![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 days ago
Closed 2 days ago
#19217 closed defect (duplicate)
ffmpeg: Permission denied
| Reported by: | 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
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Unable to save movies
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250911-ProcessingS1v2.cxs" format session
Opened cryosparc_P206_J145_010_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.647, shown at level 0.0618, step 1, values float32
Opened cryosparc_P206_J157_011_volume_map.mrc as #2, grid size 480,480,480,
pixel 0.647, shown at level 0.0514, step 1, values float32
Opened cryosparc_P206_cryosparc_P206_J45_gaussian1p9_TMs_maskbase_0p051.mrc as
#3, grid size 480,480,480, pixel 0.647, shown at level 0.00799, step 1, values
float32
Opened cryosparc_P206_J147_006_volume_map.mrc as #4, grid size 480,480,480,
pixel 0.647, shown at level 0.0781, step 1, values float32
Opened cryosparc_P206_J58_mask.mrc as #5, grid size 480,480,480, pixel 0.647,
shown at level 5e-05, step 1, values float32
Opened cryosparc_P206_J45_009_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.647, shown at level 0.0599, step 1, values float32
Opened AF-O95800-F1-model_v4.pdb map 15 as #8, grid size 480,480,480, pixel
0.647, shown at level 0.005, step 1, values float32
Opened TM-mask_onJ147_0pt005.mrc as #9, grid size 480,480,480, pixel 0.647,
shown at level 0.005, step 1, values float32
Opened cryosparc_P206_J162_005_volume_map.mrc as #10, grid size 480,480,480,
pixel 0.647, shown at level 0.0715, step 1, values float32
Opened cryosparc_P206_J162_005_volume_map_sharp.mrc as #11, grid size
480,480,480, pixel 0.647, shown at level 0.0936, step 1, values float32
Opened cryosparc_P206_J162_005_volume_mask_refine.mrc as #12, grid size
480,480,480, pixel 0.647, shown at level 0.201, step 1, values float32
Opened TM-mask_onJ162_0pt05-tight.mrc as #13, grid size 480,480,480, pixel
0.647, shown at level 0.05, step 1, values float32
Opened cryosparc_P206_J147_006_volume_mask_refine.mrc as #14, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened SubtractionMask-J162-usingfullMaskJ147.mrc as #15, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened cryosparc_P206_J177_005_volume_map.mrc as #16, grid size 480,480,480,
pixel 0.647, shown at level 0.0585, step 1, values float32
Opened cryosparc_P206_J177_005_volume_map_sharp.mrc as #17, grid size
480,480,480, pixel 0.647, shown at level 0.0855, step 1, values float32
Opened cryosparc_P206_J185_010_volume_map.mrc as #18, grid size 480,480,480,
pixel 0.647, shown at level 0.0561, step 1, values float32
Opened cryosparc_P206_J188_006_volume_map.mrc as #19, grid size 480,480,480,
pixel 0.647, shown at level 0.0717, step 1, values float32
Opened cryosparc_P206_J189_006_volume_map.mrc as #20, grid size 480,480,480,
pixel 0.647, shown at level 0.0699, step 1, values float32
Opened cryosparc_P206_J193_009_volume_map.mrc as #23, grid size 480,480,480,
pixel 0.647, shown at level 0.0642, step 1, values float32
Opened cryosparc_P206_J200_006_volume_map.mrc as #21, grid size 480,480,480,
pixel 0.647, shown at level 0.0633, step 1, values float32
Opened cryosparc_P206_J203_005_volume_map.mrc as #22, grid size 480,480,480,
pixel 0.647, shown at level 0.0723, step 1, values float32
Opened cryosparc_P206_J200_006_volume_mask_refine.mrc as #24, grid size
480,480,480, pixel 0.647, shown at level 5e-05, step 1, values float32
Opened cryosparc_P206_J203_005_volume_mask_refine.mrc as #25, grid size
480,480,480, pixel 0.647, shown at level 5e-05, step 1, values float32
Opened cryosparc_P206_J193_009_volume_mask_refine.mrc as #26, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened SubtractionMask-J193-usingfullMaskJ147.mrc as #27, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened cryosparc_P206_J209_volume_map.mrc as #28, grid size 480,480,480, pixel
0.647, shown at level 0.0553, step 1, values float32
Opened cryosparc_P206_J213_006_volume_map.mrc as #29, grid size 480,480,480,
pixel 0.647, shown at level 0.0657, step 1, values float32
Opened cryosparc_P206_J214_007_volume_map.mrc as #30, grid size 480,480,480,
pixel 0.647, shown at level 0.0677, step 1, values float32
Opened cryosparc_P206_J215_map_locres.mrc as #31, grid size 480,480,480, pixel
0.647, shown at level 0.000822, step 1, values float32
Opened cryosparc_P206_J214_007_volume_map_sharp.mrc as #33, grid size
480,480,480, pixel 0.647, shown at level 0.101, step 1, values float32
Opened cryosparc_P207_J127_008_volume_map.mrc as #34, grid size 480,480,480,
pixel 0.647, shown at level 0.0285, step 1, values float32
Opened cryosparc_P207_J137_003_volume_map.mrc as #35, grid size 480,480,480,
pixel 0.647, shown at level 0.0598, step 1, values float32
Opened cryosparc_P207_J136_005_volume_map.mrc as #36, grid size 480,480,480,
pixel 0.647, shown at level 0.0564, step 1, values float32
Opened cryosparc_P207_J138_009_volume_map.mrc as #37, grid size 480,480,480,
pixel 0.647, shown at level 0.0553, step 1, values float32
Opened cryosparc_P207_J164_011_volume_map.mrc as #38, grid size 480,480,480,
pixel 0.647, shown at level 0.0575, step 1, values float32
Opened cryosparc_P207_J170_009_volume_map.mrc as #39, grid size 480,480,480,
pixel 0.647, shown at level 0.0656, step 1, values float32
Opened cryosparc_P207_J173_010_volume_map.mrc as #40, grid size 480,480,480,
pixel 0.647, shown at level 0.0603, step 1, values float32
Opened cryosparc_P207_J172_008_volume_map.mrc as #41, grid size 480,480,480,
pixel 0.647, shown at level 0.0588, step 1, values float32
Opened cryosparc_P207_J177_007_volume_map.mrc as #42, grid size 480,480,480,
pixel 0.647, shown at level 0.0261, step 1, values float32
Opened cryosparc_P207_J177_007_volume_mask_refine.mrc as #43, grid size
480,480,480, pixel 0.647, shown at level 0.201, step 2, values float32
Opened cryosparc_P207_J171_006_volume_map.mrc as #44, grid size 480,480,480,
pixel 0.647, shown at level 0.0312, step 1, values float32
Opened cryosparc_P207_J171_006_volume_mask_refine.mrc as #45, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 2, values float32
Opened SubtractionMask-J147-usingfullMaskJ171.mrc as #46, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened cryosparc_P207_J183_006_volume_map.mrc as #47, grid size 480,480,480,
pixel 0.647, shown at level 0.0355, step 1, values float32
Opened cryosparc_P207_J186_003_volume_map.mrc as #48, grid size 480,480,480,
pixel 0.647, shown at level 0.00121, step 1, values float32
Opened SubtractionMask-J162-usingfullMaskJ171-0pt999.mrc as #49, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened cryosparc_P207_J198_004_volume_map.mrc as #50, grid size 480,480,480,
pixel 0.647, shown at level 0.0757, step 1, values float32
Opened cryosparc_P207_J206_005_volume_map.mrc as #51, grid size 480,480,480,
pixel 0.647, shown at level 0.0263, step 1, values float32
Opened cryosparc_P207_J207_008_volume_map.mrc as #52, grid size 480,480,480,
pixel 0.647, shown at level 0.0259, step 1, values float32
Opened cryosparc_P207_J208_006_volume_map.mrc as #53, grid size 480,480,480,
pixel 0.647, shown at level 0.0222, step 1, values float32
Opened cryosparc_P207_J210_008_volume_map.mrc as #54, grid size 480,480,480,
pixel 0.647, shown at level 0.0258, step 1, values float32
Opened cryosparc_P207_J211_004_volume_map.mrc as #55, grid size 480,480,480,
pixel 0.647, shown at level 0.0291, step 1, values float32
Opened cryosparc_P207_J211_004_volume_mask_refine.mrc as #56, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 2, values float32
Opened SubtractionMask-J162-usingfullMaskJ211.mrc as #57, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened cryosparc_P207_J216_volume_map.mrc as #58, grid size 480,480,480, pixel
0.647, shown at level 0.0282, step 1, values float32
Opened cryosparc_P207_J217_volume_map.mrc as #59, grid size 480,480,480, pixel
0.647, shown at level 0.0265, step 1, values float32
Opened cryosparc_P207_J220_004_volume_map.mrc as #60, grid size 480,480,480,
pixel 0.647, shown at level 0.0299, step 1, values float32
Opened cryosparc_P207_J221_003_volume_map.mrc as #61, grid size 480,480,480,
pixel 0.647, shown at level 0.0247, step 1, values float32
Opened cryosparc_P207_J225_003_volume_map.mrc as #62, grid size 480,480,480,
pixel 0.647, shown at level 0.0313, step 1, values float32
Opened cryosparc_P207_J227_004_volume_map.mrc as #63, grid size 480,480,480,
pixel 0.647, shown at level 0.0251, step 1, values float32
Log from Fri Sep 19 16:56:58 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zmotiwal@amgen.com/Library/CloudStorage/OneDrive-
> Amgen/Projects/GPR75/Processing-Apo/20250911-ProcessingS1v2.cxs
Opened cryosparc_P206_J145_010_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.647, shown at level 0.0618, step 1, values float32
Opened cryosparc_P206_J157_011_volume_map.mrc as #2, grid size 480,480,480,
pixel 0.647, shown at level 0.0514, step 1, values float32
Opened cryosparc_P206_cryosparc_P206_J45_gaussian1p9_TMs_maskbase_0p051.mrc as
#3, grid size 480,480,480, pixel 0.647, shown at level 0.00799, step 1, values
float32
Opened cryosparc_P206_J147_006_volume_map.mrc as #4, grid size 480,480,480,
pixel 0.647, shown at level 0.0781, step 1, values float32
Opened cryosparc_P206_J58_mask.mrc as #5, grid size 480,480,480, pixel 0.647,
shown at level 5e-05, step 1, values float32
Opened cryosparc_P206_J45_009_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.647, shown at level 0.0599, step 1, values float32
Opened AF-O95800-F1-model_v4.pdb map 15 as #8, grid size 480,480,480, pixel
0.647, shown at level 0.005, step 1, values float32
Opened TM-mask_onJ147_0pt005.mrc as #9, grid size 480,480,480, pixel 0.647,
shown at level 0.005, step 1, values float32
Opened cryosparc_P206_J162_005_volume_map.mrc as #10, grid size 480,480,480,
pixel 0.647, shown at level 0.0715, step 1, values float32
Opened cryosparc_P206_J162_005_volume_map_sharp.mrc as #11, grid size
480,480,480, pixel 0.647, shown at level 0.0936, step 1, values float32
Opened cryosparc_P206_J162_005_volume_mask_refine.mrc as #12, grid size
480,480,480, pixel 0.647, shown at level 0.201, step 1, values float32
Opened TM-mask_onJ162_0pt05-tight.mrc as #13, grid size 480,480,480, pixel
0.647, shown at level 0.05, step 1, values float32
Opened cryosparc_P206_J147_006_volume_mask_refine.mrc as #14, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened SubtractionMask-J162-usingfullMaskJ147.mrc as #15, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened cryosparc_P206_J177_005_volume_map.mrc as #16, grid size 480,480,480,
pixel 0.647, shown at level 0.0585, step 1, values float32
Opened cryosparc_P206_J177_005_volume_map_sharp.mrc as #17, grid size
480,480,480, pixel 0.647, shown at level 0.0855, step 1, values float32
Opened cryosparc_P206_J185_010_volume_map.mrc as #18, grid size 480,480,480,
pixel 0.647, shown at level 0.0561, step 1, values float32
Opened cryosparc_P206_J188_006_volume_map.mrc as #19, grid size 480,480,480,
pixel 0.647, shown at level 0.0717, step 1, values float32
Opened cryosparc_P206_J189_006_volume_map.mrc as #20, grid size 480,480,480,
pixel 0.647, shown at level 0.0699, step 1, values float32
Opened cryosparc_P206_J193_009_volume_map.mrc as #23, grid size 480,480,480,
pixel 0.647, shown at level 0.0642, step 1, values float32
Opened cryosparc_P206_J200_006_volume_map.mrc as #21, grid size 480,480,480,
pixel 0.647, shown at level 0.0633, step 1, values float32
Opened cryosparc_P206_J203_005_volume_map.mrc as #22, grid size 480,480,480,
pixel 0.647, shown at level 0.0723, step 1, values float32
Opened cryosparc_P206_J200_006_volume_mask_refine.mrc as #24, grid size
480,480,480, pixel 0.647, shown at level 5e-05, step 1, values float32
Opened cryosparc_P206_J203_005_volume_mask_refine.mrc as #25, grid size
