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Opened 3 years ago
Last modified 3 years ago
#8825 closed defect
Overlay model in hierarchy — at Version 1
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | Eric Pettersen, Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-
> PCNA_dssp_v14.cxs"
Opened Apo_P29_J632_004.mrc as #1.1, grid size 420,420,420, pixel 0.828, shown
at level 0.25, step 1, values float32
Opened Closed_P29_J651_004.mrc as #1.2, grid size 420,420,420, pixel 0.828,
shown at level 0.25, step 1, values float32
Opened Open_P29_J701_004.mrc as #1.3, grid size 420,420,420, pixel 0.828,
shown at level 0.2, step 1, values float32
Log from Sat Feb 18 16:30:50 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-
> PCNA_dssp_v13.cxs" format session
Opened Apo_P29_J632_004.mrc as #1.1, grid size 420,420,420, pixel 0.828, shown
at level 0.25, step 1, values float32
Opened Closed_P29_J651_004.mrc as #1.2, grid size 420,420,420, pixel 0.828,
shown at level 0.25, step 1, values float32
Opened Open_P29_J701_004.mrc as #1.3, grid size 420,420,420, pixel 0.828,
shown at level 0.2, step 1, values float32
Log from Fri Feb 10 12:12:25 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v9.cxs" format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish_5ntGap_P43_J266_sharp.mrc as #1.6, grid size 420,420,420, pixel
0.828, shown at level 0.09, step 2, values float32
Opened cryosparc_P29_J632_004_volume_map_sharp.mrc as #5.1, grid size
420,420,420, pixel 0.828, shown at level 0.28, step 1, values float32
Opened cryosparc_P29_J677_003_volume_map_sharp.mrc as #5.2, grid size
420,420,420, pixel 0.828, shown at level 0.15, step 1, values float32
Opened cryosparc_P29_J701_004_volume_map_sharp.mrc as #5.3, grid size
420,420,420, pixel 0.828, shown at level 0.2, step 1, values float32
Log from Thu Feb 2 14:25:37 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v8.cxs" format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish_5ntGap_P43_J266_sharp.mrc as #1.6, grid size 420,420,420, pixel
0.828, shown at level 0.09, step 2, values float32
Opened cryosparc_P29_J632_004_volume_map_sharp.mrc as #5.1, grid size
420,420,420, pixel 0.828, shown at level 0.28, step 1, values float32
Opened cryosparc_P29_J677_003_volume_map_sharp.mrc as #5.2, grid size
420,420,420, pixel 0.828, shown at level 0.15, step 1, values float32
Opened cryosparc_P29_J701_004_volume_map_sharp.mrc as #5.3, grid size
420,420,420, pixel 0.828, shown at level 0.2, step 1, values float32
Log from Thu Jan 12 10:32:45 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v7.cxs"
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish_5ntGap_P43_J266_sharp.mrc as #1.6, grid size 420,420,420, pixel
0.828, shown at level 0.09, step 2, values float32
Log from Tue Dec 6 12:15:53 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v4.cxs" format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish_5ntGap_P43_J266_sharp.mrc as #1.6, grid size 420,420,420, pixel
0.828, shown at level 0.09, step 2, values float32
Log from Tue Dec 6 11:47:28 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v17-Models-Compare.cxs"
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish_5ntGap_P43_J266_sharp.mrc as #1.6, grid size 420,420,420, pixel
0.828, shown at level 0.09, step 2, values float32
Log from Mon Nov 14 16:55:53 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v16-Models-Compare.cxs"
> format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish_5ntGap_P43_J266_sharp.mrc as #1.6, grid size 420,420,420, pixel
0.828, shown at level 0.2, step 2, values float32
Log from Mon Nov 14 16:29:22 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v15-Models-Compare.cxs"
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Tue Jul 5 16:32:16 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/S4-v3.cxs" format
> session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Mon Jul 4 15:09:05 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/S4-v2.cxs" format
> session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Fri Jul 1 16:33:56 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v13-Models-Compare.cxs"
> format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Wed Jun 29 11:45:15 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v14-Models-Compare.cxs"
> format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Wed Jun 29 11:25:52 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v13-Models-Compare.cxs"
> format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Wed Jun 29 10:57:53 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/0-used/Fig3-focusDNA-v11.cxs"
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Mon Jun 6 17:25:34 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs"
