![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Last modified 3 years ago
#8825 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | Eric Pettersen, Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
> lighting full
> volume #0-9 step 1 level 0.12
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> volume #0-9 step 1 level 0.2
> hide #!4 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 = 0.744, overlap = 4.798e+04
steps = 40, shift = 0.0344, angle = 0.0106 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
0.98257846 0.13415442 0.12861633 -42.92728786
-0.13432869 0.99090951 -0.00735837 24.94050738
-0.12843430 -0.01004669 0.99166713 27.21963240
Axis -0.00723238 0.69154264 -0.72229943
Axis point 173.30825708 342.60365247 0.00000000
Rotation angle (degrees) 10.71087133
Shift along axis -2.10283387
> show #!4 models
> hide #!5 models
> volume #3-4 step 1 level 0.12
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3-4 step 1 level 0.15
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3-4 step 1 level 0.2
> fitmap #3 inMap #4
Fit map polish-stat3-cs_P24_J259_sharp.mrc in map polish-
stat4-cs_P24_J260_sharp.mrc using 215387 points
correlation = 0.9632, correlation about mean = 0.8769, overlap = 4.762e+04
steps = 40, shift = 0.00656, angle = 0.00479 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
0.99892561 -0.00922543 0.04541498 -6.06312038
0.00784074 0.99950175 0.03057400 -8.01852571
-0.04567441 -0.03018506 0.99850023 15.07939955
Axis -0.54828753 0.82198746 0.15400451
Axis point 328.32122008 0.00000000 152.67478308
Rotation angle (degrees) 3.17627246
Shift along axis -0.94449873
> volume #3-4 step 1 level 0.12
> volume #0-9 step 1 level 0.2
> lighting full
> lighting soft
> graphics silhouettes true
> hide #!3 models
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting shadows false
> lighting shadows true
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!2 models
> show #!5 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 = 0.9114, correlation about mean = 0.6937, overlap = 2.679e+04
steps = 36, shift = 0.0149, angle = 0.0131 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
0.98284064 0.09437251 0.15848691 -43.40986848
-0.09430693 0.99551141 -0.00795160 18.30443788
-0.15852594 -0.00713126 0.98732906 34.84365477
Axis 0.00222367 0.85931303 -0.51144518
Axis point 189.21117102 0.00000000 294.35708437
Rotation angle (degrees) 10.62948441
Shift along axis -2.18790652
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> volume #2 step 1 level 0.12
> volume #2 step 1 level 0.1
> hide #!5 models
> show #!3 models
> hide #!3 models
> volume #2 step 1 level 0.08
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #2 step 2 level 0.07
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> volume #2 step 1 level 0.12
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #!5 models
> volume #1-2 step 2 level 0.07
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #1-2 step 2 level 0.08
> volume #0-9 step 1 level 0.2
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!5 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v2.cxs"
——— End of log from Thu May 19 10:48:15 2022 ———
opened ChimeraX session
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v2.cxs"
> show #!3 models
> hide #!5 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> graphics silhouettes true
> lighting soft
> show #!5 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v1.cxs"
> hide #!1 models
> show #!1 models
> hide #!5 models
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/0_MM/Stat1-Rsr115-Ct4.pdb"
Chain information for Stat1-Rsr115-Ct4.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
K | No description available
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/0_MM/Stat2-Rsr101-Ct1.pdb"
Summary of feedback from opening /Users/fengwei.zheng/OneDrive - Van Andel