480,480,480, pixel 0.647, shown at level 5e-05, step 1, values float32
Opened cryosparc_P206_J193_009_volume_mask_refine.mrc as #26, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened SubtractionMask-J193-usingfullMaskJ147.mrc as #27, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened cryosparc_P206_J209_volume_map.mrc as #28, grid size 480,480,480, pixel
0.647, shown at level 0.0553, step 1, values float32
Opened cryosparc_P206_J213_006_volume_map.mrc as #29, grid size 480,480,480,
pixel 0.647, shown at level 0.0657, step 1, values float32
Opened cryosparc_P206_J214_007_volume_map.mrc as #30, grid size 480,480,480,
pixel 0.647, shown at level 0.0677, step 1, values float32
Opened cryosparc_P206_J215_map_locres.mrc as #31, grid size 480,480,480, pixel
0.647, shown at level 0.000822, step 1, values float32
Opened cryosparc_P206_J214_007_volume_map_sharp.mrc as #33, grid size
480,480,480, pixel 0.647, shown at level 0.101, step 1, values float32
Opened cryosparc_P207_J127_008_volume_map.mrc as #34, grid size 480,480,480,
pixel 0.647, shown at level 0.0285, step 1, values float32
Opened cryosparc_P207_J137_003_volume_map.mrc as #35, grid size 480,480,480,
pixel 0.647, shown at level 0.0598, step 1, values float32
Opened cryosparc_P207_J136_005_volume_map.mrc as #36, grid size 480,480,480,
pixel 0.647, shown at level 0.0564, step 1, values float32
Opened cryosparc_P207_J138_009_volume_map.mrc as #37, grid size 480,480,480,
pixel 0.647, shown at level 0.0553, step 1, values float32
Opened cryosparc_P207_J164_011_volume_map.mrc as #38, grid size 480,480,480,
pixel 0.647, shown at level 0.0575, step 1, values float32
Opened cryosparc_P207_J170_009_volume_map.mrc as #39, grid size 480,480,480,
pixel 0.647, shown at level 0.0656, step 1, values float32
Opened cryosparc_P207_J173_010_volume_map.mrc as #40, grid size 480,480,480,
pixel 0.647, shown at level 0.0603, step 1, values float32
Opened cryosparc_P207_J172_008_volume_map.mrc as #41, grid size 480,480,480,
pixel 0.647, shown at level 0.0588, step 1, values float32
Opened cryosparc_P207_J177_007_volume_map.mrc as #42, grid size 480,480,480,
pixel 0.647, shown at level 0.0261, step 1, values float32
Opened cryosparc_P207_J177_007_volume_mask_refine.mrc as #43, grid size
480,480,480, pixel 0.647, shown at level 0.201, step 2, values float32
Opened cryosparc_P207_J171_006_volume_map.mrc as #44, grid size 480,480,480,
pixel 0.647, shown at level 0.0312, step 1, values float32
Opened cryosparc_P207_J171_006_volume_mask_refine.mrc as #45, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 2, values float32
Opened SubtractionMask-J147-usingfullMaskJ171.mrc as #46, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened cryosparc_P207_J183_006_volume_map.mrc as #47, grid size 480,480,480,
pixel 0.647, shown at level 0.0355, step 1, values float32
Opened cryosparc_P207_J186_003_volume_map.mrc as #48, grid size 480,480,480,
pixel 0.647, shown at level 0.00121, step 1, values float32
Opened SubtractionMask-J162-usingfullMaskJ171-0pt999.mrc as #49, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened cryosparc_P207_J198_004_volume_map.mrc as #50, grid size 480,480,480,
pixel 0.647, shown at level 0.0757, step 1, values float32
Log from Mon Sep 15 13:23:32 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs" format session
Opened cryosparc_P206_J145_010_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.647, shown at level 0.0618, step 1, values float32
Opened cryosparc_P206_J157_011_volume_map.mrc as #2, grid size 480,480,480,
pixel 0.647, shown at level 0.0514, step 1, values float32
Opened cryosparc_P206_cryosparc_P206_J45_gaussian1p9_TMs_maskbase_0p051.mrc as
#3, grid size 480,480,480, pixel 0.647, shown at level 0.00799, step 1, values
float32
Opened cryosparc_P206_J147_006_volume_map.mrc as #4, grid size 480,480,480,
pixel 0.647, shown at level 0.0781, step 1, values float32
Opened cryosparc_P206_J58_mask.mrc as #5, grid size 480,480,480, pixel 0.647,
shown at level 5e-05, step 1, values float32
Opened cryosparc_P206_J45_009_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.647, shown at level 0.0599, step 1, values float32
Opened AF-O95800-F1-model_v4.pdb map 15 as #8, grid size 480,480,480, pixel
0.647, shown at level 0.005, step 1, values float32
Opened TM-mask_onJ147_0pt005.mrc as #9, grid size 480,480,480, pixel 0.647,
shown at level 0.005, step 1, values float32
Opened cryosparc_P206_J162_005_volume_map.mrc as #10, grid size 480,480,480,
pixel 0.647, shown at level 0.0715, step 1, values float32
Opened cryosparc_P206_J162_005_volume_map_sharp.mrc as #11, grid size
480,480,480, pixel 0.647, shown at level 0.0936, step 1, values float32
Opened cryosparc_P206_J162_005_volume_mask_refine.mrc as #12, grid size
480,480,480, pixel 0.647, shown at level 0.201, step 1, values float32
Opened TM-mask_onJ162_0pt05-tight.mrc as #13, grid size 480,480,480, pixel
0.647, shown at level 0.05, step 1, values float32
Opened cryosparc_P206_J147_006_volume_mask_refine.mrc as #14, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened SubtractionMask-J162-usingfullMaskJ147.mrc as #15, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened cryosparc_P206_J177_005_volume_map.mrc as #16, grid size 480,480,480,
pixel 0.647, shown at level 0.0585, step 1, values float32
Opened cryosparc_P206_J177_005_volume_map_sharp.mrc as #17, grid size
480,480,480, pixel 0.647, shown at level 0.0855, step 1, values float32
Opened cryosparc_P206_J185_010_volume_map.mrc as #18, grid size 480,480,480,
pixel 0.647, shown at level 0.0561, step 1, values float32
Opened cryosparc_P206_J188_006_volume_map.mrc as #19, grid size 480,480,480,
pixel 0.647, shown at level 0.0717, step 1, values float32
Opened cryosparc_P206_J189_006_volume_map.mrc as #20, grid size 480,480,480,
pixel 0.647, shown at level 0.0699, step 1, values float32
Opened cryosparc_P206_J193_009_volume_map.mrc as #23, grid size 480,480,480,
pixel 0.647, shown at level 0.0642, step 1, values float32
Opened cryosparc_P206_J200_006_volume_map.mrc as #21, grid size 480,480,480,
pixel 0.647, shown at level 0.0633, step 1, values float32
Opened cryosparc_P206_J203_005_volume_map.mrc as #22, grid size 480,480,480,
pixel 0.647, shown at level 0.0723, step 1, values float32
Opened cryosparc_P206_J200_006_volume_mask_refine.mrc as #24, grid size
480,480,480, pixel 0.647, shown at level 5e-05, step 1, values float32
Opened cryosparc_P206_J203_005_volume_mask_refine.mrc as #25, grid size
480,480,480, pixel 0.647, shown at level 5e-05, step 1, values float32
Opened cryosparc_P206_J193_009_volume_mask_refine.mrc as #26, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened SubtractionMask-J193-usingfullMaskJ147.mrc as #27, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened cryosparc_P206_J209_volume_map.mrc as #28, grid size 480,480,480, pixel
0.647, shown at level 0.0553, step 1, values float32
Opened cryosparc_P206_J213_006_volume_map.mrc as #29, grid size 480,480,480,
pixel 0.647, shown at level 0.0657, step 1, values float32
Opened cryosparc_P206_J214_007_volume_map.mrc as #30, grid size 480,480,480,
pixel 0.647, shown at level 0.0677, step 1, values float32
Opened cryosparc_P206_J215_map_locres.mrc as #31, grid size 480,480,480, pixel
0.647, shown at level 0.000822, step 1, values float32
Opened cryosparc_P206_J214_007_volume_map_sharp.mrc as #33, grid size
480,480,480, pixel 0.647, shown at level 0.101, step 1, values float32
Log from Mon Aug 25 15:56:30 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs" format session
Opened cryosparc_P206_J145_010_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.647, shown at level 0.0618, step 1, values float32
Opened cryosparc_P206_J157_011_volume_map.mrc as #2, grid size 480,480,480,
pixel 0.647, shown at level 0.0514, step 1, values float32
Opened cryosparc_P206_cryosparc_P206_J45_gaussian1p9_TMs_maskbase_0p051.mrc as
#3, grid size 480,480,480, pixel 0.647, shown at level 0.00799, step 1, values
float32
Opened cryosparc_P206_J147_006_volume_map.mrc as #4, grid size 480,480,480,
pixel 0.647, shown at level 0.0781, step 1, values float32
Opened cryosparc_P206_J58_mask.mrc as #5, grid size 480,480,480, pixel 0.647,
shown at level 5e-05, step 1, values float32
Opened cryosparc_P206_J45_009_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.647, shown at level 0.0599, step 1, values float32
Opened AF-O95800-F1-model_v4.pdb map 15 as #8, grid size 480,480,480, pixel
0.647, shown at level 0.005, step 1, values float32
Opened TM-mask_onJ147_0pt005.mrc as #9, grid size 480,480,480, pixel 0.647,
shown at level 0.005, step 1, values float32
Opened cryosparc_P206_J162_005_volume_map.mrc as #10, grid size 480,480,480,
pixel 0.647, shown at level 0.0715, step 1, values float32
Opened cryosparc_P206_J162_005_volume_map_sharp.mrc as #11, grid size
480,480,480, pixel 0.647, shown at level 0.0936, step 1, values float32
Opened cryosparc_P206_J162_005_volume_mask_refine.mrc as #12, grid size
480,480,480, pixel 0.647, shown at level 0.201, step 1, values float32
Opened TM-mask_onJ162_0pt05-tight.mrc as #13, grid size 480,480,480, pixel
0.647, shown at level 0.05, step 1, values float32
Opened cryosparc_P206_J147_006_volume_mask_refine.mrc as #14, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened SubtractionMask-J162-usingfullMaskJ147.mrc as #15, grid size
480,480,480, pixel 0.647, shown at level 0.999, step 1, values float32
Opened cryosparc_P206_J177_005_volume_map.mrc as #16, grid size 480,480,480,
pixel 0.647, shown at level 0.0585, step 1, values float32
Opened cryosparc_P206_J177_005_volume_map_sharp.mrc as #17, grid size
480,480,480, pixel 0.647, shown at level 0.0855, step 1, values float32
Opened cryosparc_P206_J185_010_volume_map.mrc as #18, grid size 480,480,480,
pixel 0.647, shown at level 0.0561, step 1, values float32
Opened cryosparc_P206_J188_006_volume_map.mrc as #19, grid size 480,480,480,
pixel 0.647, shown at level 0.0717, step 1, values float32
Opened cryosparc_P206_J189_006_volume_map.mrc as #20, grid size 480,480,480,
pixel 0.647, shown at level 0.0699, step 1, values float32
Opened cryosparc_P206_J193_009_volume_map.mrc as #23, grid size 480,480,480,
pixel 0.647, shown at level 0.0642, step 1, values float32
Log from Sat Aug 23 10:02:10 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zmotiwal@amgen.com/Library/CloudStorage/OneDrive-
> Amgen/Projects/GPR75/Processing-Apo/20250820-Processing.cxs
Opened cryosparc_P206_J145_010_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.647, shown at level 0.0618, step 1, values float32
Opened cryosparc_P206_J157_011_volume_map.mrc as #2, grid size 480,480,480,
pixel 0.647, shown at level 0.0514, step 1, values float32
Opened cryosparc_P206_cryosparc_P206_J45_gaussian1p9_TMs_maskbase_0p051.mrc as
#3, grid size 480,480,480, pixel 0.647, shown at level 0.00799, step 1, values
float32
Opened cryosparc_P206_J147_006_volume_map.mrc as #4, grid size 480,480,480,
pixel 0.647, shown at level 0.0781, step 1, values float32
Opened cryosparc_P206_J58_mask.mrc as #5, grid size 480,480,480, pixel 0.647,
shown at level 5e-05, step 1, values float32
Opened cryosparc_P206_J45_009_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.647, shown at level 0.0599, step 1, values float32
Opened AF-O95800-F1-model_v4.pdb map 15 as #8, grid size 480,480,480, pixel
0.647, shown at level 0.005, step 1, values float32
Opened TM-mask_onJ147_0pt005.mrc as #9, grid size 480,480,480, pixel 0.647,
shown at level 0.005, step 1, values float32
Log from Wed Aug 20 12:37:43 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs" format session
Log from Wed Aug 20 10:49:50 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs" includeMaps true
——— End of log from Wed Aug 20 10:49:50 2025 ———
> view name session-start
