPLIVSGADDRQVKIWRMNESKAWEVDTCRGHYNNVSCAVFHPRQELILSNSEDKSIRVWDMSKRTGVQTFRRDHDRFWVLAAHPNLNLFAAGHDGGMIVFKLERERPAYAVHGNMLHYVKDRFLRQLDFNSSKDVAVMQLRSGSKFPVFNMSYNPAENAVLLCTRASNLENSTYDLYTIPKDADSQNPDAPEGKRSSGLTAVWVARNRFAVLDRMHSLLIKNLKNEITKKIQVPNCDEIFYAGTGNLLLRDADSITLFDVQQKRTLASVKISKVKYVIWSADMSHVALLAKHEHSCPLPLTAIVICNRKLDALCNIHENIRVKSGAWDESGVFIYTTSNHIKYAVTTGDHGIIRTLDLPIYVTRVKGNNVYCLDRECRPRVLTIDPTEFKFKLALINRKYDEVLHMVRNAKLVGQSIIAYLQKKGYPEVALHFVKDEKTRFSLALECGNIEIALEAAKALDDKNCWEKLGEVALLQGNHQIVEMCYQRTKNFDKLSFLYLITGNLEKLRKMMKIAEIRKDMSGHYQNALYLGDVSERVRILKNCGQKSLAYLSAATHGLDEEAESLKETFDPEKETIPDIDPNAKLLQPPAPIMPLDTNWPLLTVSKGFFEGSIASKGKGGALAADIDIDTVGTEGWGEDAELQLDEDGFVEAPEGLGEDVLGKGQEEGGGWDVEEDLELPPELDVPSGVSGSAEDGFFVPPTKGTSPTQIWCNNSQLPVDHILAGSFETAMRLLHDQVGVIQFGPYKQLFLQTYARGRTTYQALPCLPSMYSYPNRNWKDAGLKNGVPAVGLKLNDLIQRLQLCYQLTTVGKFEEAVEKFRSILLSVPLLVVDNKQEIAEAQQLITICREYIVGLCMEIERKKLPKETLDQQKRICEMAAYFTHSNLQPVHMILVLRTALNLFFKLKNFKTAATFARRLLELGPKPEVAQQTRKILSACEKNPTDACQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEFKGQICRVTTVTEIGKDVIGLRISPLQFR

AlphaFold sequence search web service failed (404) "Not Found"  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py  

No AlphaFold model with similar sequence for 1 sequences  

Opened 0 AlphaFold model  
Fetching compressed F8WHL2 UniProt info from
https://www.uniprot.org/uniprot/F8WHL2.xml  