> format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Mon Jun 6 16:50:44 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs"
> format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Mon Jun 6 14:52:02 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v9.cxs"
> format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Tue May 31 15:25:24 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v5.cxs"
> format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Fri May 27 10:46:01 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-v1.cxs" format
> session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Thu May 26 14:32:30 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_2/Fig2-1.cxs"
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Tue May 24 12:29:31 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_1/Fig1b-3.cxs" format
> session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.175, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Mon May 23 16:17:23 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_1/Fig1-v1.cxs" format
> session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Mon May 23 15:10:58 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v11-M-M-color-SS
> assigned.cxs" format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Mon May 23 12:04:10 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v4-maps-models.cxs" format
> session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1.1, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #1.2, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #1.3, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #1.4, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #1.5, grid size 420,420,420,
pixel 0.828, shown at level 0.2, step 1, values float32
Log from Thu May 19 16:17:48 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v3-maps-models.cxs"
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1, grid size 420,420,420, pixel
0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #2, grid size 420,420,420, pixel
0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #3, grid size 420,420,420, pixel
0.828, shown at level 0.2, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #4, grid size 420,420,420, pixel
0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #5, grid size 420,420,420, pixel
0.828, shown at level 0.2, step 1, values float32
Log from Thu May 19 12:06:54 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v2.cxs" format session
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1, grid size 420,420,420, pixel
0.828, shown at level 0.2, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #2, grid size 420,420,420, pixel
0.828, shown at level 0.2, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #3, grid size 420,420,420, pixel
0.828, shown at level 0.2, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #4, grid size 420,420,420, pixel
0.828, shown at level 0.2, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #5, grid size 420,420,420, pixel
0.828, shown at level 0.2, step 1, values float32
Log from Thu May 19 10:48:15 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/ScRR91-10nt/Overall-v1.cxs"
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1, grid size 420,420,420, pixel
0.828, shown at level 0.12, step 1, values float32
Opened polish-stat2-cs_P24_J258_sharp.mrc as #2, grid size 420,420,420, pixel
0.828, shown at level 0.12, step 1, values float32
Opened polish-stat3-cs_P24_J259_sharp.mrc as #3, grid size 420,420,420, pixel
0.828, shown at level 0.12, step 1, values float32
Opened polish-stat4-cs_P24_J260_sharp.mrc as #4, grid size 420,420,420, pixel
0.828, shown at level 0.12, step 1, values float32
Opened polish-stat5-cs_P24_J261_sharp.mrc as #5, grid size 420,420,420, pixel
0.828, shown at level 0.12, step 1, values float32
Log from Wed May 18 16:38:49 2022 Startup Messages
---
warnings | No presets found in custom preset folder
/Users/fengwei.zheng/Documents/Draft_PolD/manuscript
No presets found in custom preset folder
/Users/fengwei.zheng/Documents/Draft_PolD/Figure
No presets found in custom preset folder
/Users/fengwei.zheng/Documents/Draft_PolD/PolD-review
No presets found in custom preset folder
/Users/fengwei.zheng/Documents/Draft_PolD/Session
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/ScRR91-10nt/0_MM/polish-
> stat1-cs_P24_J252_sharp.mrc"
Opened polish-stat1-cs_P24_J252_sharp.mrc as #1, grid size 420,420,420, pixel
0.828, shown at level 0.0691, step 2, values float32
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/ScRR91-10nt/0_MM/polish-
> stat2-cs_P24_J258_sharp.mrc"