opened ChimeraX session
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J145_010_volume_map.mrc
Opened cryosparc_P206_J145_010_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.647, shown at level 0.0223, step 2, values float32
> volume #1 step 1
> volume #1 level 0.0633
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J157_011_volume_map.mrc
Opened cryosparc_P206_J157_011_volume_map.mrc as #2, grid size 480,480,480,
pixel 0.647, shown at level 0.0245, step 2, values float32
> hide #!1 models
> volume #2 step 1
> volume #2 level 0.0003896
> volume #2 level 0.04065
> volume #2 level 0.05139
> set bgColor white
> hide #!2 models
> show #!1 models
> volume #1 level 0.05778
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_cryosparc_P206_J45_gaussian1p9_TMs_maskbase_0p051.mrc
Opened cryosparc_P206_cryosparc_P206_J45_gaussian1p9_TMs_maskbase_0p051.mrc as
#3, grid size 480,480,480, pixel 0.647, shown at level 0.00642, step 2, values
float32
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> volume #3 step 1
> volume #3 level 0.02103
> volume #3 level 0.02889
> volume #3 level 0.007993
> volume #3 level 0.01541
> volume #3 level 0.02777
> volume #3 level -0.001222
> volume #3 level 0.0017
> volume #1 level 0.03911
> volume #1 level 0.06265
> volume #1 level 0.05616
> volume #1 level 0.06103
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.007993
> hide #!3 models
> volume #1 level 0.06184
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J147_006_volume_map.mrc
Opened cryosparc_P206_J147_006_volume_map.mrc as #4, grid size 480,480,480,
pixel 0.647, shown at level 0.0221, step 2, values float32
> hide #!1 models
> volume #4 step 1
> volume #4 level 0.06716
[Repeated 1 time(s)]
> show #!1 models
> volume #4 level 0.07007
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> volume #4 level 0.06861
> open /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J58_mask.mrc
Opened cryosparc_P206_J58_mask.mrc as #5, grid size 480,480,480, pixel 0.647,
shown at level 5e-05, step 2, values float32
> volume #5 step 1
> volume #4 level 0.06934
> volume #4 level 0.0737
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J45_009_volume_map.mrc
Opened cryosparc_P206_J45_009_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.647, shown at level 0.0223, step 2, values float32
> volume #6 step 1
> volume #6 level 0.07497
> hide #!4 models
> volume #6 level 0.05992
> show #!4 models
> hide #!5 models
> volume #4 level 0.08388
> select add #5
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-1.6574,0,1,0,0.2643,0,0,1,31.074
> view matrix models #5,1,0,0,3.3212,0,1,0,4.7702,0,0,1,35.862
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.75011,0.27576,0.60108,-80.899,-0.22138,0.96118,-0.16469,67.77,-0.62316,-0.0095257,0.78204,164.72
> view matrix models
> #5,0.22677,-0.96804,0.10713,262.05,0.75319,0.24404,0.61086,-77.584,-0.61748,-0.057828,0.78446,171.05
> view matrix models
> #5,-0.22408,0.50787,0.83178,5.4147,-0.069089,0.84306,-0.53337,111.61,-0.97212,-0.17698,-0.15383,371.2
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> view matrix models
> #5,-0.1588,-0.70263,-0.69361,388.56,-0.98304,0.17783,0.044914,282.09,0.091788,0.68898,-0.71895,143.97
> view matrix models
> #5,0.38531,-0.0094359,0.92274,-21.945,0.14496,-0.98691,-0.070625,301.85,0.91133,0.16097,-0.3789,51.81
> view matrix models
> #5,0.35384,0.77896,0.5177,-85.928,0.15635,-0.59498,0.78838,123.77,0.92214,-0.19802,-0.33232,99.96
> view matrix models
> #5,-0.065879,0.91209,0.40466,-25.466,0.089519,-0.3985,0.91279,86.934,0.9938,0.096358,-0.055396,5.5863
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.065879,0.91209,0.40466,-25.867,0.089519,-0.3985,0.91279,87.726,0.9938,0.096358,-0.055396,6.3968
> view matrix models
> #5,-0.065879,0.91209,0.40466,-25.254,0.089519,-0.3985,0.91279,87.28,0.9938,0.096358,-0.055396,7.8082
> view matrix models
> #5,-0.065879,0.91209,0.40466,-25.937,0.089519,-0.3985,0.91279,83.413,0.9938,0.096358,-0.055396,2.838
> view matrix models
> #5,-0.065879,0.91209,0.40466,-24.414,0.089519,-0.3985,0.91279,89.777,0.9938,0.096358,-0.055396,6.3724
> view matrix models
> #5,-0.065879,0.91209,0.40466,-25.178,0.089519,-0.3985,0.91279,86.876,0.9938,0.096358,-0.055396,3.9237
> view matrix models
> #5,-0.065879,0.91209,0.40466,-25.545,0.089519,-0.3985,0.91279,89.277,0.9938,0.096358,-0.055396,3.8231
> view matrix models
> #5,-0.065879,0.91209,0.40466,-26.085,0.089519,-0.3985,0.91279,89.361,0.9938,0.096358,-0.055396,2.3021
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.95881,0.14663,0.24328,-46.303,-0.28374,0.53444,0.79615,18.015,-0.013281,-0.83239,0.55403,224.46
> hide #!5 models
> open /Users/zmotiwal@amgen.com/Downloads/AF-O95800-F1-model_v4.pdb
AF-O95800-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for probable G-protein coupled receptor 75
(O95800) [more info...]
Chain information for AF-O95800-F1-model_v4.pdb #7
---
Chain | Description | UniProt
A | probable G-protein coupled receptor 75 | GPR75_HUMAN 1-540
Computing secondary structure
> select subtract #5
Nothing selected
> select add #7
4169 atoms, 4270 bonds, 540 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,148.92,0,1,0,149.12,0,0,1,173.79
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.43372,0.14831,-0.88876,139.14,-0.7207,0.53492,0.44097,137.45,0.54082,0.83178,-0.12512,188.6
> view matrix models
> #7,0.42311,-0.86153,0.28062,140,-0.89374,-0.3459,0.28561,136.41,-0.14899,-0.37165,-0.91634,186.31
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.42311,-0.86153,0.28062,141.04,-0.89374,-0.3459,0.28561,144.32,-0.14899,-0.37165,-0.91634,173.03
> view matrix models
> #7,0.42311,-0.86153,0.28062,152.88,-0.89374,-0.3459,0.28561,135.12,-0.14899,-0.37165,-0.91634,166.81
> view matrix models
> #7,0.42311,-0.86153,0.28062,156.46,-0.89374,-0.3459,0.28561,142.3,-0.14899,-0.37165,-0.91634,168.23
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.42311,-0.86153,0.28062,157.59,-0.89374,-0.3459,0.28561,144.79,-0.14899,-0.37165,-0.91634,168.39
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.8836,-0.045967,-0.46598,148.37,-0.3739,0.66833,0.64306,148.33,0.28187,0.74244,-0.60772,171.29
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.8836,-0.045967,-0.46598,148.68,-0.3739,0.66833,0.64306,148.56,0.28187,0.74244,-0.60772,171.95
> view matrix models
> #7,-0.8836,-0.045967,-0.46598,153.86,-0.3739,0.66833,0.64306,151.23,0.28187,0.74244,-0.60772,171.18
> view matrix models
> #7,-0.8836,-0.045967,-0.46598,152.04,-0.3739,0.66833,0.64306,150.84,0.28187,0.74244,-0.60772,167.02
> view matrix models
> #7,-0.8836,-0.045967,-0.46598,151.92,-0.3739,0.66833,0.64306,150.21,0.28187,0.74244,-0.60772,166.39
> view matrix models
> #7,-0.8836,-0.045967,-0.46598,149.74,-0.3739,0.66833,0.64306,149.71,0.28187,0.74244,-0.60772,164.53
> view matrix models
> #7,-0.8836,-0.045967,-0.46598,148.95,-0.3739,0.66833,0.64306,148.62,0.28187,0.74244,-0.60772,170.46
> view matrix models
> #7,-0.8836,-0.045967,-0.46598,149.29,-0.3739,0.66833,0.64306,148.91,0.28187,0.74244,-0.60772,170.59
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.63333,0.72961,0.25799,161.47,0.016845,-0.34629,0.93797,150.96,0.7737,-0.5897,-0.23161,173.11
> view matrix models
> #7,0.63594,0.72196,0.27268,161.39,0.0060486,-0.35799,0.93371,150.86,0.77172,-0.59213,-0.23203,173.09
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.63594,0.72196,0.27268,161.07,0.0060486,-0.35799,0.93371,151.35,0.77172,-0.59213,-0.23203,174.22
> view matrix models
> #7,0.63594,0.72196,0.27268,160.18,0.0060486,-0.35799,0.93371,151.38,0.77172,-0.59213,-0.23203,174.52
> select subtract #7
Nothing selected
> fitmap #7 inMap #4
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P206_J147_006_volume_map.mrc (#4) using 4169 atoms
average map value = 0.03034, steps = 124
shifted from previous position = 1.34
rotated from previous position = 4.18 degrees
atoms outside contour = 3792, contour level = 0.083878
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P206_J147_006_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.63957808 0.74142966 0.20303186 162.04296027
0.05836207 -0.31018529 0.94888300 151.71333845
0.76650750 -0.59503541 -0.24165908 173.94603911
Axis -0.86745611 -0.31659082 -0.38378398
Axis point 0.00000000 73.03948657 26.16194541
Rotation angle (degrees) 117.13786649
Shift along axis -255.35391007
> select add #7
4169 atoms, 4270 bonds, 540 residues, 1 model selected
> view matrix models
> #7,0.63958,0.74143,0.20303,162.26,0.058362,-0.31019,0.94888,151.49,0.76651,-0.59504,-0.24166,173.24
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.54101,0.82891,0.14218,161.6,0.054841,-0.20347,0.97754,151.26,0.83923,-0.52107,-0.15554,173.45
> view matrix models
> #7,0.58857,0.79687,0.13631,162.18,0.096952,-0.23696,0.96667,151.82,0.80261,-0.55573,-0.21673,173.47
> view matrix models
> #7,0.56679,0.81271,0.13511,161.95,0.087282,-0.22231,0.97106,151.68,0.81923,-0.53859,-0.19694,173.52
> view matrix models
> #7,0.60166,0.7901,0.11722,162.48,0.13043,-0.24197,0.96148,152.24,0.78803,-0.5632,-0.24863,173.54
> view matrix models
> #7,0.61653,0.7754,0.13654,162.5,0.12162,-0.26513,0.95651,152.17,0.77788,-0.57311,-0.25776,173.49
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.61653,0.7754,0.13654,161.84,0.12162,-0.26513,0.95651,153.31,0.77788,-0.57311,-0.25776,172.49
> view matrix models
> #7,0.61653,0.7754,0.13654,162.31,0.12162,-0.26513,0.95651,154.8,0.77788,-0.57311,-0.25776,173.49
> fitmap #7 inMap #4
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P206_J147_006_volume_map.mrc (#4) using 4169 atoms
average map value = 0.03034, steps = 128
shifted from previous position = 2.22
rotated from previous position = 4.64 degrees
atoms outside contour = 3793, contour level = 0.083878
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P206_J147_006_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.63958223 0.74139495 0.20314553 162.03190784
0.05828748 -0.31027454 0.94885841 151.71995757
0.76650972 -0.59503213 -0.24166012 173.94384203
Axis -0.86746197 -0.31653605 -0.38381591
Axis point 0.00000000 73.04621742 26.15369011
Rotation angle (degrees) 117.14063989
Shift along axis -255.34376861
> select subtract #7
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 7/A
> select /A:24-399
2905 atoms, 2973 bonds, 376 residues, 1 model selected
> molmap sel 15 onGrid #4
Opened AF-O95800-F1-model_v4.pdb map 15 as #8, grid size 480,480,480, pixel
0.647, shown at level 0.0249, step 1, values float32
> volume #8 level 0.04109
> volume #8 level 0.01169
> volume #8 level 0.001
> volume #8 level 0.005
> volume #8 level 0.0001
> volume #8 level 0.005
> hide #!8 models
> hide #!4 models
> select /A:24-237
1658 atoms, 1696 bonds, 214 residues, 1 model selected
> select /A:24-237,299-399
2438 atoms, 2491 bonds, 315 residues, 1 model selected
> show #!4 models
> fitmap #7 inMap #4
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P206_J147_006_volume_map.mrc (#4) using 4169 atoms
average map value = 0.03034, steps = 36
shifted from previous position = 0.00329
rotated from previous position = 0.00156 degrees
atoms outside contour = 3793, contour level = 0.083878
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P206_J147_006_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.63958679 0.74138514 0.20316695 162.03410234
0.05828211 -0.31029964 0.94885053 151.72209640
0.76650631 -0.59503127 -0.24167304 173.94319406
Axis -0.86746542 -0.31652515 -0.38381711
Axis point 0.00000000 73.04681914 26.15196521
Rotation angle (degrees) 117.14171663
Shift along axis -255.34521400
> fitmap #7 inMap #4
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P206_J147_006_volume_map.mrc (#4) using 4169 atoms
average map value = 0.03034, steps = 44
shifted from previous position = 0.00218
rotated from previous position = 0.00269 degrees