> alphafold match F8WHL2

Fetching compressed AlphaFold F8WHL2 from
https://alphafold.ebi.ac.uk/files/AF-F8WHL2-F1-model_v4.cif  
1 AlphaFold model found using UniProt identifier: F8WHL2 (UniProt F8WHL2)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
F8WHL2 | F8WHL2 | 100.0 | 100.0    
Opened 1 AlphaFold model  
> select add #39810 atoms, 10032 bonds, 1233 residues, 1 model selected  
> ui mousemode right "translate selected models"> view matrix models
> #3,1,0,0,303.28,0,1,0,304.96,0,0,1,11.166> view matrix models
> #3,1,0,0,324.74,0,1,0,283.74,0,0,1,319.33> view matrix models
> #3,1,0,0,209.64,0,1,0,387.4,0,0,1,429.36> ui mousemode right "translate
> selected models"[Repeated 1 time(s)]> view matrix models
> #3,1,0,0,222.42,0,1,0,405.56,0,0,1,420.95> ui mousemode right "rotate
> selected models"> view matrix models
> #3,0.32639,-0.23212,-0.91629,218.55,-0.93865,-0.1938,-0.28526,399.27,-0.11137,0.95319,-0.28113,421.32>
> view matrix models
> #3,-0.60439,0.30546,-0.7358,196.12,-0.51637,-0.85352,0.069815,409.29,-0.60669,0.42214,0.67359,409.09>
> view matrix models
> #3,-0.96723,0.14467,-0.20868,186.74,-0.15733,-0.9865,0.045344,417.05,-0.1993,0.076689,0.97693,416.89>
> view matrix models
> #3,-0.9522,0.23336,-0.19714,186.28,-0.23562,-0.97177,-0.01224,415.93,-0.19443,0.034795,0.9803,417.26>
> view matrix models
> #3,-0.97348,-0.079573,-0.21447,188.33,0.038436,-0.98112,0.18956,419.54,-0.2255,0.17629,0.95816,415.81>
> view matrix models
> #3,-0.22693,-0.37305,-0.89963,209.3,0.58137,0.68921,-0.43244,421.75,0.78135,-0.62115,0.060477,446.87>
> view matrix models
> #3,0.21155,-0.58135,-0.78567,218.06,0.9196,-0.15386,0.36146,428.33,-0.33102,-0.79897,0.50207,424.47>
> view matrix models
> #3,-0.12158,-0.084379,-0.98899,209.76,-0.25211,-0.96108,0.11299,414.62,-0.96003,0.26307,0.095579,408.05>
> view matrix models
> #3,0.84817,0.13727,0.51163,214.82,-0.089352,-0.91493,0.3936,415.19,0.52213,-0.37955,-0.76375,446.42>
> view matrix models
> #3,0.32531,0.49583,-0.80518,212.31,0.69626,0.45057,0.55876,418.28,0.63984,-0.74239,-0.19865,447.08>
> view matrix models
> #3,0.4134,0.56919,-0.71072,212.69,0.6828,0.32261,0.65552,418.27,0.6024,-0.75627,-0.25528,446.92>
> view matrix models
> #3,-0.13517,-0.24305,-0.96055,210.47,0.45069,0.84827,-0.27806,417.02,0.88239,-0.4705,-0.0051158,448.09>
> view matrix models
> #3,-0.8766,0.28966,-0.38428,188.63,0.43236,0.82468,-0.36465,417.5,0.21128,-0.4858,-0.84815,442.12>
> view matrix models
> #3,-0.75554,0.47772,0.44827,183.3,-0.087054,0.60499,-0.79146,412.75,-0.6493,-0.637,-0.4155,424.22>
> view matrix models
> #3,-0.17993,0.68527,0.70571,190.43,-0.77714,0.3408,-0.52907,400.08,-0.60306,-0.64363,0.47123,418.55>
> view matrix models
> #3,0.38482,0.64397,0.66123,201.45,-0.54337,0.73715,-0.40169,400.49,-0.7461,-0.20471,0.63358,411.47>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.38482,0.64397,0.66123,209.11,-0.54337,0.73715,-0.40169,352.77,-0.7461,-0.20471,0.63358,346.78>
> view matrix models
> #3,0.38482,0.64397,0.66123,272.84,-0.54337,0.73715,-0.40169,341.51,-0.7461,-0.20471,0.63358,359.04>
> view matrix models
> #3,0.38482,0.64397,0.66123,275.5,-0.54337,0.73715,-0.40169,343.71,-0.7461,-0.20471,0.63358,340.28>
> volume #1 level 0.009245> volume #1 transparency .5> view matrix models
> #3,0.38482,0.64397,0.66123,277.74,-0.54337,0.73715,-0.40169,343.45,-0.7461,-0.20471,0.63358,342.76>
> view matrix models
> #3,0.38482,0.64397,0.66123,274.73,-0.54337,0.73715,-0.40169,335.94,-0.7461,-0.20471,0.63358,326.51>
> view matrix models
> #3,0.38482,0.64397,0.66123,273,-0.54337,0.73715,-0.40169,338.08,-0.7461,-0.20471,0.63358,327.8>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.2206,0.77424,0.5932,269.52,-0.66437,0.56456,-0.48978,337.79,-0.7141,-0.28606,0.63893,328.95>
> view matrix models
> #3,0.46242,0.64706,0.60621,274.81,-0.30974,0.75851,-0.57335,343.48,-0.8308,0.077362,0.55116,324.76>
> view matrix models
> #3,0.1596,0.83662,0.52402,268.45,-0.68532,0.47596,-0.55117,338.51,-0.71054,-0.27116,0.64932,328.83>
> view matrix models
> #3,0.48141,0.60575,0.63349,275.26,-0.24765,0.78731,-0.56464,344.35,-0.84078,0.11494,0.52903,324.46>
> view matrix models
> #3,0.22271,0.44453,0.86764,269.97,-0.69434,0.69705,-0.1789,333.95,-0.68431,-0.56259,0.4639,332.84>
> view matrix models
> #3,0.25107,0.90985,0.33037,271.02,-0.74263,0.39997,-0.53714,337.92,-0.62085,-0.11048,0.7761,328.35>
> view matrix models
> #3,0.60545,0.57661,0.54859,278.39,-0.6801,0.73285,-0.01969,332.77,-0.41339,-0.36117,0.83586,333.57>
> view matrix models
> #3,0.5141,0.75687,0.40355,276.45,-0.8383,0.54295,0.049627,330.76,-0.18154,-0.3638,0.91361,337.28>
> view matrix models
> #3,0.68948,0.49522,0.52856,280.68,-0.57485,0.81809,-0.016621,334.05,-0.44064,-0.29238,0.84873,332.47>
> view matrix models
> #3,0.76356,0.52587,0.37475,282.96,-0.51319,0.84643,-0.14212,335.9,-0.39194,-0.083795,0.91617,331.32>
> view matrix models
> #3,0.20308,0.96515,0.16504,270.96,-0.89543,0.25126,-0.36754,334.96,-0.3962,-0.073139,0.91525,331.17>
> select clear> volume #1 level 0.007668> volume #1 level 0.008528> select add
> #39810 atoms, 10032 bonds, 1233 residues, 1 model selected  
> select subtract #3Nothing selected  
> select add #39810 atoms, 10032 bonds, 1233 residues, 1 model selected  
> view matrix models
> #3,0.24506,0.95994,0.13585,271.98,-0.89492,0.27787,-0.34914,334.63,-0.3729,-0.036017,0.92717,331.23>
[deleted to fit within ticket limits]


> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_alum_bottom_job073_soft_silwid1_5_T65_view4_memremoved.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #a9a9a940 models

> color #5 #a9a9a959 models

> color #5 #a9a9a940 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_alum_bottom_job073_soft_silwid1_5_T75_view4_memremoved.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #929292ff models

> color #5 #92929259 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_nickel_bottom_job073_soft_silwid1_5_T65_view4_memremoved.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #92929240 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_nickel_bottom_job073_soft_silwid1_5_T75_view4_memremoved.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #919191ff models

> color #5 #91919159 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_tin_bottom_job073_soft_silwid1_5_T65_view4_memremoved.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #91919140 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_tin_bottom_job073_soft_silwid1_5_T75_view4_memremoved.png"
> width 782 height 613 supersample 3 transparentBackground true

> hide #!5 models

> set silhouetteWidth 5

> show #!11 models

> hide #!30 models

> color #11 #a9a9a900 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/leaf_outlines/leaf_outline_bottom_job073_lp15_silwid5_T100_view4_memremoved.png"
> width 782 height 613 supersample 3 transparentBackground true

> set silhouetteWidth 1.5

> hide #!11 models

> show #!5 models

> show #!30 models

> view view3

> color #5 darkgrey models

> color #5 #a9a9a959 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_alum_top_job073_soft_silwid1_5_T65_view3.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #a9a9a940 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_alum_top_job073_soft_silwid1_5_T75_view3.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #929292ff models

> color #5 #92929259 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_nickel_top_job073_soft_silwid1_5_T65_view3.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #92929240 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_nickel_top_job073_soft_silwid1_5_T75_view3.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #919191ff models

> color #5 #91919159 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_tin_top_job073_soft_silwid1_5_T65_view3.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #91919140 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_tin_top_job073_soft_silwid1_5_T75_view3.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view4

> color #5 darkgrey models

> color #5 #a9a9a959 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_alum_bottom_job073_soft_silwid1_5_T65_view4.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #a9a9a940 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_alum_bottom_job073_soft_silwid1_5_T75_view4.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #929292ff models

> color #5 #92929259 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_nickel_bottom_job073_soft_silwid1_5_T65_view4.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #92929240 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_nickel_bottom_job073_soft_silwid1_5_T75_view4.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #919191ff models

> color #5 #91919159 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_tin_bottom_job073_soft_silwid1_5_T65_view4.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #91919140 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_tin_bottom_job073_soft_silwid1_5_T75_view4.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view18

> color #5 darkgrey models

> color #5 #a9a9a959 models

> color #5 darkgrey models

> color #5 #a9a9a959 models

> color #5 darkgrey models

> color #5 #a9a9a959 models

> color #5 #a9a9a940 models

> color #5 #a9a9a959 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_alum_top_job073_soft_silwid1_5_T65_view18.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #a9a9a940 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_alum_top_job073_soft_silwid1_5_T75_view18.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #929292ff models