Opened polish-stat2-cs_P24_J258_sharp.mrc as #2, grid size 420,420,420, pixel
0.828, shown at level 0.0607, step 2, values float32
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/ScRR91-10nt/0_MM/polish-
> stat3-cs_P24_J259_sharp.mrc"
Opened polish-stat3-cs_P24_J259_sharp.mrc as #3, grid size 420,420,420, pixel
0.828, shown at level 0.109, step 2, values float32
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/ScRR91-10nt/0_MM/polish-
> stat4-cs_P24_J260_sharp.mrc"
Opened polish-stat4-cs_P24_J260_sharp.mrc as #4, grid size 420,420,420, pixel
0.828, shown at level 0.0981, step 2, values float32
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/ScRR91-10nt/0_MM/polish-
> stat5-cs_P24_J261_sharp.mrc"
Opened polish-stat5-cs_P24_J261_sharp.mrc as #5, grid size 420,420,420, pixel
0.828, shown at level 0.109, step 2, values float32
> surface hidePatches #0-9 size 10
Expected a keyword
> surface dust #0-9 size 10
> volume #0-9 step 1 level 0.12
> fitmap #0-4 inMap #5
Multiple maps for #0-4
> fitmap #0 inMap #5
No atoms or maps for #0
> fitmap #0 into #5
Expected a keyword
> fitmap #0 inMap #5
No atoms or maps for #0
> fitmap #1 inMap #5
Fit map polish-stat1-cs_P24_J252_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 298859 points
correlation = 0.8628, correlation about mean = 0.7346, overlap = 3.617e+04
steps = 100, shift = 1.99, angle = 3.16 degrees
Position of polish-stat1-cs_P24_J252_sharp.mrc (#1) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99869014 0.02395107 0.04521441 -11.99555770
-0.02487573 0.99949047 0.01999985 1.05709615
-0.04471235 -0.02109839 0.99877708 13.57181162
Axis -0.37269835 0.81549845 -0.44278461
Axis point 289.19774714 0.00000000 279.25909904
Rotation angle (degrees) 3.16066681
Shift along axis -0.67660446
> fitmap #2 inMap #5
Fit map polish-stat2-cs_P24_J258_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 236547 points
correlation = 0.8728, correlation about mean = 0.7147, overlap = 2.888e+04
steps = 204, shift = 4.33, angle = 10.7 degrees
Position of polish-stat2-cs_P24_J258_sharp.mrc (#2) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.98276280 0.09477082 0.15873177 -43.51303304
-0.09468661 0.99547409 -0.00811065 18.40164401
-0.15878202 -0.00705893 0.98728843 34.87375114
Axis 0.00284446 0.85874076 -0.51240239
Axis point 188.97694280 0.00000000 294.61169144
Rotation angle (degrees) 10.65365418
Shift along axis -2.19092257
> fitmap #3 inMap #5
Fit map polish-stat3-cs_P24_J259_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 555341 points
correlation = 0.8502, correlation about mean = 0.8187, overlap = 4.953e+04
steps = 220, shift = 2.16, angle = 10.7 degrees
Position of polish-stat3-cs_P24_J259_sharp.mrc (#3) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.98257101 0.13422036 0.12860443 -42.92958717
-0.13439642 0.99090040 -0.00734796 24.95916960
-0.12842043 -0.01006408 0.99166875 27.22762933
Axis -0.00730562 0.69132649 -0.72250558
Axis point 173.34604304 342.46816394 0.00000000
Rotation angle (degrees) 10.71317352
Shift along axis -2.10355172
> fitmap #4 inMap #5
Fit map polish-stat4-cs_P24_J260_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 410574 points
correlation = 0.8805, correlation about mean = 0.8253, overlap = 4.235e+04
steps = 180, shift = 0.467, angle = 9.67 degrees
Position of polish-stat4-cs_P24_J260_sharp.mrc (#4) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.98611068 0.14583526 0.07948460 -36.99899607
-0.14377499 0.98912206 -0.03108553 32.48843896
-0.08315334 0.01922587 0.99635129 11.85475921
Axis 0.14976255 0.48412633 -0.86208635
Axis point 205.40357915 273.23338169 0.00000000
Rotation angle (degrees) 9.66984417
Shift along axis -0.03238136
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/ScRR91-10nt/Overall-v1.cxs"
——— End of log from Wed May 18 16:38:49 2022 ———
opened ChimeraX session
> volume #0-9 step 2 level 0.15
> volume #0-9 step 1 level 0.15
> fitmap #1 inMap #5
Fit map polish-stat1-cs_P24_J252_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 232532 points
correlation = 0.8798, correlation about mean = 0.7194, overlap = 3.55e+04
steps = 28, shift = 0.0139, angle = 0.00431 degrees
Position of polish-stat1-cs_P24_J252_sharp.mrc (#1) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99869069 0.02388653 0.04523659 -11.99847626
-0.02481034 0.99949267 0.01997134 1.04682350
-0.04473659 -0.02106753 0.99877665 13.56202997
Axis -0.37230073 0.81622817 -0.44177341
Axis point 288.90562138 0.00000000 279.11329471
Rotation angle (degrees) 3.15946993
Shift along axis -0.66985591
> fitmap #2 inMap #5
Fit map polish-stat2-cs_P24_J258_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 188644 points