atoms outside contour = 3793, contour level = 0.083878
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P206_J147_006_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.63955697 0.74141539 0.20315045 162.03504759
0.05830796 -0.31028656 0.94885322 151.72070631
0.76652923 -0.59500040 -0.24167635 173.94335641
Axis -0.86745460 -0.31654912 -0.38382180
Axis point 0.00000000 73.04254964 26.15395280
Rotation angle (degrees) 117.14236192
Shift along axis -255.34835557
> select /A:24-237,299-399
2438 atoms, 2491 bonds, 315 residues, 1 model selected
> volume #4 level 0.07806
> select /A:24-237,299-399
2438 atoms, 2491 bonds, 315 residues, 1 model selected
> molmap sel 15 onGrid #4
Opened AF-O95800-F1-model_v4.pdb map 15 as #9, grid size 480,480,480, pixel
0.647, shown at level 0.0319, step 1, values float32
> volume #9 level 0.005
> volume #9 level 0.001
> volume #9 level 0.0001
> volume #9 level 0.005
> volume #9 level 0.002
> volume #9 level 0.005
> volume #9 level 0.009
> volume #9 level 0.005
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/TM-mask_onJ147_0pt005.mrc" models #9
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs"
——— End of log from Wed Aug 20 12:37:43 2025 ———
> view name session-start
opened ChimeraX session
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J162_005_volume_map.mrc
Opened cryosparc_P206_J162_005_volume_map.mrc as #10, grid size 480,480,480,
pixel 0.647, shown at level 0.0233, step 2, values float32
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J162_005_volume_map_sharp.mrc
Opened cryosparc_P206_J162_005_volume_map_sharp.mrc as #11, grid size
480,480,480, pixel 0.647, shown at level 0.0226, step 2, values float32
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J162_005_volume_mask_refine.mrc
Opened cryosparc_P206_J162_005_volume_mask_refine.mrc as #12, grid size
480,480,480, pixel 0.647, shown at level 0.201, step 2, values float32
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> volume #12 step 1
> volume #11 step 1
> volume #10 step 1
> volume #10 level 0.02332
> volume #10 level 0.06183
> transparency #10.1 50
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.63956,0.74142,0.20315,161.26,0.058308,-0.31029,0.94885,150.39,0.76653,-0.595,-0.24168,173.33
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.6193,0.7591,0.20058,161.05,-0.0081794,-0.24922,0.96841,149.49,0.78511,-0.60138,-0.14813,172.84
> view matrix models
> #7,0.72191,0.64109,0.26047,161.75,-0.050588,-0.3265,0.94384,149.17,0.69013,-0.69455,-0.20328,172.14
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.72191,0.64109,0.26047,158.05,-0.050588,-0.3265,0.94384,147.46,0.69013,-0.69455,-0.20328,173.82
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.99068,0.13541,-0.014747,163.07,0.10392,-0.6814,0.72449,150.79,0.088055,-0.71927,-0.68913,170.53
> view matrix models
> #7,0.95929,0.015201,0.28201,160.47,-0.1449,-0.83061,0.53767,149.3,0.24241,-0.55665,-0.79459,173.13
> volume #10 level 0.09285
> view matrix models
> #7,0.91211,-0.20056,0.35754,159.31,-0.34057,-0.85617,0.38857,148.16,0.22818,-0.47619,-0.84922,173.39
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.91211,-0.20056,0.35754,164.31,-0.34057,-0.85617,0.38857,152.16,0.22818,-0.47619,-0.84922,174.82
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.7391,-0.59042,0.32424,162.48,-0.65335,-0.51127,0.55833,147.38,-0.16388,-0.62451,-0.76363,169.64
> view matrix models
> #7,0.53763,-0.7921,0.28902,160.39,-0.84031,-0.47505,0.26117,147.47,-0.069573,-0.38327,-0.92101,171.96
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.53763,-0.7921,0.28902,160.9,-0.84031,-0.47505,0.26117,148.19,-0.069573,-0.38327,-0.92101,173.94
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.53197,-0.7976,0.28433,160.87,-0.83883,-0.45054,0.30556,147.88,-0.11562,-0.40105,-0.90873,173.32
> view matrix models
> #7,0.55258,-0.7763,0.30334,160.97,-0.82432,-0.45529,0.33647,147.81,-0.12309,-0.43598,-0.8915,173.1
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.55258,-0.7763,0.30334,164.54,-0.82432,-0.45529,0.33647,147.04,-0.12309,-0.43598,-0.8915,175.16
> fitmap #7 inMap #10
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P206_J162_005_volume_map.mrc (#10) using 4169 atoms
average map value = 0.02882, steps = 432
shifted from previous position = 5.27
rotated from previous position = 16.7 degrees
atoms outside contour = 3922, contour level = 0.092848
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P206_J162_005_volume_map.mrc (#10) coordinates:
Matrix rotation and translation
0.70470421 -0.56570731 0.42821399 163.50352036
-0.70947275 -0.55645277 0.43244507 146.32974922
-0.00635648 -0.60855202 -0.79348853 171.43220925
Axis -0.91541393 0.38214503 -0.12642195
Axis point 0.00000000 134.01745178 41.97579766
Rotation angle (degrees) 145.34778552
Shift along axis -115.42700837
> volume #10 level 0.06611
> view matrix models
> #7,0.7047,-0.56571,0.42821,163.21,-0.70947,-0.55645,0.43245,145.95,-0.0063565,-0.60855,-0.79349,171.27
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.73766,-0.11613,0.6651,161.92,-0.61108,-0.53373,0.58456,145.94,0.2871,-0.83765,-0.46468,172.12
> view matrix models
> #7,0.76388,-0.098937,0.63773,162.43,-0.58832,-0.51294,0.62512,145.91,0.26527,-0.8527,-0.45004,171.76
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.76388,-0.098937,0.63773,162.64,-0.58832,-0.51294,0.62512,140.3,0.26527,-0.8527,-0.45004,171.62
> view matrix models
> #7,0.76388,-0.098937,0.63773,162.83,-0.58832,-0.51294,0.62512,140.03,0.26527,-0.8527,-0.45004,173.36
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.86499,-0.30661,0.39721,165.74,-0.49253,-0.67019,0.55522,141.62,0.095969,-0.6759,-0.73072,173.56
> view matrix models
> #7,0.87014,-0.33018,0.36585,166.03,-0.48782,-0.68248,0.54429,141.75,0.069963,-0.65208,-0.75492,173.44
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.87014,-0.33018,0.36585,164.86,-0.48782,-0.68248,0.54429,144.64,0.069963,-0.65208,-0.75492,174.6
> view matrix models
> #7,0.87014,-0.33018,0.36585,164.38,-0.48782,-0.68248,0.54429,142.82,0.069963,-0.65208,-0.75492,174.49
> fitmap #7 inMap #10
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P206_J162_005_volume_map.mrc (#10) using 4169 atoms
average map value = 0.0296, steps = 132
shifted from previous position = 6.25
rotated from previous position = 9.52 degrees
atoms outside contour = 3602, contour level = 0.066107
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P206_J162_005_volume_map.mrc (#10) coordinates:
Matrix rotation and translation
0.81596929 -0.28562646 0.50260486 162.72601710
-0.53481333 -0.70304519 0.46872398 148.08261520
0.21947396 -0.65126415 -0.72642012 173.35677516
Axis -0.94770384 0.23957776 -0.21085523
Axis point 0.00000000 118.87219172 36.60491229
Rotation angle (degrees) 143.77940870
Shift along axis -155.29195348
> view matrix models
> #7,0.81597,-0.28563,0.5026,162.1,-0.53481,-0.70305,0.46872,154.2,0.21947,-0.65126,-0.72642,179.68
> view matrix models
> #7,0.81597,-0.28563,0.5026,163.39,-0.53481,-0.70305,0.46872,150.16,0.21947,-0.65126,-0.72642,182.91
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.94111,-0.071806,0.33037,166.16,-0.2786,-0.7183,0.63752,151.84,0.19153,-0.69202,-0.69601,182.36
> view matrix models
> #7,0.90397,-0.26821,0.33302,165.67,-0.40305,-0.79456,0.45412,151.76,0.14281,-0.54474,-0.82636,182.8
> view matrix models
> #7,0.95759,0.15073,0.24556,167.03,-0.037183,-0.78047,0.62409,154.69,0.28572,-0.60675,-0.74177,183.8
> view matrix models
> #7,0.95432,0.16052,0.252,166.95,-0.035954,-0.7756,0.6302,154.66,0.29661,-0.61048,-0.7344,183.87
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.95432,0.16052,0.252,167.48,-0.035954,-0.7756,0.6302,153.92,0.29661,-0.61048,-0.7344,182.59
> view matrix models
> #7,0.95432,0.16052,0.252,167.25,-0.035954,-0.7756,0.6302,153.53,0.29661,-0.61048,-0.7344,182.19
> fitmap #7 inMap #10
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P206_J162_005_volume_map.mrc (#10) using 4169 atoms
average map value = 0.02911, steps = 148
shifted from previous position = 2.9
rotated from previous position = 7.39 degrees
atoms outside contour = 3634, contour level = 0.066107
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P206_J162_005_volume_map.mrc (#10) coordinates:
Matrix rotation and translation
0.91864610 0.28059035 0.27813380 167.43301247
0.02865647 -0.74945953 0.66142969 156.06013242
0.39404081 -0.59964946 -0.69652880 185.58416279
Axis -0.97666392 -0.08976613 -0.19511442
Axis point 0.00000000 97.29891515 50.41719342
Rotation angle (degrees) 139.78891274
Shift along axis -213.74484134
> volume #10 level 0.05755
> transparency #10.1 0
> view matrix models
> #7,0.91865,0.28059,0.27813,167.49,0.028656,-0.74946,0.66143,156.03,0.39404,-0.59965,-0.69653,185.45
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.77953,0.55124,0.29745,165.82,0.134,-0.61065,0.78048,156.38,0.61187,-0.56855,-0.54988,186.86
> view matrix models
> #7,0.87464,0.46588,0.134,168.11,0.045004,-0.35327,0.93444,154.27,0.48267,-0.81127,-0.32995,183.68
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.87464,0.46588,0.134,173.72,0.045004,-0.35327,0.93444,148.54,0.48267,-0.81127,-0.32995,177.02
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.5808,0.70366,0.4093,168.35,-0.20785,-0.35795,0.91031,145.81,0.78706,-0.61379,-0.06164,178.55
> view matrix models
> #7,0.58459,0.70764,0.39688,168.49,-0.19473,-0.3525,0.91533,145.93,0.78762,-0.61237,-0.068268,178.61
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.58459,0.70764,0.39688,167.64,-0.19473,-0.3525,0.91533,145.25,0.78762,-0.61237,-0.068268,180.99
> view matrix models
> #7,0.58459,0.70764,0.39688,161.39,-0.19473,-0.3525,0.91533,140.78,0.78762,-0.61237,-0.068268,177.08
> view matrix models
> #7,0.58459,0.70764,0.39688,158.07,-0.19473,-0.3525,0.91533,138.89,0.78762,-0.61237,-0.068268,174.36
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.58634,0.74181,0.32545,158.63,-0.04822,-0.36908,0.92814,140.47,0.80863,-0.5599,-0.18064,175.46
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.58634,0.74181,0.32545,160.76,-0.04822,-0.36908,0.92814,144.98,0.80863,-0.5599,-0.18064,179.42
> view matrix models
> #7,0.58634,0.74181,0.32545,160.3,-0.04822,-0.36908,0.92814,145.55,0.80863,-0.5599,-0.18064,179.23
> transparency #10.1 50
> volume #10 level 0.07146
> view matrix models
> #7,0.58634,0.74181,0.32545,160.66,-0.04822,-0.36908,0.92814,145.37,0.80863,-0.5599,-0.18064,178.93
> fitmap #7 inMap #10
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P206_J162_005_volume_map.mrc (#10) using 4169 atoms
average map value = 0.0401, steps = 608
shifted from previous position = 8.85
rotated from previous position = 29.9 degrees
atoms outside contour = 3216, contour level = 0.071455
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P206_J162_005_volume_map.mrc (#10) coordinates:
Matrix rotation and translation
0.86236205 0.34174007 0.37355779 162.31424413
-0.10250977 -0.60469360 0.78983378 154.02649056
0.49580585 -0.71941600 -0.48643311 177.31910621
Axis -0.95642180 -0.07746942 -0.28152413
Axis point 0.00000000 100.12958805 29.71368741
Rotation angle (degrees) 127.90705286
Shift along axis -217.09283070
> select add #7
4169 atoms, 4270 bonds, 540 residues, 1 model selected
> select subtract #7
Nothing selected
> show #!11 models
> volume #11 level 0.09361
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs"
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/AFmodel-on-J162.pdb" relModel #10
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> select /A:24-237,299-399
2438 atoms, 2491 bonds, 315 residues, 1 model selected
> molmap sel 15 onGrid #10
Opened AF-O95800-F1-model_v4.pdb map 15 as #13, grid size 480,480,480, pixel
0.647, shown at level 0.0319, step 1, values float32
> volume #13 level 0.03
> volume #13 level 0.05