> color #5 #92929259 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_nickel_top_job073_soft_silwid1_5_T65_view18.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #92929240 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_nickel_top_job073_soft_silwid1_5_T75_view18.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #919191ff models

> color #5 #91919159 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_tin_top_job073_soft_silwid1_5_T65_view18.png"
> width 782 height 613 supersample 3 transparentBackground true

> color #5 #91919140 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/soft_lighting/leaf_model_density/leaf_modelfit_tin_top_job073_soft_silwid1_5_T75_view18.png"
> width 782 height 613 supersample 3 transparentBackground true

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20250109_chimera_for_figures.cxs" includeMaps true

> color #5 #929292ff models

> color #5 #92929259 models

> view view5

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure2/Golph_coatomer_interactions_overview_nickel_soft_T65_view5.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view8

> show #20 models

> select #30/Q

1971 atoms, 2002 bonds, 244 residues, 1 model selected  

> cartoon hide sel

> view view9

> view view10

> view view11

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure2/GOLPH_PI4P_nickel_soft_T65_view11.png" width
> 782 height 613 supersample 3 transparentBackground true

> hide #20 models

> show #21 models

> show #23 models

> show #15 models

> show #16 models

> view view12

> view view13

> view view14

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure2/GOLPH_alpha_nickel_soft_T65_view14.png" width
> 782 height 613 supersample 3 transparentBackground true

> view view23

> view view17

> view view114

Expected an objects specifier or a view name or a keyword  

> view view14

> view view15

> view view16

> view view17

> view view18

> view view19

> view view20

> view view21

> view view22

> view view23

> view view24

> view view25

> view view26

> view view27

> view view28

> view view23

> hide #16 models

> hide #15 models

> hide #23 models

> hide #21 models

> show #25 models

> show #28 models

> show #29 models

> show #18 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure2/GOLPH_zeta_nickel_soft_T65_view23.png" width
> 782 height 613 supersample 3 transparentBackground true

> view name view23

> view name view15

> view view15

> view view16

> show #!54 models

> select #30/A

138 atoms, 135 bonds, 2 pseudobonds, 18 residues, 2 models selected  

> cartoon hide (#!30 & sel)

> view name view15

> view view15

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure2/GOLPH_beta_nickel_soft_T65_view15.png" width
> 782 height 613 supersample 3 transparentBackground true

> view view16

> view view17

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure3/GOLPH3-alpha_interaction_overview_nickel_T65_view17.png"
> width 782 height 613 supersample 3 transparentBackground true

> hide #29 models

> select add #30

33939 atoms, 34555 bonds, 6 pseudobonds, 4256 residues, 2 models selected  

> select subtract #30

Nothing selected  

> hide #28 models

> hide #18 models

> hide #25 models

> show #27 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure3/GOLPH3-alpha_interaction_overview_nickel_T65_view17.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view18

> view view19

> view view 22

Expected an objects specifier or a view name or a keyword  

> view view22

> view view23

> view view24

> view view25

> view view26

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure3/GOLPH3-alpha_interaction_E183-K179_nickel_T65_view26.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view28

> view view29

> view view23

> view view30

> view view3

> hide #27 models

> show #!32 models

> select add #32

1971 atoms, 2002 bonds, 244 residues, 1 model selected  

> coulombic sel

Coulombic values for copy of 20240711_copi_golph3_golph3_.cif_A SES surface
#32.1: minimum, -23.57, mean -1.11, maximum 10.20  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select subtract #32

1 model selected  

> hide #!5 models

> show #!11 models

> show #!33 models

> hide #!33 models

> show #!61 models

> hide #!61 models

> hide #!30 models

> hide #!54 models

> show #!61 models

> hide #!61 models

> color #61 #d6d6d6ff

> show #!61 models

> hide #!11 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure4/electro_golph_w_ribbon.png" width 782 height
> 613 supersample 3 transparentBackground true

> hide #!61 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure4/electro_golph_wout_ribbon.png" width 782
> height 613 supersample 3 transparentBackground true

> show #!61 models

> hide #!61 models

> show #!61 models

> view view4

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure4/electro_golph_w_ribbon_bottom.png" width 782
> height 613 supersample 3 transparentBackground true

> hide #!61 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure4/electro_golph_wout_ribbon_bottom.png" width
> 782 height 613 supersample 3 transparentBackground true