correlation = 0.8896, correlation about mean = 0.707, overlap = 2.815e+04
steps = 36, shift = 0.0136, angle = 0.014 degrees
Position of polish-stat2-cs_P24_J258_sharp.mrc (#2) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.98280664 0.09459975 0.15856226 -43.45125592
-0.09451836 0.99549040 -0.00807176 18.36869397
-0.15861079 -0.00705406 0.98731599 34.84797917
Axis 0.00275593 0.85890300 -0.51213088
Axis point 189.08692708 0.00000000 294.49795119
Rotation angle (degrees) 10.64005453
Shift along axis -2.18954841
> fitmap #3 inMap #5
Fit map polish-stat3-cs_P24_J259_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 319391 points
correlation = 0.8817, correlation about mean = 0.7855, overlap = 4.903e+04
steps = 40, shift = 0.0162, angle = 0.00392 degrees
Position of polish-stat3-cs_P24_J259_sharp.mrc (#3) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.98255840 0.13426795 0.12865115 -42.95275035
-0.13444303 0.99089397 -0.00736236 24.95920889
-0.12846818 -0.01006231 0.99166258 27.22955953
Axis -0.00725952 0.69133280 -0.72250000
Axis point 173.28076624 342.52654523 0.00000000
Rotation angle (degrees) 10.71705821
Shift along axis -2.10642050
> fitmap #4 inMap #5
Fit map polish-stat4-cs_P24_J260_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 262070 points
correlation = 0.9069, correlation about mean = 0.7921, overlap = 4.171e+04
steps = 28, shift = 0.0188, angle = 0.00568 degrees
Position of polish-stat4-cs_P24_J260_sharp.mrc (#4) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.98612655 0.14576388 0.07941869 -36.96642423
-0.14370610 0.98913261 -0.03106838 32.48117544
-0.08308426 0.01922440 0.99635708 11.85399935
Axis 0.14979143 0.48399690 -0.86215401
Axis point 205.49334666 273.12574979 0.00000000
Rotation angle (degrees) 9.66434956
Shift along axis -0.03643827
> hide #!2 models
> hide #!3 models
> hide #!4 models
> volume #0-9 step 1 level 0.2
> fitmap #1 inMap #5
Fit map polish-stat1-cs_P24_J252_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 171098 points
correlation = 0.9011, correlation about mean = 0.7042, overlap = 3.417e+04
steps = 28, shift = 0.00298, angle = 0.00569 degrees
Position of polish-stat1-cs_P24_J252_sharp.mrc (#1) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99869255 0.02379239 0.04524500 -11.98531631
-0.02471512 0.99949555 0.01994505 1.03287798
-0.04474764 -0.02103721 0.99877679 13.55717977
Axis -0.37208657 0.81706224 -0.44040989
Axis point 288.78365592 0.00000000 278.73017318
Rotation angle (degrees) 3.15692509
Shift along axis -0.66721521
> fitmap #1 inMap #5
Fit map polish-stat1-cs_P24_J252_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 171098 points
correlation = 0.9012, correlation about mean = 0.7046, overlap = 3.417e+04
steps = 40, shift = 0.0115, angle = 0.00569 degrees
Position of polish-stat1-cs_P24_J252_sharp.mrc (#1) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99869687 0.02370865 0.04519361 -11.95437166
-0.02462977 0.99949786 0.01993475 1.02779771
-0.04469829 -0.02102188 0.99877933 13.54911814
Axis -0.37241605 0.81738143 -0.43953826
Axis point 289.00128287 0.00000000 278.31333202
Rotation angle (degrees) 3.15215479
Shift along axis -0.66325323
> hide #!1 models
> show #!2 models
> fitmap #2 inMap #5
Fit map polish-stat2-cs_P24_J258_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 138689 points
correlation = 0.9115, correlation about mean = 0.6945, overlap = 2.679e+04
steps = 36, shift = 0.00825, angle = 0.0259 degrees
Position of polish-stat2-cs_P24_J258_sharp.mrc (#2) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.98288207 0.09423494 0.15831176 -43.34976964
-0.09416590 0.99552474 -0.00795418 18.28517381
-0.15835283 -0.00708955 0.98735714 34.80986396
Axis 0.00234651 0.85939784 -0.51130212
Axis point 189.27332941 0.00000000 294.25867381
Rotation angle (degrees) 10.61661159
Shift along axis -2.18583875
> hide #!2 models
> show #!3 models
> fitmap #3 inMap #5
Fit map polish-stat3-cs_P24_J259_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 215387 points
correlation = 0.9024, correlation about mean = 0.7439, overlap = 4.798e+04
steps = 28, shift = 0.0102, angle = 0.00119 degrees
Position of polish-stat3-cs_P24_J259_sharp.mrc (#3) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.98255962 0.13426844 0.12864125 -42.94550654
-0.13444108 0.99089410 -0.00738045 24.96982143
-0.12846082 -0.01004294 0.99166373 27.22793937
Axis -0.00715905 0.69131105 -0.72252182
Axis point 173.35012147 342.47702980 0.00000000
Rotation angle (degrees) 10.71667190
Shift along axis -2.10341773
> hide #!3 models
> show #!4 models
> fitmap #3 inMap #5
Fit map polish-stat3-cs_P24_J259_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 215387 points
correlation = 0.9024, correlation about mean = 0.7441, overlap = 4.798e+04