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J147_006_volume_mask_refine.mrc
Opened cryosparc_P206_J147_006_volume_mask_refine.mrc as #14, grid size
480,480,480, pixel 0.647, shown at level 1, step 2, values float32
> volume #14 step 1
> volume #14 level 0.999
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs"
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> volume subtract #14 #13 onGrid #14
Opened volume difference as #15, grid size 480,480,480, pixel 0.647, shown at
step 1, values float32
> show #!13 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs"
No map chosen to save
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/TM-mask_onJ162_0pt05-tight.mrc" models #13
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/SubtractionMask-J162-usingfullMaskJ147.mrc" models #15
> hide #!15 models
> hide #!13 models
> show #!10 models
> select add #7
4169 atoms, 4270 bonds, 540 residues, 1 model selected
> select subtract #7
Nothing selected
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J177_005_volume_map.mrc
Opened cryosparc_P206_J177_005_volume_map.mrc as #16, grid size 480,480,480,
pixel 0.647, shown at level 0.0237, step 2, values float32
> volume #16 step 1
> volume #16 level 0.0585
> transparency #10.1#16.1 0
> transparency #10.1#16.1 50
> transparency #11.1 50
> volume #16 level 0.07168
> volume #16 level 0.0585
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs"
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J177_005_volume_map_sharp.mrc
Opened cryosparc_P206_J177_005_volume_map_sharp.mrc as #17, grid size
480,480,480, pixel 0.647, shown at level 0.023, step 2, values float32
> volume #17 step 1
> volume #17 level 0.06279
> transparency #11.1#17.1 0
> transparency #11.1#17.1 50
> volume #17 level 0.08838
> volume #17 level 0.1197
> volume #17 level 0.08554
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J185_010_volume_map.mrc
Opened cryosparc_P206_J185_010_volume_map.mrc as #18, grid size 480,480,480,
pixel 0.647, shown at level 0.0241, step 2, values float32
> volume #18 step 1
> volume #18 level 0.05693
> volume #18 level 0.06494
> volume #18 level 0.05613
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J188_006_volume_map.mrc
Opened cryosparc_P206_J188_006_volume_map.mrc as #19, grid size 480,480,480,
pixel 0.647, shown at level 0.0224, step 2, values float32
> volume #19 step 1
> volume #19 level 0.05637
> volume #19 level 0.07011
[Repeated 1 time(s)]
> volume #19 level 0.07172
> transparency #19.1 50
> volume #19 level 0.07172
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J189_006_volume_map.mrc
Opened cryosparc_P206_J189_006_volume_map.mrc as #20, grid size 480,480,480,
pixel 0.647, shown at level 0.0241, step 2, values float32
> volume #20 level 0.06845
> volume #20 step 1
> transparency #20.1 50
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs"
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J47_003_volume_map.mrc
Opened cryosparc_P207_J47_003_volume_map.mrc as #21, grid size 240,240,240,
pixel 1.29, shown at level 0.0667, step 1, values float32
> volume #21 level 0.1172
> volume #21 level 0.07475
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J49_003_volume_map.mrc
Opened cryosparc_P207_J49_003_volume_map.mrc as #22, grid size 240,240,240,
pixel 1.29, shown at level 0.0569, step 1, values float32
> volume #22 level 0.06645
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J193_009_volume_map.mrc
Opened cryosparc_P206_J193_009_volume_map.mrc as #23, grid size 480,480,480,
pixel 0.647, shown at level 0.023, step 2, values float32
> volume #23 step 1
> volume #23 level 0.07147
> volume #23 level 0.07604
> volume #23 level 0.07147
> volume #23 level 0.07421
> close #21
> close #22
> volume #20 level 0.06988
> volume #23 level 0.06416
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs"
——— End of log from Sat Aug 23 10:02:10 2025 ———
> view name session-start
opened ChimeraX session
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J200_006_volume_map.mrc
Opened cryosparc_P206_J200_006_volume_map.mrc as #21, grid size 480,480,480,
pixel 0.647, shown at level 0.0245, step 2, values float32
> volume #21 step 1
> volume #21 level 0.07084
> transparency #20.1#21.1 0
> transparency #20.1#21.1 50
> volume #21 level 0.06868
> volume #21 level 0.05789
> volume #21 level 0.08162
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J203_005_volume_map.mrc
Opened cryosparc_P206_J203_005_volume_map.mrc as #22, grid size 480,480,480,
pixel 0.647, shown at level 0.0241, step 2, values float32
> volume #22 step 1
> volume #22 level 0.08429
> transparency #22.1 50
> volume #22 level 0.07225
> volume #21 level 0.06329
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J200_006_volume_mask_refine.mrc
Opened cryosparc_P206_J200_006_volume_mask_refine.mrc as #24, grid size
480,480,480, pixel 0.647, shown at level 5e-05, step 2, values float32
> volume #24 step 1
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J203_005_volume_mask_refine.mrc
Opened cryosparc_P206_J203_005_volume_mask_refine.mrc as #25, grid size
480,480,480, pixel 0.647, shown at level 5e-05, step 2, values float32
> volume #25 step 1
> show #!15 models
> hide #!25 models
> hide #!15 models
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J193_009_volume_mask_refine.mrc
Opened cryosparc_P206_J193_009_volume_mask_refine.mrc as #26, grid size
480,480,480, pixel 0.647, shown at level 1, step 2, values float32
> volume #26 step 1
> volume #26 level 0.999
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!26 models
> hide #!15 models
> show #!13 models
> show #!26 models
> hide #!21 models
> volume subtract #26 #13 onGrid #26
Opened volume difference as #27, grid size 480,480,480, pixel 0.647, shown at
step 1, values float32
> show #!13 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs"
No map chosen to save
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/SubtractionMask-J193-usingfullMaskJ147.mrc" models #27
> hide #!27 models
> hide #!13 models
> open /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J209_volume_map.mrc
Opened cryosparc_P206_J209_volume_map.mrc as #28, grid size 480,480,480, pixel
0.647, shown at level 0.00395, step 2, values float32
> volume #28 step 1
> volume #28 level 0.04407
> transparency #28.1 50
> volume #28 level 0.0553
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J213_006_volume_map.mrc
Opened cryosparc_P206_J213_006_volume_map.mrc as #29, grid size 480,480,480,
pixel 0.647, shown at level 0.00127, step 2, values float32
> volume #29 step 1
> volume #29 level 0.04456
> transparency #29.1 50
> volume #29 level 0.06851
> volume #29 level 0.07035
> volume #29 level 0.07956
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J214_007_volume_map.mrc
Opened cryosparc_P206_J214_007_volume_map.mrc as #30, grid size 480,480,480,
pixel 0.647, shown at level 0.0013, step 2, values float32
> volume #30 step 1
> volume #30 level 0.06045
> transparency #29.1#30.1 0
> transparency #29.1#30.1 50
> volume #30 level 0.06235
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Destroying pre-existing alignment with identifier 7/A
Alignment identifier is 7/A
> select /A:24-67,70-72,78-106,115-147,158-182,201-237,299-346,352-379,381-399
2080 atoms, 2119 bonds, 266 residues, 1 model selected
> select add #7
4169 atoms, 4270 bonds, 540 residues, 1 model selected
> select subtract #7
Nothing selected
> select /A:118
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:118
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:189
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:189
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:118-119,189
23 atoms, 22 bonds, 3 residues, 1 model selected
> select /A:118-119,189
23 atoms, 22 bonds, 3 residues, 1 model selected
> select /A:118-119,189
23 atoms, 22 bonds, 3 residues, 1 model selected
> select /A:118
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:118,189-190
20 atoms, 18 bonds, 3 residues, 1 model selected
> show sel atoms
> volume #29 level 0.06299
> volume #29 level 0.06575
> open /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J215_map_locres.mrc
Opened cryosparc_P206_J215_map_locres.mrc as #31, grid size 480,480,480, pixel
0.647, shown at level 0.000822, step 2, values float32
> volume #31 step 1
> ui tool show "Surface Color"
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> ui mousemode right "color key"
> color sample #30.1 map #31 palette #0000ff:#00ff00:#ff0000:#808080:#808080
> outsideColor #808080
Map values for surface "surface": minimum 3.096, mean 4.389, maximum 8.422
> key blue:3.10 lime:4.43 red:5.76 grey:7.09 grey:8.42 showTool true
> transparency #30.1 50
> transparency #30.1 0
> transparency #30.1 50
> color sample #30.1 map #31 palette
> 3.096,#0000ff:4.428,#00ff00:5.759,#ff0000:7.091,#808080:8.422,#808080
> outsideColor #808080
Map values for surface "surface": minimum 3.096, mean 4.389, maximum 8.422
> color sample #30.1 map #31 palette
> 3.096,#0000ff:4.428,#00ff00:5.759,#ff0000:7.091,#808080:8.422,#808080
> outsideColor #808080
Map values for surface "surface": minimum 3.096, mean 4.389, maximum 8.422
> color sample #30.1 map #31 palette
> 3.096,#0000ff:4.428,#0091ff:5.759,#00ffda:7.091,#00ff48:8.422,#48ff00
> outsideColor #808080
Map values for surface "surface": minimum 3.096, mean 4.389, maximum 8.422
> color sample #30.1 map #31 palette
> 3.096,#0000ff:3.5,#0091ff:4,#00ffda:4.5,#00ff48:5,#48ff00:6,#daff00:7.091,#ff9100:8.422,#ff0000
> outsideColor #808080
Map values for surface "surface": minimum 3.096, mean 4.389, maximum 8.422
> key blue:3.10 #0091ff:3.50 #00ffda:4.00 #00ff48:4.50 #48ff00:5.00
> #daff00:6.00 #ff9100:7.09 red:8.42 showTool true
> key pos 0.952838,0.103709 size 0.00209344,0
> key blue:3.10 #0091ff:3.50 #00ffda:4.00 #00ff48:4.50 #48ff00:5.00
> #daff00:6.00 #ff9100:7.09 red:8.42 showTool true
> key pos 0.965728,0.124599 size 0,0
> key blue:3.10 #0091ff:3.50 #00ffda:4.00 #00ff48:4.50 #48ff00:5.00
> #daff00:6.00 #ff9100:7.09 red:8.42 showTool true
> key pos 0.981362,0.145008 size 0.00224827,0.000547252
> key pos 0.981362,0.145008 size 0,0
> key blue:3.10 #0091ff:3.50 #00ffda:4.00 #00ff48:4.50 #48ff00:5.00
> #daff00:6.00 #ff9100:7.09 red:8.42 showTool true
> key pos 0.663459,0.137209 size 0.327828,0.0238479
> key fontSize 23
> key fontSize 22
> key fontSize 21
> key fontSize 20
> key fontSize 19
> key fontSize 18
> key fontSize 17
> key fontSize 16
> key fontSize 15
> key fontSize 14
> key fontSize 13
> key fontSize 12
> key bold true
> key numericLabelSpacing proportional
> key numericLabelSpacing equal
> key justification left
> key justification right
> key justification decimal
> key ticks true
> key ticks false
> key ticks true
> key ticks false
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs"
> volume #30 level 0.06414
> show #!22 models
> hide #!30 models
> show #!30 models
> hide #!22 models
> color single #30.1
> show #!25 models
> hide #!25 models
> show #!24 models
> hide #!24 models
> show #!23 models
> show #!18 models
> show #!16 models
> transparency #16.1#18.1#23.1#30.1 0
> transparency #16.1#18.1#23.1#30.1 50
> color sample #30.1 map #31 palette
> 3.096,#0000ff:3.5,#0091ff:4,#00ffda:4.5,#00ff48:5,#48ff00:6,#daff00:7.091,#ff9100:8.422,#ff0000
> outsideColor #808080
Map values for surface "surface": minimum 3.096, mean 4.363, maximum 8.214
> hide #!23 models
> hide #!18 models
> hide #!16 models
> volume #30 level 0.02128
> volume #30 level 0.04093
> volume #30 level 0.032
> color single #30.1
> volume #30 level 0.04182
> color sample #30.1 map #31 palette
> 3.096,#0000ff:3.5,#0091ff:4,#00ffda:4.5,#00ff48:5,#48ff00:6,#daff00:7.091,#ff9100:8.422,#ff0000
> outsideColor #808080
Map values for surface "surface": minimum 3.099, mean 4.665, maximum 8.498
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs"
> color single #30.1