Institute/Documents/Draft/3_ScRR91-10nt/0_MM/Stat2-Rsr101-Ct1.pdb
---
warning | End residue of secondary structure not found: HELIX 96 96 HIS F 74
VAL F 76 1 3
Chain information for Stat2-Rsr101-Ct1.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/0_MM/Stat3-Ref88-Ct3.pdb"
Chain information for Stat3-Ref88-Ct3.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/0_MM/Stat4-Ref80-Ct6.pdb"
Chain information for Stat4-Ref80-Ct6.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/0_MM/Stat5-ref59-v3.pdb"
Chain information for Stat5-ref59-v3.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
> hide #6-10
> show cartoons
> hide #!1 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> dssp
> undo
> dssp
> undo
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> show #!7 models
> dssp #6
> undo
> hide #!7 models
> dssp #6
> undo
> dssp #6
> undo
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!8 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> show #!5 models
> fitmap #10 inMap #5
Fit molecule Stat5-ref59-v3.pdb (#10) to map polish-
stat5-cs_P24_J261_sharp.mrc (#5) using 22190 atoms
average map value = 0.4749, steps = 40
shifted from previous position = 0.0118
rotated from previous position = 0.0154 degrees
atoms outside contour = 4549, contour level = 0.2
Position of Stat5-ref59-v3.pdb (#10) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999996 -0.00023189 -0.00013098 0.07248581
0.00023189 0.99999997 0.00003749 -0.03958209
0.00013098 -0.00003752 0.99999999 -0.01549584
Axis -0.13944471 -0.48700260 0.86219699
Axis point 179.53137965 310.04211664 0.00000000
Rotation angle (degrees) 0.01540985
Shift along axis -0.00419165
> hide #!10 models
> hide #!5 models
> show #!4 models
> show #!9 models
> fitmap #9 inMap #4
Fit molecule Stat4-Ref80-Ct6.pdb (#9) to map polish-
stat4-cs_P24_J260_sharp.mrc (#4) using 22260 atoms
average map value = 0.394, steps = 116
shifted from previous position = 0.393
rotated from previous position = 9.66 degrees
atoms outside contour = 7049, contour level = 0.2
Position of Stat4-Ref80-Ct6.pdb (#9) relative to polish-
stat4-cs_P24_J260_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99999996 -0.00020731 0.00019735 -0.00273479
0.00020730 0.99999998 0.00005282 -0.02601563
-0.00019736 -0.00005277 0.99999998 0.03690394
Axis -0.18139255 0.67806855 0.71226384
Axis point 155.39639231 -5.22421209 0.00000000
Rotation angle (degrees) 0.01667605
Shift along axis 0.00914104
> fitmap #9 inMap #4
Fit molecule Stat4-Ref80-Ct6.pdb (#9) to map polish-
stat4-cs_P24_J260_sharp.mrc (#4) using 22260 atoms
average map value = 0.394, steps = 28
shifted from previous position = 0.0124
rotated from previous position = 0.00991 degrees
atoms outside contour = 7040, contour level = 0.2
Position of Stat4-Ref80-Ct6.pdb (#9) relative to polish-
stat4-cs_P24_J260_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99999998 -0.00007086 0.00020828 -0.02653646
0.00007083 0.99999998 0.00015866 -0.03295482
-0.00020829 -0.00015864 0.99999997 0.05873668
Axis -0.58489918 0.76790127 0.26119070
Axis point 275.00727809 -0.00000000 111.83556729
Rotation angle (degrees) 0.01554089
Shift along axis 0.00555658
> hide #!9 models
> show #!8 models
> hide #!4 models
> show #!3 models
> fitmap #8 inMap #3
Fit molecule Stat3-Ref88-Ct3.pdb (#8) to map polish-
stat3-cs_P24_J259_sharp.mrc (#3) using 22206 atoms
average map value = 0.5003, steps = 112
shifted from previous position = 2.15
rotated from previous position = 10.7 degrees
atoms outside contour = 4839, contour level = 0.2
Position of Stat3-Ref88-Ct3.pdb (#8) relative to polish-
stat3-cs_P24_J259_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999998 -0.00003724 0.00017100 -0.02704958
0.00003728 0.99999998 -0.00021766 0.04254268
-0.00017099 0.00021767 0.99999996 -0.00638064
Axis 0.77933426 0.61224054 0.13341527
Axis point 0.00000000 31.86795610 183.87738750