> hide #!32 models

> show #!30 models

> select ~sel & ##selected

Nothing selected  

> view view26

> view view16

> view view18

> view view14

> show #27 models

> show #!5 models

> view view26

> view view17

> hide #27 models

> select #30/Q

1971 atoms, 2002 bonds, 244 residues, 1 model selected  

> cartoon sel

> select add #30

33939 atoms, 34555 bonds, 6 pseudobonds, 4256 residues, 2 models selected  

> select subtract #30

Nothing selected  

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20250109_chimera_for_figures_v2.cxs" includeMaps true

> view view1

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20250109_chimera_for_figures_v3.cxs"

> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/7s22_yeast_alphaCOPI_WD40.cif"

7s22_yeast_alphaCOPI_WD40.cif title:  
Crystal structure of alpha-COP-WD40 domain [more info...]  
  
Chain information for 7s22_yeast_alphaCOPI_WD40.cif #36  
---  
Chain | Description | UniProt  
A B C | Coatomer subunit alpha | COPA_SCHPO 1-327  
  
Non-standard residues in 7s22_yeast_alphaCOPI_WD40.cif #36  
---  
ACE — acetyl group  
  
7s22_yeast_alphaCOPI_WD40.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select add #36

8243 atoms, 7672 bonds, 3 pseudobonds, 1724 residues, 2 models selected  

> view matrix models #36,1,0,0,-147.42,0,1,0,223.48,0,0,1,306.58

> view matrix models #36,1,0,0,330.99,0,1,0,400.1,0,0,1,242.77

> view matrix models #36,1,0,0,330.73,0,1,0,400.07,0,0,1,242.79

> view matrix models #36,1,0,0,281.12,0,1,0,421.92,0,0,1,241.73

> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/4j86_yeast_betaprimeCOPI_yWbp1.cif"

4j86_yeast_betaprimeCOPI_yWbp1.cif title:  
Crystal structure of beta'-COP/yWbp1 complex [more info...]  
  
Chain information for 4j86_yeast_betaprimeCOPI_yWbp1.cif #37  
---  
Chain | Description | UniProt  
A B | Coatomer subunit beta' | COPB2_YEAST 1-301  
C D | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 | OSTB_YEAST 1-6  
  
4j86_yeast_betaprimeCOPI_yWbp1.cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> view matrix models #36,1,0,0,281.96,0,1,0,432,0,0,1,239.76

> select add #37

13861 atoms, 12723 bonds, 3 pseudobonds, 3042 residues, 3 models selected  

> select subtract #36

5618 atoms, 5051 bonds, 1318 residues, 1 model selected  

> view matrix models #37,1,0,0,155.93,0,1,0,343.73,0,0,1,-75.49

> view matrix models #37,1,0,0,180.79,0,1,0,433.89,0,0,1,306.03

> view matrix models #37,1,0,0,308.87,0,1,0,464.24,0,0,1,322.97

> view matrix models #37,1,0,0,317.78,0,1,0,455.14,0,0,1,282.45

> select subtract #37

Nothing selected  

> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/4j84_yeast_betaprimeCOPI_Scyl1.cif"

4j84_yeast_betaprimeCOPI_Scyl1.cif title:  
Crystal structure of beta'-COP/Scyl1 complex [more info...]  
  
Chain information for 4j84_yeast_betaprimeCOPI_Scyl1.cif #58  
---  
Chain | Description | UniProt  
A B | Coatomer subunit beta' | COPB2_YEAST 1-301  
C D | SCYL1 |   
  
4j84_yeast_betaprimeCOPI_Scyl1.cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select add #58

5629 atoms, 4977 bonds, 1 pseudobond, 1390 residues, 2 models selected  

> view matrix models #58,1,0,0,321.38,0,1,0,537.86,0,0,1,10.829

> view matrix models #58,1,0,0,212.79,0,1,0,544.05,0,0,1,90.406

> view matrix models #58,1,0,0,282.97,0,1,0,565.35,0,0,1,134.13

> select subtract #58

Nothing selected  

> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/4j8g_yeast_alphaCOPI_E19.cif"

4j8g_yeast_alphaCOPI_E19.cif title:  
Crystal structure of alpha-COP/E19 complex [more info...]  
  