> toolshed show
> volume #30 level 0.06771
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P206_J214_007_volume_map_sharp.mrc
Opened cryosparc_P206_J214_007_volume_map_sharp.mrc as #33, grid size
480,480,480, pixel 0.647, shown at level 0.00564, step 2, values float32
> volume #33 step 1
> volume #33 level 0.08392
> volume #33 level 0.08773
> transparency #33.1 50
> volume #33 level 0.1011
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250820-Processing.cxs"
——— End of log from Mon Aug 25 15:56:30 2025 ———
> view name session-start
opened ChimeraX session
> select add #7
4169 atoms, 4270 bonds, 540 residues, 1 model selected
> select subtract #7
Nothing selected
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J127_008_volume_map.mrc
Opened cryosparc_P207_J127_008_volume_map.mrc as #34, grid size 480,480,480,
pixel 0.647, shown at level 0.0215, step 2, values float32
> volume #34 step 1
> volume #34 level 0.04957
> volume #34 level 0.06081
> hide #!34 models
> show #!34 models
> hide #32 models
> hide #!30 models
> show #!27 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> fitmap #7 inMap #34
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P207_J127_008_volume_map.mrc (#34) using 4169 atoms
average map value = 0.03225, steps = 68
shifted from previous position = 0.457
rotated from previous position = 1.91 degrees
atoms outside contour = 3423, contour level = 0.060806
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P207_J127_008_volume_map.mrc (#34) coordinates:
Matrix rotation and translation
0.85296521 0.34141409 0.39482499 161.80411212
-0.13002626 -0.59358963 0.79419426 153.18374039
0.50551313 -0.72875769 -0.46191850 177.39307498
Axis -0.95298280 -0.06926279 -0.29500245
Axis point 0.00000000 100.38497049 27.48481236
Rotation angle (degrees) 126.96101367
Shift along axis -217.13785997
> show #!9 models
> hide #!9 models
> volume #34 level 0.05027
> show #!9 models
> volume #34 level 0.02849
> hide #!9 models
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J137_003_volume_map.mrc
Opened cryosparc_P207_J137_003_volume_map.mrc as #35, grid size 480,480,480,
pixel 0.647, shown at level 0.0214, step 2, values float32
> hide #!34 models
> volume #35 step 1
> volume #35 level 0.05302
> transparency #35.1 50
> volume #35 level 0.05976
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J136_005_volume_map.mrc
Opened cryosparc_P207_J136_005_volume_map.mrc as #36, grid size 480,480,480,
pixel 0.647, shown at level 0.0215, step 2, values float32
> volume #36 step 1
> volume #36 level 0.0509
> volume #36 level 0.05641
> transparency #35.1#36.1 0
> transparency #35.1#36.1 50
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J138_009_volume_map.mrc
Opened cryosparc_P207_J138_009_volume_map.mrc as #37, grid size 480,480,480,
pixel 0.647, shown at level 0.022, step 2, values float32
> volume #37 step 1
> volume #37 level 0.05026
> transparency #36.1#37.1 0
> transparency #36.1#37.1 50
> volume #37 level 0.05616
> volume #37 level 0.05532
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J164_011_volume_map.mrc
Opened cryosparc_P207_J164_011_volume_map.mrc as #38, grid size 480,480,480,
pixel 0.647, shown at level 0.0214, step 2, values float32
> volume #38 step 1
> volume #38 level 0.0541
> volume #38 level 0.05754
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> transparency #38.1 50
> show #!30 models
> show #!36 models
> hide #!36 models
> hide #!30 models
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J170_009_volume_map.mrc
Opened cryosparc_P207_J170_009_volume_map.mrc as #39, grid size 480,480,480,
pixel 0.647, shown at level 0.0221, step 2, values float32
> hide #!39 models
> show #!39 models
> hide #!38 models
> hide #!39 models
> show #!38 models
> hide #!38 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> volume #39 step 1
> volume #39 level 0.03463
> volume #39 level 0.06563
> hide #!39 models
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J173_010_volume_map.mrc
Opened cryosparc_P207_J173_010_volume_map.mrc as #40, grid size 480,480,480,
pixel 0.647, shown at level 0.0217, step 2, values float32
> volume #40 step 1
> volume #40 level 0.06534
> volume #40 level 0.06031
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J172_008_volume_map.mrc
Opened cryosparc_P207_J172_008_volume_map.mrc as #41, grid size 480,480,480,
pixel 0.647, shown at level 0.0223, step 2, values float32
> volume #41 step 1
> volume #41 level 0.06608
> volume #41 level 0.05878
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J177_007_volume_map.mrc
Opened cryosparc_P207_J177_007_volume_map.mrc as #42, grid size 480,480,480,
pixel 0.647, shown at level 0.0226, step 2, values float32
> volume #42 step 1
> volume #42 level 0.05126
> volume #42 level 0.06167
> volume #42 level 0.07382
> volume #42 level 0.04952
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!9 models
> volume #42 level 0.02609
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J177_007_volume_mask_refine.mrc
Opened cryosparc_P207_J177_007_volume_mask_refine.mrc as #43, grid size
480,480,480, pixel 0.647, shown at level 0.201, step 2, values float32
> hide #!43 models
> hide #!42 models
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J171_006_volume_map.mrc
Opened cryosparc_P207_J171_006_volume_map.mrc as #44, grid size 480,480,480,
pixel 0.647, shown at level 0.0216, step 2, values float32
> hide #!9 models
> volume #44 step 1
> volume #44 level 0.06068
> show #!9 models
> volume #44 level 0.03118
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J171_006_volume_mask_refine.mrc
Opened cryosparc_P207_J171_006_volume_mask_refine.mrc as #45, grid size
480,480,480, pixel 0.647, shown at level 1, step 2, values float32
> volume #45 level 0.999
> hide #!9 models
> show #!9 models
> volume subtract #45 #9 onGrid #45
Opened volume difference as #46, grid size 480,480,480, pixel 0.647, shown at
step 1, values float32
> hide #!44 models
> show #!44 models
> hide #!44 models
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250911-ProcessingS1.cxs"
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/SubtractionMask-J147-usingfullMaskJ171.mrc" models #46
> show #!9 models
> hide #!46 models
> hide #!9 models
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J183_006_volume_map.mrc
Opened cryosparc_P207_J183_006_volume_map.mrc as #47, grid size 480,480,480,
pixel 0.647, shown at level 0.00128, step 2, values float32
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J186_003_volume_map.mrc
Opened cryosparc_P207_J186_003_volume_map.mrc as #48, grid size 480,480,480,
pixel 0.647, shown at level 0.00121, step 2, values float32
> volume #47 step 1
> volume #48 step 1
> hide #!48 models
> volume #47 level 0.03549
> transparency #47.1 50
> show #!13 models
> show #!45 models
> hide #!45 models
> show #!45 models
> hide #!47 models
> volume subtract #45 #13 onGrid #45
Opened volume difference as #49, grid size 480,480,480, pixel 0.647, shown at
step 1, values float32
> show #!46 models
> hide #!49 models
> show #!49 models
> hide #!46 models
> show #!13 models
> volume #49 level 0.99
> volume #49 level 0.999
> volume #49 level 0.9999
> volume #49 level 0.999
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/SubtractionMask-J162-usingfullMaskJ171-0pt999.mrc" models #49
> hide #!49 models
> hide #!13 models
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J198_004_volume_map.mrc
Opened cryosparc_P207_J198_004_volume_map.mrc as #50, grid size 480,480,480,
pixel 0.647, shown at level 0.00126, step 2, values float32
> volume #50 step 1
> volume #50 level 0.04329
> transparency #50.1 50
> volume #50 level 0.05978
> volume #50 level 0.07574
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250911-ProcessingS1v2.cxs"
——— End of log from Mon Sep 15 13:23:32 2025 ———
> view name session-start
opened ChimeraX session
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J206_005_volume_map.mrc
Opened cryosparc_P207_J206_005_volume_map.mrc as #51, grid size 480,480,480,
pixel 0.647, shown at level 0.00873, step 2, values float32
> volume #51 step 1
> volume #51 level 0.02778
> transparency #51.1 50
> volume #51 level 0.02359
> volume #51 level 0.02778
> fitmap #7 inMap #51
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P207_J206_005_volume_map.mrc (#51) using 4169 atoms
average map value = 0.01515, steps = 60
shifted from previous position = 0.905
rotated from previous position = 2.09 degrees
atoms outside contour = 3216, contour level = 0.027777
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P207_J206_005_volume_map.mrc (#51) coordinates:
Matrix rotation and translation
0.85974828 0.33380156 0.38653514 161.91579954
-0.11056235 -0.61725084 0.77895916 154.38745132
0.49860693 -0.71244503 -0.49377446 178.02582024
Axis -0.95588972 -0.07183047 -0.28480737
Axis point 0.00000000 100.31449006 30.04305245
Rotation angle (degrees) 128.72906768
Shift along axis -216.56643573
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J207_008_volume_map.mrc
Opened cryosparc_P207_J207_008_volume_map.mrc as #52, grid size 480,480,480,
pixel 0.647, shown at level 0.00917, step 2, values float32
> volume #52 step 1
> volume #52 level 0.02592
> transparency #52.1 50
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J208_006_volume_map.mrc
Opened cryosparc_P207_J208_006_volume_map.mrc as #53, grid size 480,480,480,
pixel 0.647, shown at level 0.00888, step 2, values float32
> volume #53 step 1
> volume #53 level 0.02221
> volume #51 level 0.02625
> show #!49 models
> hide #!49 models
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J210_008_volume_map.mrc
Opened cryosparc_P207_J210_008_volume_map.mrc as #54, grid size 480,480,480,
pixel 0.647, shown at level 0.00928, step 2, values float32
> volume #54 step 1
> volume #54 level 0.02807
> transparency #54.1 50
> volume #54 level 0.01867
> volume #54 level 0.02619
> volume #54 level 0.01567
> volume #54 level 0.02582
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J211_004_volume_map.mrc
Opened cryosparc_P207_J211_004_volume_map.mrc as #55, grid size 480,480,480,
pixel 0.647, shown at level 0.00934, step 2, values float32
> volume #55 step 1
> volume #55 level 0.02797
> transparency #55.1 50
> volume #55 level 0.02379
> volume #55 level 0.02911
> show #!31 models
> hide #!31 models
> show #!30 models
> hide #!30 models
> show #!49 models
> hide #!49 models
> show #!45 models
> hide #!45 models
> show #!13 models
> hide #!13 models
> show #!13 models
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J211_004_volume_mask_refine.mrc
Opened cryosparc_P207_J211_004_volume_mask_refine.mrc as #56, grid size
480,480,480, pixel 0.647, shown at level 1, step 2, values float32
> volume #56 level 0.999
> volume subtract #56 #13 onGrid #56
Opened volume difference as #57, grid size 480,480,480, pixel 0.647, shown at
step 1, values float32
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250911-ProcessingS1v2.cxs"
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/SubtractionMask-J162-usingfullMaskJ211.mrc" models #57
> open /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J216_volume_map.mrc
Opened cryosparc_P207_J216_volume_map.mrc as #58, grid size 480,480,480, pixel
0.647, shown at level 0.00138, step 2, values float32
> volume #58 step 1
> volume #58 level 0.01524
> volume #58 level 0.02208
> transparency #55.1#58.1 0
> transparency #55.1#58.1 50
> volume #58 level 0.02406
> volume #58 level 0.0282
> open /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J217_volume_map.mrc
Opened cryosparc_P207_J217_volume_map.mrc as #59, grid size 480,480,480, pixel
0.647, shown at level 0.00118, step 2, values float32
> volume #59 step 1
> volume #59 level 0.02389
> transparency #55.1#58.1#59.1 0
> transparency #55.1#58.1#59.1 50
> volume #59 level 0.02649