Rotation angle (degrees) 0.01600241
Shift along axis 0.00411441
> fitmap #8 inMap #3
Fit molecule Stat3-Ref88-Ct3.pdb (#8) to map polish-
stat3-cs_P24_J259_sharp.mrc (#3) using 22206 atoms
average map value = 0.5003, steps = 40
shifted from previous position = 0.00299
rotated from previous position = 0.00503 degrees
atoms outside contour = 4833, contour level = 0.2
Position of Stat3-Ref88-Ct3.pdb (#8) relative to polish-
stat3-cs_P24_J259_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999998 -0.00001612 0.00021454 -0.03743634
0.00001616 0.99999999 -0.00014440 0.03068096
-0.00021453 0.00014440 0.99999997 0.01462916
Axis 0.55729248 0.82797633 0.06229190
Axis point 66.57801523 0.00000000 188.66655366
Rotation angle (degrees) 0.01484581
Shift along axis 0.00545140
> hide #!3 models
> show #!2 models
> hide #!8 models
> show #!7 models
> fitmap #7 inMap #2
Fit molecule Stat2-Rsr101-Ct1.pdb (#7) to map polish-
stat2-cs_P24_J258_sharp.mrc (#2) using 21450 atoms
average map value = 0.2812, steps = 124
shifted from previous position = 4.43
rotated from previous position = 10.7 degrees
atoms outside contour = 9695, contour level = 0.2
Position of Stat2-Rsr101-Ct1.pdb (#7) relative to polish-
stat2-cs_P24_J258_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999971 -0.00033689 0.00068872 -0.06283759
0.00033697 0.99999994 -0.00011560 -0.04225239
-0.00068868 0.00011583 0.99999976 0.05695438
Axis 0.14923236 0.88820430 0.43453748
Axis point 96.65069623 0.00000000 86.47841398
Rotation angle (degrees) 0.04442630
Shift along axis -0.02215735
> fitmap #7 inMap #2
Fit molecule Stat2-Rsr101-Ct1.pdb (#7) to map polish-
stat2-cs_P24_J258_sharp.mrc (#2) using 21450 atoms
average map value = 0.2812, steps = 28
shifted from previous position = 0.00926
rotated from previous position = 0.00543 degrees
atoms outside contour = 9694, contour level = 0.2
Position of Stat2-Rsr101-Ct1.pdb (#7) relative to polish-
stat2-cs_P24_J258_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999976 -0.00035258 0.00059576 -0.03904426
0.00035265 0.99999993 -0.00012583 -0.04023357
-0.00059572 0.00012604 0.99999981 0.04605711
Axis 0.17897638 0.84666029 0.50113252
Axis point 92.41276833 0.00000000 60.17480644
Rotation angle (degrees) 0.04031540
Shift along axis -0.01797145
> hide #!7 models
> show #!6 models
> hide #!2 models
> show #!1 models
> fitmap #6 inMap #1
Fit molecule Stat1-Rsr115-Ct4.pdb (#6) to map polish-
stat1-cs_P24_J252_sharp.mrc (#1) using 21221 atoms
average map value = 0.3671, steps = 64
shifted from previous position = 1.96
rotated from previous position = 3.15 degrees
atoms outside contour = 7031, contour level = 0.2
Position of Stat1-Rsr115-Ct4.pdb (#6) relative to polish-
stat1-cs_P24_J252_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999989 -0.00039481 0.00023409 0.03368282
0.00039486 0.99999990 -0.00019020 -0.02899819
-0.00023401 0.00019029 0.99999995 -0.00137993
Axis 0.38290067 0.47106031 0.79466299
Axis point 71.24272862 87.09758706 0.00000000
Rotation angle (degrees) 0.02846790
Shift along axis -0.00185931
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-maps-models-v3.cxs"
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!7 models
> hide #!6 models
> show #!8 models
> hide #!7 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!10 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> show #!10 models
> hide #!8 models
> show #!8 models
> hide #!10 models
> hide #!8 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!10 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v3-maps-models.cxs"
——— End of log from Thu May 19 12:06:54 2022 ———
opened ChimeraX session
> rename #1-5 maps id #1
> rename #6-10 models id #2
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v4-maps-models.cxs"
——— End of log from Thu May 19 16:17:48 2022 ———
opened ChimeraX session
> hide #!1 models