Chain information for 4j8g_yeast_alphaCOPI_E19.cif #59  
---  
Chain | Description | UniProt  
A B | coatomer subunit alpha | COPA_SCHPO 1-327  
C D | membrane glycoprotein E3 gp19K |   
  
4j8g_yeast_alphaCOPI_E19.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_defined_assembly  
  

> select add #59

5422 atoms, 5101 bonds, 2 pseudobonds, 1089 residues, 2 models selected  

> view matrix models #59,1,0,0,309.29,0,1,0,452.46,0,0,1,334.15

> select subtract #59

Nothing selected  

> hide #!58 models

> hide #37 models

> hide #!36 models

> ui tool show Matchmaker

> matchmaker #!59 to #38

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 20240711_copi_golph3_alpha_M1-T591.cif, chain D (#38) with
4j8g_yeast_alphaCOPI_E19.cif, chain B (#59), sequence alignment score = 1352.5  
RMSD between 295 pruned atom pairs is 0.445 angstroms; (across all 300 pairs:
0.809)  
  

> select #59/D

78 atoms, 73 bonds, 15 residues, 1 model selected  

> cartoon hide sel

> select #59/D

78 atoms, 73 bonds, 15 residues, 1 model selected  

> select #59/D

78 atoms, 73 bonds, 15 residues, 1 model selected  

> select add #59

5422 atoms, 5101 bonds, 2 pseudobonds, 1089 residues, 2 models selected  

> select subtract #59

Nothing selected  

> hide #!5 models

> select #59/C

87 atoms, 83 bonds, 16 residues, 1 model selected  

> select add #59

5422 atoms, 5101 bonds, 2 pseudobonds, 1089 residues, 2 models selected  

> select subtract #59

Nothing selected  

> select #59/A

2636 atoms, 2456 bonds, 1 pseudobond, 551 residues, 2 models selected  

> cartoon hide (#!59 & sel)

> color #59 label_red

> view matrix models
> #59,-0.44074,-0.2599,-0.85919,220.3,0.13706,-0.96543,0.22173,400.67,-0.88711,-0.020035,0.46113,327.07

> view view17

> view view14

> hide #!59 models

> show #!59 models

> view view14

> show #!5 models

> close #58

> hide #!5 models

> hide #!30 models

> color #59 label_redv2

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color list

30 custom colors: alphav1

, alphav2

, alphav3

, arf1v1

, arf1v2

, arf1v3

, betapv1

, betapv2

, betapv3

, betav1

, betav2

, betav3

, deltav1

, deltav2

, deltav3

, epsilonv1

, epsilonv3

, gammav1

, gammav2

, gammav3

, label_purple

, label_purple_v3

, label_purple_v4

, label_purplev2

, label_red

, label_red_v3

, lable_purple_v4

, zetav1

, zetav2

, and zetav3

.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color #59 label_red_v3

> color #59 crimson

> show #!30 models

> view view14

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20250109_chimera_for_figures_v4.cxs"

> hide #!30 models

> hide #!59 models

> close #36

> close #37

> view view3

> show #!11 models

> set silhouetteWidth 3

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/leaf_outlines/leaf_outline_side_job073_lp15_silwid3_T100_view3.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view4

> show #!30 models

> show #!5 models

> hide #!5 models

> hide #!30 models

> show #!30 models

> hide #!11 models

> show #!5 models

> hide #!5 models

> hide #!30 models

> show #!11 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/leaf_outlines/leaf_outline_bottom_job073_lp15_silwid3_T100_view4_memremoved.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view18

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/leaf_outlines/leaf_outline_top_job073_lp15_silwid3_T100_view18.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view1

> hide #!11 models

> show #!13 models

> color #13 #a9a9a900 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/triad_outlines/triad_outline_top_job020_lp20_silwid3_T100_view1.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view2

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/triad_outlines/triad_outline_side_job020_lp20_silwid3_T100_view2.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view21

> view view22

> view view20

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/triad_outlines/triad_outline_bottom_job020_lp20_silwid3_T100_view20_withmem.png"
> width 782 height 613 supersample 3 transparentBackground true

> set silhouetteWidth 4

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/triad_outlines/triad_outline_bottom_job020_lp20_silwid4_T100_view20_withmem.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view1

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/triad_outlines/triad_outline_top_job020_lp20_silwid4_T100_view1.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view2

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure1/triad_outlines/triad_outline_side_job020_lp20_silwid4_T100_view2.png"
> width 782 height 613 supersample 3 transparentBackground true

> view view17

> hide #!13 models

> show #!5 models

> show #!30 models

> set silhouetteWidth 1.5

> view view17

> view view14

[Repeated 1 time(s)]