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J220_004_volume_map.mrc
Opened cryosparc_P207_J220_004_volume_map.mrc as #60, grid size 480,480,480,
pixel 0.647, shown at level 0.000594, step 2, values float32
> volume #60 step 1
> volume #60 level 0.02446
> transparency #55.1#60.1 0
> transparency #55.1#60.1 50
> volume #60 level 0.02753
> volume #60 level 0.02989
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J221_003_volume_map.mrc
Opened cryosparc_P207_J221_003_volume_map.mrc as #61, grid size 480,480,480,
pixel 0.647, shown at level 0.000635, step 2, values float32
> volume #61 step 1
> volume #61 level 0.02626
> transparency #55.1#60.1#61.1 0
> transparency #55.1#60.1#61.1 50
> hide #!55 models
> volume #61 level 0.02809
> volume #61 level 0.02469
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J225_003_volume_map.mrc
Opened cryosparc_P207_J225_003_volume_map.mrc as #62, grid size 480,480,480,
pixel 0.647, shown at level 0.000628, step 2, values float32
> volume #62 step 1
> volume #62 level 0.005434
> volume #62 level 0.02626
> transparency #60.1#61.1#62.1 0
> transparency #60.1#61.1#62.1 50
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J227_004_volume_map.mrc
Opened cryosparc_P207_J227_004_volume_map.mrc as #63, grid size 480,480,480,
pixel 0.647, shown at level 0.000592, step 2, values float32
> volume #63 step 1
> volume #63 level 0.004913
> volume #63 level 0.02076
> transparency #62.1#63.1 0
> transparency #62.1#63.1 50
> volume #63 level 0.02604
> volume #63 level 0.02508
> volume #62 level 0.03133
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!33 models
> hide #!33 models
> show #!30 models
> color #30 #9437ffff models
> transparency #30.1#62.1 0
> transparency #30.1#62.1 50
> volume #62 level 0.02759
> hide #!30 models
> show #!30 models
> hide #!30 models
> volume #62 level -0.001508
> volume #62 level 0.001429
> volume #62 level 0.004633
> volume #62 level 0.02866
> volume #62 level 0.01798
> volume #62 level 0.02546
> volume #62 level 0.01691
> volume #62 level 0.03133
> save "/Users/zmotiwal@amgen.com/OneDrive - Amgen/Projects/GPR75/Processing-
> Apo/20250911-ProcessingS1v2.cxs"
——— End of log from Fri Sep 19 16:56:58 2025 ———
> view name session-start
opened ChimeraX session
> show #!55 models
> hide #!62 models
> volume #55 level 0.01805
> volume #55 level 0.02516
> volume #55 level 0.02674
> volume #55 level 0.02358
> show #!57 models
> hide #!57 models
> show #!57 models
> hide #!57 models
> volume #55 level 0.01608
> volume #55 level 0.03464
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J411_004_volume_map.mrc
Opened cryosparc_P207_J411_004_volume_map.mrc as #64, grid size 480,480,480,
pixel 0.647, shown at level 0.0283, step 2, values float32
> volume #60 level -0.003311
> volume #60 level 0.006507
> volume #60 level 0.02369
> volume #64 level 0.05964
> transparency #64.1 50
> volume #64 step 1
> fitmap #7 inMap #64
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P207_J411_004_volume_map.mrc (#64) using 4169 atoms
average map value = 0.03553, steps = 120
shifted from previous position = 3.46
rotated from previous position = 8.16 degrees
atoms outside contour = 3245, contour level = 0.059642
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P207_J411_004_volume_map.mrc (#64) coordinates:
Matrix rotation and translation
0.85750091 0.34915272 0.37786846 165.15896162
-0.02467207 -0.70571118 0.70806993 157.26884381
0.51389053 -0.61649341 -0.59653366 180.33536501
Axis -0.95773994 -0.09835224 -0.27029808
Axis point 0.00000000 95.35295453 38.48270608
Rotation angle (degrees) 136.25066285
Shift along axis -222.39137898
> volume #64 level 0.06502
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J416_008_volume_map.mrc
Opened cryosparc_P207_J416_008_volume_map.mrc as #65, grid size 480,480,480,
pixel 0.647, shown at level 0.0289, step 2, values float32
> volume #65 step 1
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J418_006_volume_map.mrc
Opened cryosparc_P207_J418_006_volume_map.mrc as #66, grid size 480,480,480,
pixel 0.647, shown at level 0.0281, step 2, values float32
> volume #66 step 1
> volume #66 level 0.06117
> transparency #64.1#66.1 0
> transparency #64.1#66.1 50
> volume #66 level 0.06078
> save "/Users/zmotiwal@amgen.com/OneDrive -
> Amgen/Projects/GPR75/Processing_FITC_S1/20251017_v1.cxs" includeMaps true
> close #1
> close #2
> close #3
> close #4
> close #5
> close #6
> close #11
> close #14
> close #16
> close #17
> close #18
> close #19
> close #20
> close #23
> close #21
> close #22
> close #25
> close #26
> close #28
> close #31
> close #33
> volume #34 level 0.05589
> close #34
> close #35
> close #36
> close #37
> close #38
> close #39
> close #40
> close #41
> close #42
> close #44
> close #45
> close #47
> close #48
> close #49
> close #50
> close #51
> close #52
> close #54
> close #55
> close #56
> close #57
> close #58
> close #59
> close #62
> close #63
> close #65
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #7 models
> show #7 models
> save "/Users/zmotiwal@amgen.com/OneDrive -
> Amgen/Projects/GPR75/Processing_FITC_S1/20251017_v1.cxs" includeMaps true
> hide #7 models
> show #7 models
> select add #7
4169 atoms, 4270 bonds, 540 residues, 1 model selected
> select subtract #7
Nothing selected
> select /A:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:24-67,70-72,78-106,115-147,158-182,201-237,299-346,352-379,381-399
2080 atoms, 2119 bonds, 266 residues, 1 model selected
> select /A:24-237
1658 atoms, 1696 bonds, 214 residues, 1 model selected
> select /A:24-67,70-72,78-106,115-147,158-182,201-237,299-346,352-379,381-399
2080 atoms, 2119 bonds, 266 residues, 1 model selected
> select /A:24-237,299-399
2438 atoms, 2491 bonds, 315 residues, 1 model selected
> molmap sel 15 onGrid #66
Opened AF-O95800-F1-model_v4.pdb map 15 as #1, grid size 480,480,480, pixel
0.647, shown at level 0.0319, step 1, values float32
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #66 level 0.05408
> select /A:24-237,299-399,472-539
2974 atoms, 3043 bonds, 383 residues, 1 model selected
> molmap sel 15 onGrid #66
Opened AF-O95800-F1-model_v4.pdb map 15 as #2, grid size 480,480,480, pixel
0.647, shown at level 0.0239, step 1, values float32
> hide #!2 models
> select /A:24-237,299-399,472-500
2667 atoms, 2726 bonds, 344 residues, 1 model selected
> volume #66 level 0.04659
> select /A:24-237,299-399,472-520
2828 atoms, 2894 bonds, 364 residues, 1 model selected
> select /A:24-237,299-399,472-520
2828 atoms, 2894 bonds, 364 residues, 1 model selected
> molmap sel 15 onGrid #66
Opened AF-O95800-F1-model_v4.pdb map 15 as #3, grid size 480,480,480, pixel
0.647, shown at level 0.0264, step 1, values float32
> close #2
> close #1
> volume #66 level 0.06196
> volume #3 level 0.001
> volume #3 level 0.005
> volume #3 level 0.0001
> volume #3 level 0.005
> volume #3 level 0.001
> volume #3 level 0.005
> volume #3 level 0.001
> volume #3 level 0.0001
> volume #3 level 0.001
> volume #3 level 0.005
> volume #3 level 0.03311
> volume #3 level 0.005
> save "/Users/zmotiwal@amgen.com/OneDrive -
> Amgen/Projects/GPR75/Processing_FITC_S1/FocusMaskonJ418_0pt005.mrc" models
> #3
> save "/Users/zmotiwal@amgen.com/OneDrive -
> Amgen/Projects/GPR75/Processing_FITC_S1/20251017_v1.cxs" includeMaps true
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J418_006_volume_mask_refine.mrc
Opened cryosparc_P207_J418_006_volume_mask_refine.mrc as #1, grid size
480,480,480, pixel 0.647, shown at level 1, step 2, values float32
> volume #1 level 1
> volume #1 level 0.99
> volume #1 step 1
> hide #!3 models
> show #!3 models
> hide #!66 models
> show #!66 models
> hide #!66 models
> show #!66 models
> hide #!1 models
> show #!1 models
> volume subtract #1 #3 onGrid #1
Opened volume difference as #2, grid size 480,480,480, pixel 0.647, shown at
step 1, values float32
> save "/Users/zmotiwal@amgen.com/OneDrive -
> Amgen/Projects/GPR75/Processing_FITC_S1/SubMaskonJ418_0pt99.mrc" models #2
> hide #!2 models
> select add #7
4169 atoms, 4270 bonds, 540 residues, 1 model selected
> select subtract #7
Nothing selected
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J441_006_volume_map.mrc
Opened cryosparc_P207_J441_006_volume_map.mrc as #4, grid size 480,480,480,
pixel 0.647, shown at level 0.0275, step 2, values float32
> volume #4 step 1
> volume #4 level 0.06207
> transparency #4.1#66.1 0
> transparency #4.1#66.1 50
> hide #!66 models
> volume #4 level 0.06057
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J446_006_volume_map.mrc
Opened cryosparc_P207_J446_006_volume_map.mrc as #5, grid size 480,480,480,
pixel 0.647, shown at level 0.0276, step 2, values float32
> volume #5 step 1
> volume #5 level 0.05571
> transparency #5.1 50
> volume #5 level 0.06092
> volume #5 level 0.06665
> volume #5 level 0.05518
> volume #5 level 0.04215
> volume #5 level 0.0531
> volume #5 level 0.06352
> volume #5 level 0.06404
> volume #5 level 0.03694
> volume #5 level 0.03225
> volume #5 level 0.05049
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> volume #5 level 0.06457
> volume #5 level 0.05571
> volume #5 level 0.06404
> volume #5 level 0.05362
> volume #5 level 0.04476
> volume #5 level 0.03851
> volume #5 level 0.06509
> hide #!5 models
> show #!66 models
> volume #66 level 0.06984
> volume #66 level 0.03911
> volume #66 level 0.03438
> volume #66 level 0.06078
> surface dust #66 size 6.47
[Repeated 2 time(s)]
> volume #66 level 0.04581
> hide #!66 models
> show #!66 models
> show #!64 models
> hide #!66 models
> show #!66 models
> hide #!64 models
> show #!64 models
> hide #!66 models
> volume #64 level 0.0454
> hide #!64 models
> show #!66 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> select add #7
4169 atoms, 4270 bonds, 540 residues, 1 model selected
> select subtract #7
Nothing selected
> volume #!66 hide
> volume show
[Repeated 1 time(s)]
> volume hide
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!66 models
> volume #66 level 0.05605
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J460_006_volume_map.mrc
Opened cryosparc_P207_J460_006_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.647, shown at level 0.0276, step 2, values float32
> volume #64 level 0.05679
> volume #6 step 1
> volume #6 level 0.0354
> transparency #6.1#66.1 0
> transparency #6.1#66.1 50
> volume #6 level 0.03881
> select /A:71
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:71-77
65 atoms, 66 bonds, 7 residues, 1 model selected
> select /A:68
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:68-76
84 atoms, 87 bonds, 9 residues, 1 model selected
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J460_006_volume_map_sharp.mrc
Opened cryosparc_P207_J460_006_volume_map_sharp.mrc as #11, grid size
480,480,480, pixel 0.647, shown at level 0.0273, step 2, values float32
> volume #11 step 1
> transparency #11.1 50
> volume #11 level 0.04411
> volume #11 level 0.04115
> volume #11 color #d6d6d6
> volume #11 color #d6d6d653
> volume #11 color #d6d6d644
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J458_012_volume_map_sharp.mrc
Opened cryosparc_P207_J458_012_volume_map_sharp.mrc as #14, grid size
480,480,480, pixel 0.647, shown at level 0.0273, step 2, values float32
> transparency #11.1#14.1 0
> transparency #11.1#14.1 50
> volume #14 step 1
> volume #14 level 0.05482
> volume #14 level 0.04847
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J464_007_volume_map_sharp.mrc
Opened cryosparc_P207_J464_007_volume_map_sharp.mrc as #16, grid size
480,480,480, pixel 0.647, shown at level 0.0111, step 2, values float32
> volume #16 step 1
> transparency #14.1#16.1 0
> transparency #14.1#16.1 50
> volume #16 level 0.01406
> volume #16 level 0.01796
> volume #16 level 0.01926
> save "/Users/zmotiwal@amgen.com/OneDrive -