> cartoon style nucleic xsection oval width 2.5 thickness 2.5
> cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true
> xsection oval width 2.75 thickness 1 arrowScale 1.5
> select /I-K
5046 atoms, 5628 bonds, 5 pseudobonds, 251 residues, 10 models selected
> show sel & #!2.5 atoms
> nucleotides sel & #!2.5 stubs
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v5-maps-models.cxs"
> hide #!2 models
> show #!2.1 models
> hide #!2.5 models
> hide #!2.1 models
> show #!2.3 models
> show #!2.5 models
> hide #!2.3 models
> hide #!2.5 models
> show #!2.1 models
> select #2.1-5/I-K
5046 atoms, 5628 bonds, 5 pseudobonds, 251 residues, 10 models selected
> show sel & #!2.1 atoms
> nucleotides sel & #!2.1 stubs
> select clear
> show #!2.2 models
> hide #!2.1 models
> show #!2.1 models
> show #!2.3 models
> show #!2.4 models
> show #!2.5 models
> select #2.1-5/I-K
5046 atoms, 5628 bonds, 5 pseudobonds, 251 residues, 10 models selected
> show sel atoms
> nucleotides sel stubs
> hide #!2.1 models
> hide #!2.2 models
> hide #!2.3 models
> hide #!2.4 models
> hide #!2.5 models
> show #!2.1 models
> show #!2.5 models
> select clear
> hide #!2.1 models
> show #!2.1 models
> hide #!2.5 models
> view name v1
> color /F plum
> show #!2.5 models
> hide #!2.1 models
> hide #!2.5 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.5 models
> color /I #8E8CDF
> show #!2.1 models
> hide #!2.5 models
> color /I magenta
> show #!2.5 models
> hide #!2.1 models
> hide #!2.5 models
> show #!2.1 models
> show #!2.5 models
> hide #!2.1 models
> color /I dark magenta
> show #!2.1 models
> hide #!2.5 models
> color /I purple
[Repeated 1 time(s)]
> show #!2.5 models
> color /I medium orchid
> hide #!2.1 models
> show #!2.1 models
> hide #!2.5 models
> hide #!2.1 models
> show #!2.5 models
> color /J teel
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color /J teal
> show #!2.3 models
> hide #!2 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.3 models
> hide #!2.3 models
> color /J steel blue
> color /J dark sea green
> color /J sea green
> color /J aquamarine
> show #!2.1 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.1 models
> show #!2.1 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v6-maps-models.cxs"
> hide #!2.1 models
> show #!2.1 models
> hide #!2.5 models
> color /K dark slate grey
> color /K light cyan
> show #!2.5 models
> color /K wheat
> color /K gold
> hide #!2.1 models
> show #!2.1 models
> hide #!2.5 models
> color /K orange
> show #!2.5 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.5 models
> color /K olive
> color /K pale goldenrod
> show #!2.5 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.5 models
> hide #!2.1 models
> show #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> hide #!2.2 models
> show #!2.5 models
> color /J light cyan
> color /J light blue
> color /J powder blue
> color /J sky blue
> show #!2.3 models
> hide #!2.5 models
> hide #!2.3 models
> show #!2.5 models
> color /J light sky blue
> show #!2.3 models
> hide #!2.5 models
> hide #!2.3 models
> show #!2.1 models
> color /I palegreen purple
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /I #CAC6FD
> undo
> color /I violet
> show #!2.5 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.5 models
> hide #!2.1 models
> show #!2.2 models
> show #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> hide #!2.1 models
> show #!2.2 models
> show #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.5 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.5 models
> hide #!2.1 models
> show #!2.2 models
> show #!2.1 models
> hide #!2.2 models
> show #!2.5 models
> hide #!2.1 models
> show #!2.1 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v7-maps-models.cxs"
> view v1
> hide #!2.1 models
> show #!2.1 models
> hide #!2.5 models
> undo
[Repeated 1 time(s)]