> show #23 models

> show #21 models

> hide #21 models

> show #21 models

> hide #21 models

> show #21 models

> select #30/Q

1971 atoms, 2002 bonds, 244 residues, 1 model selected  

> cartoon hide sel

> show #15 models

> show #16 models

> view view14

[Repeated 1 time(s)]

> view name view31

> view view31

> show #!59 models

> hide #!59 models

> show #!59 models

> hide #!59 models

> show #!59 models

> hide #!59 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure2/GOLPH_alpha_nickel_soft_T65_view31.png" width
> 782 height 613 supersample 3 transparentBackground true

> hide #23 models

> hide #21 models

> hide #15 models

> hide #16 models

> select #30/Q

1971 atoms, 2002 bonds, 244 residues, 1 model selected  

> cartoon sel

> select add #30

33939 atoms, 34555 bonds, 6 pseudobonds, 4256 residues, 2 models selected  

> select subtract #30

Nothing selected  

> view view31

> show #!59 models

> select #59/B

2621 atoms, 2489 bonds, 1 pseudobond, 507 residues, 2 models selected  

> cartoon hide (#!59 & sel)

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure2/GOLPH_alpha_with_KKXX_peptidenickel_soft_T65_view31.png"
> width 782 height 613 supersample 3 transparentBackground true

> hide #!59 models

> select add #59

5422 atoms, 5101 bonds, 2 pseudobonds, 1089 residues, 2 models selected  

> select subtract #59

Nothing selected  

> view view3

> hide #!5 models

> show #!11 models

> hide #!30 models

> show #!32 models

> show #!61 models

> hide #!61 models

> show #!61 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure4/electro_golph_w_ribbon_side_v2.png" width 782
> height 613 supersample 3 transparentBackground true

> hide #!61 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure4/electro_golph_wout_ribbon_side_v2.png" width
> 782 height 613 supersample 3 transparentBackground true

> view view4

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure4/electro_golph_wout_ribbon_bottom_nomem_v2.png"
> width 782 height 613 supersample 3 transparentBackground true

> show #!61 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure4/electro_golph_w_ribbon_bottom_nomem_v2.png"
> width 782 height 613 supersample 3 transparentBackground true

> hide #!61 models

> hide #!32 models

> set silhouetteWidth 4

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure4/leaf_outline_silwid4_no_mem_view4.png" width
> 782 height 613 supersample 3 transparentBackground true

> view view3

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2025_Jan/Figure4/leaf_outline_silwid4_view3.png" width 782
> height 613 supersample 3 transparentBackground true

> hide #!11 models

> show #!5 models

> show #!30 models

> set silhouetteWidth 1.5

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20250101_chimera_for_figures.cxs" includeMaps true

——— End of log from Thu Jan 9 16:57:06 2025 ———

> view name session-start

opened ChimeraX session  

> save /Users/sean/Desktop/image1.png supersample 3

> save /Users/sean/Desktop/image2.png supersample 3

> save /Users/sean/Desktop/image3.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/sean/Desktop/movie1.mp4

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 185, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run  
f(s)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1312, in save_spin_movie  
run(session, cmd)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 202, in movie_encode  
encode_op(session, output[-1], format, quality, qscale, bitrate,  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 260, in encode_op  
movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'],
"yuv420p", f['size_restriction'],  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 324, in start_encoding  
self.encoder.run(Status_Reporter())  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/encode.py", line 232, in run  
p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__  
self._execute_child(args, executable, preexec_fn, close_fds,  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'  
  
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: Z14V000GPB/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 2 days, 19 hours, 26 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL U3219Q:
          Resolution: 6016 x 3384
          UI Looks like: 3008 x 1692 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (3)

comment:1 by Eric Pettersen, 5 weeks ago

Cc:	Eric Pettersen added
Component:	Unassigned → Build System
Description:	modified (diff)
Owner:	set to Zach Pearson
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ffmpeg: Permission denied

comment:2 by Eric Pettersen, 5 weeks ago

Resolution:	→ duplicate
Status:	assigned → closed

Hi Sean,

Thanks for reporting this problem. It is fixed in the 1.10.1 release, so if you get that then you will be able to save movies.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by sean@…, 5 weeks ago

It is now working!

Many thanks,

Sean



Sean Munro
Division of Cell Biology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge CB2 0QH, UK

Phone:  +44 1223 267028
Fax:    +44 1223 268306

LMB Cell Biology on Bluesky: @cellbiol-mrclmb.bsky.social

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