steps = 28, shift = 0.0101, angle = 0.00975 degrees
Position of polish-stat3-cs_P24_J259_sharp.mrc (#3) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.98258937 0.13411580 0.12857325 -42.90523434
-0.13429069 0.99091474 -0.00734768 24.94045529
-0.12839057 -0.01004644 0.99167279 27.22035934
Axis -0.00726274 0.69152361 -0.72231734
Axis point 173.37668417 342.53314814 0.00000000
Rotation angle (degrees) 10.70750994
Shift along axis -2.10321438
> fitmap #4 inMap #5
Fit map polish-stat4-cs_P24_J260_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 186407 points
correlation = 0.9247, correlation about mean = 0.7591, overlap = 4.047e+04
steps = 40, shift = 0.011, angle = 0.00374 degrees
Position of polish-stat4-cs_P24_J260_sharp.mrc (#4) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.98613120 0.14571304 0.07945422 -36.96936656
-0.14365643 0.98914058 -0.03104429 32.46005321
-0.08311495 0.01919963 0.99635500 11.85709413
Axis 0.14967351 0.48428340 -0.86201359
Axis point 205.41802467 273.22957531 0.00000000
Rotation angle (degrees) 9.66255080
Shift along axis -0.03444617
> fitmap #4 inMap #5
Fit map polish-stat4-cs_P24_J260_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 186407 points
correlation = 0.9247, correlation about mean = 0.7591, overlap = 4.047e+04
steps = 28, shift = 0.0151, angle = 0.00235 degrees
Position of polish-stat4-cs_P24_J260_sharp.mrc (#4) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.98613557 0.14570408 0.07941642 -36.95320600
-0.14364720 0.98914156 -0.03105581 32.46896325
-0.08307904 0.01921729 0.99635765 11.85623466
Axis 0.14978141 0.48413162 -0.86208010
Axis point 205.50967675 273.13572274 0.00000000
Rotation angle (degrees) 9.66118481
Shift along axis -0.03667546
> hide #!5 models
> show #!3 models
> volume #0-9 step 1 level 0.1
> volume #0-9 step 1 level 0.2
> volume #0-9 step 1 level 0.12
> volume #0-9 step 1 level 0.15
> volume #0-9 step 1 level 0.12
> fitmap #3 inMap #4
Fit map polish-stat3-cs_P24_J259_sharp.mrc in map polish-
stat4-cs_P24_J260_sharp.mrc using 555341 points
correlation = 0.9181, correlation about mean = 0.9078, overlap = 4.916e+04
steps = 28, shift = 0.019, angle = 0.00749 degrees
Position of polish-stat3-cs_P24_J259_sharp.mrc (#3) relative to polish-
stat4-cs_P24_J260_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99892728 -0.00931263 0.04536031 -6.03469912
0.00792911 0.99950070 0.03058571 -8.02563753
-0.04562250 -0.03019323 0.99850236 15.07510675
Axis -0.54871201 0.82139247 0.15565841
Axis point 328.62582230 0.00000000 152.11301547
Rotation angle (degrees) 3.17485228
Shift along axis -0.93431924
> volume #0-9 step 1 level 0.15
> lighting simple
> hide #!3 models
> show #!5 models
> volume #0-9 step 1 level 0.2
> fitmap #4 inMap #5
Fit map polish-stat4-cs_P24_J260_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 186407 points
correlation = 0.9246, correlation about mean = 0.759, overlap = 4.047e+04
steps = 28, shift = 0.0203, angle = 0.00302 degrees
Position of polish-stat4-cs_P24_J260_sharp.mrc (#4) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.98612866 0.14572561 0.07946263 -36.97573506
-0.14366871 0.98913873 -0.03104623 32.45999541
-0.08312380 0.01919928 0.99635427 11.85555869
Axis 0.14966484 0.48429151 -0.86201054
Axis point 205.39163717 273.25176894 0.00000000
Rotation angle (degrees) 9.66342289
Shift along axis -0.03348377
[truncated to fit within ticket limits]
> hide #!1 models
> view position #6 sameAsModels #5
> show #!6 models
> color #6 #b2ffff84 models
> color #6 #b2ffff80 models
> color #6 #b2ffffff models
> hide #!6 models
> color sample #5 map #6 palette 2.5,blue:3.5,cyan:4.5,lime:5.5,yellow:6.5,red
Map values for surface "surface": minimum 2.789, mean 3.422, maximum 6.616
> rename #5-7 "Local Res" id #5
> hide #5.3 models
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/0-half/J677-Cplx-
> Closed/cryosparc_P29_J677_003_volume_map_sharp.mrc"
Opened cryosparc_P29_J677_003_volume_map_sharp.mrc as #6, grid size
420,420,420, pixel 0.828, shown at level 0.0613, step 2, values float32
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/0-half/J677-Cplx-
> Closed/cryosparc_P47_J330_map_locres.mrc"
Opened cryosparc_P47_J330_map_locres.mrc as #7, grid size 420,420,420, pixel
0.828, shown at level 6.08, step 2, values float32
> surface dust #0-9 size 10
> hide #!5 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> show #!6 models
> volume #6-7 step 1 level 0.25
> hide #!7 models
> volume #6-7 step 1 level 0.2
> volume #6-7 step 1 level 0.15
> hide #!6 models
> show #!1 models
> hide #!1.1 models
> show #!1.2 models
> hide #!1 models
> show #!6 models
> show #!7 models
> hide #!7 models