> Amgen/Projects/GPR75/Processing_FITC_S1/20251017_v2.cxs"
> volume #16 level 0.02966
> volume #16 level 0.02414
> volume #16 level 0.01991
> ui tool show "Map Eraser"
> volume #16 level 0.01178
> volume erase #16 center 155.37,157.36,174.58 radius 28.572 outside true
Opened cryosparc_P207_J464_007_volume_map_sharp.mrc copy as #18, grid size
480,480,480, pixel 0.647, shown at step 1, values float32
> volume #18 level 0.0087
> volume #18 level 0.001
> volume #18 level 0.0001
> volume #18 level 0.001
> volume #18 level 0.01
> volume #18 level 0.05
> volume #18 level 0.01
> volume #18 level 0.02
> volume #18 level 0.01
> volume #18 level 0.005
> volume #18 level 0.008
> volume #18 level 0
> volume #18 level 0.008
> volume #18 level 0.001
> volume #18 level 0.01
No map chosen to save
> save "/Users/zmotiwal@amgen.com/OneDrive -
> Amgen/Projects/GPR75/Processing_FITC_S1/FocusMaskonJ464_0pt01-Sphere.mrc"
> models #18
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J464_007_volume_mask_refine.mrc
Opened cryosparc_P207_J464_007_volume_mask_refine.mrc as #19, grid size
480,480,480, pixel 0.647, shown at level 1, step 2, values float32
> volume #19 step 1
> volume #19 level 1
> save "/Users/zmotiwal@amgen.com/OneDrive -
> Amgen/Projects/GPR75/Processing_FITC_S1/20251017_v2.cxs" includeMaps true
> volume subtract #19 #18 onGrid #19
Opened volume difference as #20, grid size 480,480,480, pixel 0.647, shown at
step 1, values float32
> volume #20 level 0.9948
> volume #20 level 0.999
No map chosen to save
> save "/Users/zmotiwal@amgen.com/OneDrive -
> Amgen/Projects/GPR75/Processing_FITC_S1/SubMaskonJ464-Sphere_0pt999.mrc"
> models #20
> show #!61 models
> hide #!61 models
> show #!61 models
> hide #!61 models
> show #!60 models
> open "/Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J210_008_volume_map
> (1).mrc"
Opened cryosparc_P207_J210_008_volume_map (1).mrc as #21, grid size
480,480,480, pixel 0.647, shown at level 0.00928, step 2, values float32
> volume #21 step 1
> volume #21 level 0.0167
> transparency #21.1 50
> volume #21 level 0.02372
> fitmap #7 inMap #21
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P207_J210_008_volume_map (1).mrc (#21) using 4169 atoms
average map value = 0.01608, steps = 120
shifted from previous position = 3.36
rotated from previous position = 8.56 degrees
atoms outside contour = 2833, contour level = 0.023724
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P207_J210_008_volume_map (1).mrc (#21) coordinates:
Matrix rotation and translation
0.86022416 0.32620280 0.39192617 161.94936217
-0.12091463 -0.61619644 0.77825549 154.43624105
0.49537263 -0.71686378 -0.49062437 177.79984034
Axis -0.95597800 -0.06614358 -0.28588651
Axis point 0.00000000 100.86408896 29.37089656
Rotation angle (degrees) 128.55739759
Shift along axis -215.86556827
> volume #21 level 0.02646
> volume #21 level 0.02021
> volume #21 level 0.02685
> save "/Users/zmotiwal@amgen.com/OneDrive -
> Amgen/Projects/GPR75/Processing_FITC_S1/20251017_v2.cxs" includeMaps true
> hide #!21 models
> show #!21 models
> hide #!18 models
> volume #21 level 0.02177
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> hide #!21 models
> show #!21 models
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> volume erase #21 center 152.6,166.94,164.02 radius 27.174 outside true
Opened cryosparc_P207_J210_008_volume_map (1).mrc copy as #22, grid size
480,480,480, pixel 0.647, shown at step 1, values float32
> hide #17 models
> volume #22 level 0.02461
> volume #22 level 0.01823
> volume #22 level 0.02201
> volume #22 level 0.01988
> volume erase #22 center 179.53,160.53,154.19 radius 12.578
[Repeated 1 time(s)]
> volume erase #22 center 175.86,177.25,167.92 radius 12.578
> volume erase #22 center 157.79,148.74,141.18 radius 12.578
> volume erase #22 center 163.2,148.11,140.7 radius 12.578
[Repeated 1 time(s)]
> volume erase #22 center 176.39,175.95,156.11 radius 12.578
[Repeated 1 time(s)]
> save "/Users/zmotiwal@amgen.com/OneDrive -
> Amgen/Projects/GPR75/Processing_FITC_S1/FocusMaskonJ210_0pt0199-Sphere.mrc"
> models #22
> open /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J474_mask.mrc
Opened cryosparc_P207_J474_mask.mrc as #17, grid size 480,480,480, pixel
0.647, shown at level 5e-05, step 2, values float32
> volume #17 step 1
> volume #17 level 0.9686
> volume #17 level 0.9908
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J479_006_volume_map_sharp.mrc
Opened cryosparc_P207_J479_006_volume_map_sharp.mrc as #23, grid size
480,480,480, pixel 0.647, shown at level 0.0256, step 2, values float32
> volume #23 step 1
> volume #23 level 0.06381
> transparency #23.1 50
> fitmap #7 inMap #23
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P207_J479_006_volume_map_sharp.mrc (#23) using 4169 atoms
average map value = 0.0481, steps = 176
shifted from previous position = 3.12
rotated from previous position = 9.92 degrees
atoms outside contour = 2743, contour level = 0.063813
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P207_J479_006_volume_map_sharp.mrc (#23) coordinates:
Matrix rotation and translation
0.85463833 0.36480127 0.36947715 165.10798333
0.00035712 -0.71200804 0.70217122 157.38700494
0.51922365 -0.59997049 -0.60863964 180.33924656
Axis -0.95714241 -0.11007153 -0.26788555
Axis point 0.00000000 93.89157035 39.84123969
Rotation angle (degrees) 137.13888153
Shift along axis -223.66595874
> volume #23 level 0.1066
> volume #23 level 0.08976
> volume #23 level 0.07603
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J480_006_volume_map_sharp.mrc
Opened cryosparc_P207_J480_006_volume_map_sharp.mrc as #25, grid size
480,480,480, pixel 0.647, shown at level 0.026, step 2, values float32
> volume #25 step 1
> volume #25 level 0.07493
> transparency #25.1 50
> volume #25 level 0.07027
> volume #25 level 0.09126
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J469_005_volume_map_sharp.mrc
Opened cryosparc_P207_J469_005_volume_map_sharp.mrc as #26, grid size
480,480,480, pixel 0.647, shown at level 0.00943, step 2, values float32
> volume #26 step 1
> volume #26 level 0.05413
> transparency #26.1 50
> volume #26 level 0.04692
> volume #26 level 0.06855
> close #26
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J469_005_volume_map.mrc
Opened cryosparc_P207_J469_005_volume_map.mrc as #26, grid size 480,480,480,
pixel 0.647, shown at level 0.00916, step 2, values float32
> volume #26 step 1
> transparency #26.1 50
> volume #26 level 0.01842
> volume #26 level 0.02445
> close #26
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J482_003_volume_map.mrc
Opened cryosparc_P207_J482_003_volume_map.mrc as #26, grid size 480,480,480,
pixel 0.647, shown at level 0.0109, step 2, values float32
> volume #26 step 1
> volume #26 level 0.02188
> transparency #26.1 50
> volume #26 level 0.02157
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J482_003_volume_map_sharp.mrc
Opened cryosparc_P207_J482_003_volume_map_sharp.mrc as #28, grid size
480,480,480, pixel 0.647, shown at level 0.0106, step 2, values float32
> volume #28 step 1
> volume #28 level 0.04328
> transparency #28.1 50
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J481_012_volume_map_sharp.mrc
Opened cryosparc_P207_J481_012_volume_map_sharp.mrc as #31, grid size
480,480,480, pixel 0.647, shown at level 0.00899, step 2, values float32
> volume #31 step 1
> volume #31 level 0.04927
> transparency #28.1#31.1 0
> transparency #28.1#31.1 50
> fitmap #7 inMap #31
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P207_J481_012_volume_map_sharp.mrc (#31) using 4169 atoms
average map value = 0.0166, steps = 164
shifted from previous position = 3.22
rotated from previous position = 8.8 degrees
atoms outside contour = 3750, contour level = 0.049266
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P207_J481_012_volume_map_sharp.mrc (#31) coordinates:
Matrix rotation and translation
0.85107268 0.34101950 0.39922549 161.86376009
-0.10920730 -0.62875698 0.76989508 154.31886150
0.51356504 -0.69883501 -0.49787607 177.85708626
Axis -0.95345035 -0.07422541 -0.29227215
Axis point 0.00000000 99.02556723 30.04760157
Rotation angle (degrees) 129.62649155
Shift along axis -217.76611298
> fitmap #7 inMap #28
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P207_J482_003_volume_map_sharp.mrc (#28) using 4169 atoms
average map value = 0.02399, steps = 140
shifted from previous position = 3.82
rotated from previous position = 8.29 degrees
atoms outside contour = 3130, contour level = 0.043284
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P207_J482_003_volume_map_sharp.mrc (#28) coordinates:
Matrix rotation and translation
0.86497601 0.33986107 0.36920313 165.51122452
-0.01844813 -0.71370438 0.70020406 156.81560890
0.50147399 -0.61247082 -0.61106737 180.96290939
Axis -0.96018063 -0.09675200 -0.26209198
Axis point 0.00000000 95.35825183 40.03536432
Rotation angle (degrees) 136.87783259
Shift along axis -221.52182328
> fitmap #7 inMap #31
Fit molecule AF-O95800-F1-model_v4.pdb (#7) to map
cryosparc_P207_J481_012_volume_map_sharp.mrc (#31) using 4169 atoms
average map value = 0.0166, steps = 196
shifted from previous position = 3.82
rotated from previous position = 8.29 degrees
atoms outside contour = 3750, contour level = 0.049266
Position of AF-O95800-F1-model_v4.pdb (#7) relative to
cryosparc_P207_J481_012_volume_map_sharp.mrc (#31) coordinates:
Matrix rotation and translation
0.85106915 0.34113489 0.39913443 161.85257062
-0.10911335 -0.62867154 0.76997817 154.32211835
0.51359087 -0.69885556 -0.49782058 177.86362856
Axis -0.95344722 -0.07429580 -0.29226448
Axis point 0.00000000 99.02698141 30.05208559
Rotation angle (degrees) 129.62138143
Shift along axis -217.76659011
> volume #31 level 0.02913
> volume #31 level 0.04121
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J481_012_volume_map.mrc
Opened cryosparc_P207_J481_012_volume_map.mrc as #33, grid size 480,480,480,
pixel 0.647, shown at level 0.00882, step 2, values float32
> close #31
> volume #33 step 1
> volume #33 level 0.03086
> transparency #33.1 50
> close #33
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J483_006_volume_map.mrc
Opened cryosparc_P207_J483_006_volume_map.mrc as #31, grid size 480,480,480,
pixel 0.647, shown at level 0.00972, step 2, values float32
> volume #31 step 1
> volume #31 level 0.02021
> transparency #28.1#31.1 0
> transparency #28.1#31.1 50
> volume #31 level 0.02564
> volume #31 level 0.026
> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P207_J483_006_volume_map_sharp.mrc
Opened cryosparc_P207_J483_006_volume_map_sharp.mrc as #33, grid size
480,480,480, pixel 0.647, shown at level 0.00946, step 2, values float32
> volume #33 step 1
> volume #33 level 0.03341
> transparency #31.1#33.1 0
> transparency #31.1#33.1 50
> volume #33 level 0.04212
> volume #33 level 0.02906
> show #!16 models
> show #!19 models
> hide #!19 models
> volume #18 level 0.01545
> volume #18 level 0.01995
> volume #18 level 0.02871
> volume #18 level 0.01237
> hide #!18 models
> show #!18 models
> hide #!18 models
> volume #16 level 0.01698
> show sel atoms
> volume #16 level 0.01406
> volume #16 level 0.01666
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/zmotiwal@amgen.com/Desktop/movie3.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 - 89.4
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: Mac15,6
Model Number: Z1AY001HWLL/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 23 days, 7 hours, 13 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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 (2)
comment:1 by , 2 days ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Build System |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ffmpeg: Permission denied |
comment:2 by , 2 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Hi Zenia,
--Eric