Opened 3 years ago

Closed 3 years ago

#8825 closed defect (fixed)

Session restore fails when 2D label id changed to be a submodel of a 3D model

Reported by: chimerax-bug-report@… 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 Tom Goddard) 

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 (4)

comment:1 by Eric Pettersen, 3 years ago

Cc: Eric Pettersen added
Component: Unassigned → General Controls
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Overlay model in hierarchy

comment:2 by Tom Goddard, 3 years ago

It appears the user changed the 2d label model number from an integer to be under another model so its id became #5.3. The log shows they used the "rename" command to change many id numbers. The problem is that overlay models such as 2d labels are not part of the 3D scene Drawing hierarchy. Instead they are part of their own hierarchy for overlays which is only 1 level deep. This is because those overlays are not located in 3 dimensions. They don't use the position transform hierarchy (in fact don't use the position transform at all when rendering since they render in screen rectangle coordinates). Putting an overlay model in the 3D hierarchy is likely to cause chaos. The code requires that model #5.3 have model #5 as a parent. But if #5.3 is an overlay it cannot have a parent in the 3D scene. Conversely an overlay cannot have child models from the 3D scene.

So I think the solution to this bug is that the rename command should not allow changing the id of an overlay to be anything but an integer, and also rename cannot make any model a child of an overlay. The rule is that 2D models are not part of a hierarchy. This is a bit annoying. Eric points out that it is pretty reasonable to want to put a 2D overlay that labels a specific structure as a child of that structure so that deleting or hiding the structure deletes or hides the label.

It might be possible to allow overlays to be in any hierarchy. But it is perhaps confusing that they are not effected by their parent's transform. And this would likely involve the model id numbers not having the same hierarchy as the Drawing parent / child relations which is a complication.

Last edited 3 years ago by Tom Goddard (previous) (diff)

comment:3 by Tom Goddard, 3 years ago

Description: modified (diff)
Summary: Overlay model in hierarchy → Session restore fails when 2D label id changed to be a submodel of a 3D model

comment:4 by Tom Goddard, 3 years ago

Cc: Elaine Meng added
Resolution: → fixed
Status: assigned → closed

Fixed.

Made the rename command give an error when attempting to change the id of a 3D scene model that would make it a child of a 2D label (or other overlay, eg scalebar). And also it gives an error when attempting to make any change to the id of a 2D label (or other overlay model). These are slightly annoying restrictions, but it is too complex to change the code to allow these operations.

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