> volume #6 level 0.1
> color sample #6 map #7 palette 2.5,blue:3.5,cyan:4.5,lime:5.5,yellow:6.5,red
Map values for surface "surface": minimum 0, mean 3.964, maximum 37.77
> volume #6 level 0.15
> volume #6 level 0.175
> rename #6-7 id #5
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5.1 models
> show #!5.1 models
> hide #!5 models
> show #!5 models
> hide #!5.1 models
> show #!5.5 models
> color #5.5 #ffb2ff86 models
> color #5.5 #ffb2ffff models
> hide #!5.5 models
> show #!1 models
> fitmap #5.4 inMap #1.2
Fit map cryosparc_P29_J677_003_volume_map_sharp.mrc in map
Closed_P29_J651_004.mrc using 148240 points
correlation = 0.9837, correlation about mean = 0.9026, overlap = 3.669e+04
steps = 72, shift = 2.28, angle = 0.0815 degrees
Position of cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.4) relative to
Closed_P29_J651_004.mrc (#1.2) coordinates:
Matrix rotation and translation
0.99999900 -0.00008261 -0.00141238 0.57381699
0.00008281 0.99999999 0.00014151 -0.16140408
0.00141237 -0.00014162 0.99999899 -0.13693395
Axis -0.09956319 -0.99332941 0.05817086
Axis point 101.16985535 0.00000000 412.91663607
Rotation angle (degrees) 0.08146682
Shift along axis 0.09523081
> fitmap #5.4 inMap #1.2
Fit map cryosparc_P29_J677_003_volume_map_sharp.mrc in map
Closed_P29_J651_004.mrc using 148240 points
correlation = 0.9837, correlation about mean = 0.9026, overlap = 3.676e+04
steps = 44, shift = 0.0174, angle = 0.0137 degrees
Position of cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.4) relative to
Closed_P29_J651_004.mrc (#1.2) coordinates:
Matrix rotation and translation
0.99999869 -0.00003187 -0.00162028 0.59335413
0.00003227 0.99999997 0.00024834 -0.17479036
0.00162028 -0.00024839 0.99999866 -0.17058832
Axis -0.15148674 -0.98826577 0.01955864
Axis point 106.55316821 0.00000000 373.55206898
Rotation angle (degrees) 0.09393747
Shift along axis 0.07951757
> view position #5.5 sameAsModels #5.4
> show #!5.5 models
> color #5.5 #ffb2ffff models
> hide #!5.5 models
> fitmap #5.4 inMap #1.2
Fit map cryosparc_P29_J677_003_volume_map_sharp.mrc in map
Closed_P29_J651_004.mrc using 148240 points
correlation = 0.9837, correlation about mean = 0.9026, overlap = 3.675e+04
steps = 40, shift = 0.00322, angle = 0.00362 degrees
Position of cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.4) relative to
Closed_P29_J651_004.mrc (#1.2) coordinates:
Matrix rotation and translation
0.99999874 -0.00005250 -0.00158956 0.59195956
0.00005281 0.99999998 0.00019716 -0.16802029
0.00158955 -0.00019724 0.99999872 -0.17110435
Axis -0.12304903 -0.99185653 0.03285679
Axis point 109.77196826 0.00000000 379.14339327
Rotation angle (degrees) 0.09182277
Shift along axis 0.08819002
> color sample #5.5 map #1.2 palette
> 2.5,blue:3.5,cyan:4.5,lime:5.5,yellow:6.5,red
Map values for surface "surface": minimum -0.2242, mean -0.00374, maximum
0.2303
> hide #!5.4 models
> show #!5.5 models
> undo
[Repeated 1 time(s)]
> show #!5.5 models
> hide #!5.5 models
> show #!5.5 models
> hide #!5.5 models
> color sample #1.2 map #5.5 palette
> 2.5,blue:3.5,cyan:4.5,lime:5.5,yellow:6.5,red
Map values for surface "surface": minimum 0, mean 3.871, maximum 11.89
> hide #!5.4 models
> show #!5.4 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!5.4 models
> show #!5.4 models
> hide #!5.4 models
> show #!2 models
> fitmap #2.1 inMap #1.2
Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Closed_P29_J651_004.mrc (#1.2)
using 14334 atoms
average map value = 0.5937, steps = 40
shifted from previous position = 0.0553
rotated from previous position = 0.0748 degrees
atoms outside contour = 3298, contour level = 0.25
Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
-0.53184913 0.84069819 -0.10179912 138.41549107
-0.59446545 -0.45625438 -0.66215011 467.38614460
-0.60311469 -0.29164790 0.74242452 181.06436695
Axis 0.23678812 0.32039100 -0.91721371
Axis point 214.02368031 229.96468089 0.00000000
Rotation angle (degrees) 128.52378718
Shift along axis 16.44674088
> hide #!1 models
> volume zone #1.2 nearAtoms #2.2/F-H range 5 newMap true
Opened Closed_P29_J651_004.mrc zone as #6, grid size 420,420,420, pixel 0.828,
shown at step 1, values float32
> surface dust #0-9 size 10
> rename #6 id #5
> volume #5.6 level 0.2784
> volume #5.6 level 0.25
> show #!1.2 models
> color sample #5.6 map #5.5 palette
> 2.5,blue:3.5,cyan:4.5,lime:5.5,yellow:6.5,red
Map values for surface "surface": minimum 3.089, mean 4.636, maximum 8.725
> hide #!1.2 models
> show #!1.2 models
> hide #!5 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!5.6 models
> show #!5.6 models
> hide #!5.6 models
> show #!5.6 models
> volume #1.2 level 0.3
> volume #1.2 level 0.35
> volume #1.2 level 0.3
> hide #!5 models
> show #!5 models
> hide #!1.2 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> volume #1.1 level 0.35
> hide #!5.6 models
> show #!5.1 models
> fitmap #5.1 inMap #1.1
Fit map Apo_P29_J632_004.mrc in map Apo_P29_J632_004.mrc using 125313 points
correlation = 1, correlation about mean = 1, overlap = 6.742e+04
steps = 40, shift = 0.00463, angle = 0.00327 degrees
Position of Apo_P29_J632_004.mrc (#5.1) relative to Apo_P29_J632_004.mrc
(#1.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00006838 0.00001720 0.00725213
0.00006838 0.99999999 -0.00011245 0.00734629
-0.00001720 0.00011245 1.00000000 -0.01797227
Axis 0.84722263 0.12957492 0.51519332
Axis point 0.00000000 149.91487326 67.80973045
Rotation angle (degrees) 0.00760486
Shift along axis -0.00216313
> view position #5.2 sameAsModels #5.1
> show #!5.2 models
> hide #!5.2 models
> hide #!5.1 models
> color sample #1.1 map #5.2 palette
> 2.5,blue:3.5,cyan:4.5,lime:5.5,yellow:6.5,red
Map values for surface "surface": minimum 2.789, mean 3.422, maximum 6.617
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> show #!5.6 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.1 models
> hide #!5.6 models
> show #5.3 models
> hide #5.3 models
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Open_P29_J701_004.mrc"
Opened Open_P29_J701_004.mrc as #6, grid size 420,420,420, pixel 0.828, shown
at level 0.0759, step 2, values float32
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/0-half/J701_Cplx-
> Open/cryosparc_P47_J332_map_locres.mrc"
Opened cryosparc_P47_J332_map_locres.mrc as #7, grid size 420,420,420, pixel
0.828, shown at level 7.69, step 2, values float32
> surface dust #0-9 size 10
> hide #!7 models
> rename #6-7 id #5
> volume #5.7-8 step 1 level 0.15
> hide #!1 models
> volume #5.7 level 0.175
> volume #5.7 level 0.25
> volume #5.7 level 0.2
> show #!5.8 models
> volume #5.8 level 0.2
> hide #!5.8 models
> color sample #5.7 map #5.8 palette
> 2.5,blue:3.5,cyan:4.5,lime:5.5,yellow:6.5,red
Map values for surface "surface": minimum 3.296, mean 4.64, maximum 13.48
> volume #5.7 level 0.25
> show #!1 models
> show #!1.3 models
> hide #!1.2 models
> fitmap #5.7 inMap #1.3
Fit map Open_P29_J701_004.mrc in map Open_P29_J701_004.mrc using 171594 points
correlation = 1, correlation about mean = 0.9999, overlap = 3.114e+04
steps = 72, shift = 3.3, angle = 3.63 degrees
Position of Open_P29_J701_004.mrc (#5.7) relative to Open_P29_J701_004.mrc
(#1.3) coordinates:
Matrix rotation and translation
1.00000000 -0.00007034 0.00005648 -0.00633461
0.00007034 0.99999999 -0.00007673 -0.00113877
-0.00005647 0.00007673 1.00000000 -0.01189309
Axis 0.64792252 0.47688240 0.59395251
Axis point -0.00000000 64.34419249 57.94098086
Rotation angle (degrees) 0.00678540
Shift along axis -0.01171133
> volume #5.7 level 0.2
> fitmap #5.7 inMap #1.3
Fit map Open_P29_J701_004.mrc in map Open_P29_J701_004.mrc using 237652 points
correlation = 1, correlation about mean = 0.9999, overlap = 3.445e+04
steps = 48, shift = 0.021, angle = 0.0116 degrees
Position of Open_P29_J701_004.mrc (#5.7) relative to Open_P29_J701_004.mrc
(#1.3) coordinates:
Matrix rotation and translation
1.00000000 0.00001259 0.00007592 -0.01499612
-0.00001260 0.99999999 0.00010768 -0.00481413
-0.00007592 -0.00010768 0.99999999 0.03613283
Axis -0.81358041 0.57361109 -0.09516951
Axis point 0.00000000 340.85012116 76.68998918
Rotation angle (degrees) 0.00758335
Shift along axis 0.00600037
> view position #5.8 sameAsModels #5.7
> show #!5.8 models
> hide #!5.8 models
> hide #!5.7 models
> show #!5.7 models
> hide #!5.7 models
> color sample #1.3 map #5.8 palette
> 2.5,blue:3.5,cyan:4.5,lime:5.5,yellow:6.5,red
Map values for surface "surface": minimum 3.296, mean 4.64, maximum 13.5
> hide #!1 models
> show #!5.7 models
> hide #!5.7 models
> show #!1 models
> volume #1.3 level 0.25
> hide #!2.2 models
> show #!2.3 models
> fitmap #2.3 inMap #1.3
Fit molecule Open_Rsr35-Ct2.pdb (#2.3) to map Open_P29_J701_004.mrc (#1.3)
using 20430 atoms
average map value = 0.2949, steps = 44
shifted from previous position = 0.00244
rotated from previous position = 0.00371 degrees
atoms outside contour = 10074, contour level = 0.25
Position of Open_Rsr35-Ct2.pdb (#2.3) relative to Open_P29_J701_004.mrc (#1.3)
coordinates:
Matrix rotation and translation
0.99999959 -0.00018451 -0.00088168 0.18061458
0.00018453 0.99999998 0.00002230 -0.04754907
0.00088168 -0.00002246 0.99999961 -0.13878320
Axis -0.02483967 -0.97849219 0.20478288
Axis point 160.66172146 0.00000000 205.16184059
Rotation angle (degrees) 0.05162699
Shift along axis 0.01361957
> volume zone #1.3 nearAtoms #2.3/F-H range 5 newMap true
Opened Open_P29_J701_004.mrc zone as #6, grid size 420,420,420, pixel 0.828,
shown at step 1, values float32
> rename #6-7 id #5
> surface dust #0-9 size 10
> volume #5.9 level 0.15
> hide #!2 models
> show #!1.3 models
> color sample #5.9 map #5.8 palette
> 2.5,blue:3.5,cyan:4.5,lime:5.5,yellow:6.5,red
Map values for surface "surface": minimum 3.44, mean 6.37, maximum 18.98
> show #5.3 models
> hide #5.3 models
> show #5.3 models
> volume #5.9 level 0.175
> show #!1.1 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.3 models
> hide #!1.1 models
> hide #!5 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/S3/S3-v1.cxs"
> close #5.1
> close #5.2
> show #!5.4 models
> hide #!5.4 models
> show #!5.4 models
> hide #!1.2 models
> hide #!5.4 models
> show #!5.4 models
> hide #!5.9 models
> close #5.4
> show #!5.6 models
> hide #!5.6 models
> close #5.5
> show #!5.7 models
> close #5.7
> close #5.8
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> hide #!1.3 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.1 models
> view
> show #!1.1 models
> show #!1.3 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> show #!1.2 models
> show #!5.6 models
> hide #!1.2 models
> hide #!5.6 models
> show #!1.3 models
> show #!5.9 models
> volume #5.9 level 0.15
> volume #5.9 level 0.175
> hide #5.3 models
> close all
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/S3/S3-v1.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 407, in restore_snapshot
session.models.add([key], root_model = True)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 699, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 751, in _parent_for_added_model
raise ValueError('Tried to add model %s as a root model but id is not a single
integer'
ValueError: Tried to add model Color key #5.3 as a root model but id is not a
single integer
opened ChimeraX session
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/S3/S3-v1.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 407, in restore_snapshot
session.models.add([key], root_model = True)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 699, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 751, in _parent_for_added_model
raise ValueError('Tried to add model %s as a root model but id is not a single
integer'
ValueError: Tried to add model Color key #5.3 as a root model but id is not a
single integer
opened ChimeraX session
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/S3/S3-v1.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 407, in restore_snapshot
session.models.add([key], root_model = True)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 699, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 751, in _parent_for_added_model
raise ValueError('Tried to add model %s as a root model but id is not a single
integer'
ValueError: Tried to add model Color key #5.3 as a root model but id is not a
single integer
opened ChimeraX session
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/S3/S3-v1.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 407, in restore_snapshot
session.models.add([key], root_model = True)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 699, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 751, in _parent_for_added_model
raise ValueError('Tried to add model %s as a root model but id is not a single
integer'
ValueError: Tried to add model Color key #5.3 as a root model but id is not a
single integer
opened ChimeraX session
> close all
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/S3/S3-v1.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 407, in restore_snapshot
session.models.add([key], root_model = True)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 699, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 751, in _parent_for_added_model
raise ValueError('Tried to add model %s as a root model but id is not a single
integer'
ValueError: Tried to add model Color key #5.3 as a root model but id is not a
single integer
opened ChimeraX session
OpenGL version: 4.1 ATI-4.10.12
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 32 GB
System Firmware Version: 509.0.0.0.0
OS Loader Version: 577~129
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 13.3.1 (22E261)
Kernel Version: Darwin 22.4.0
Time since boot: 3 hours, 11 minutes
Graphics/Displays:
Radeon Pro 580:
Chipset Model: Radeon Pro 580
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1X-025
EFI Driver Version: 01.00.931
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (1)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → General Controls |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Overlay model in hierarchy |
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