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.1 models
> show #!2.2 models
> hide #!2.1 models
> hide #!2.2 models
> show #!2.4 models
> show #!2.5 models
> hide #!2.4 models
> hide #!2.5 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.2 models
> show #!2.1 models
> hide #!2.2 models
> hide #!2.1 models
> show #!2.2 models
> combine #2.2 modelId #3
> hide #!2.2 models
> delete #3 & ~/B
> hide #!3 models
> show #!2.5 models
> show #!2.1 models
> hide #!2.5 models
> color /H #E0F49C
> close #3
> show #!2.2 models
> hide #!2.1 models
> combine #2.2 modelId #3
> hide #!2.2 models
> delete #3 & ~/G
> show #!2.5 models
> hide #!3 models
> show #!2.1 models
> hide #!2.5 models
> color /F #B48FE3
> undo
> hide #!2.1 models
> show #!2.2 models
> show #!2.1 models
> hide #!2.2 models
> color /F #B48FE3
> undo
> color /I #B48FE3
> show #!3 models
> hide #!2.1 models
> close #3
> show #!2.5 models
> show #!2.3 models
> hide #!2.5 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> undo
[Repeated 1 time(s)]
> hide #!2.2 models
> show #!2.1 models
> color /G #B48FE3
> color /I medium orchid
> color /F plum
> show #!2.3 models
> hide #!2.1 models
> show #!2.5 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.5 models
> show #!2.1 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.1 models
> color /I violet
> undo
> color /I #CAC6FD
> undo
> show #!2.1 models
> hide #!2.3 models
> color /K #CAC6FD
> undo
> color /G #CAC6FD
> undo
> color /C #CAC6FD
> hide #!2.1 models
> show #!2.3 models
> hide #!2 models
> show #!2.1 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.1 models
> hide #!2.2 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.4 models
> show #!2.1 models
> hide #!2.4 models
> show #!2.4 models
> hide #!2.1 models
> show #!2.5 models
> hide #!2.4 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.4 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.4 models
> hide #!2.5 models
> show #!2.1 models
> show #!2.3 models
> hide #!2.1 models
> hide #!2.3 models
> show #!2.1 models
> color /H yellow green
> color /H light green
> color /H pale green
> show #!2.3 models
> hide #!2.1 models
> hide #!2.3 models
> show #!2.5 models
> show #!2.1 models
> hide #!2.5 models
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting full
> lighting simple
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> lighting soft
> hide #!2.1 models
> show #!2.2 models
> show #!2.3 models
> hide #!2.2 models
> hide #!2.3 models
> show #!2.4 models
> show #!2.5 models
> hide #!2.4 models
> show #!2.1 models
> hide #!2.5 models
> color /K #E7F981
> show #!2.3 models
> hide #!2.1 models
> show #!2.1 models
> show #!2.4 models
> hide #!2.3 models
> hide #!2.1 models
> show #!2.5 models
> hide #!2.4 models
> hide #!2.5 models
> show #!2.1 models
> color /H olive drab
> color /H olive
> color /H dark khaki
> color /H light salmon
> color /H light coral
> show #!2.5 models
> hide #!2.1 models
> color /H hot pink
> color /H indian red
> show #!2.1 models
> hide #!2.5 models
> color /H misty rose
> color /H moccasin
> color /H navajo white
> show #!2.5 models
> hide #!2.1 models
> show #!2.4 models
> hide #!2.5 models
> hide #!2.4 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.1 models
> color /G #CAC6FD
> color /C #B48FE3
> view v1
[Repeated 1 time(s)]
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v8-maps-models.cxs"
> show #!2.4 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.4 models
> show #!2.4 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.4 models
> color /E #EB9BC1
> color /E salmon
> color /E light salmon
> color /E dark salmon
> color /E salmon
> color /E light coral
> undo
> color /B #EB9BC1
> undo
> show #!2.2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.2 models
> combine #2.1 modelId #3
> delete #3 & ~/B
> close #3
> combine #2.1 modelId #3
> delete #3 & ~/D
> close #3
> color /A #FFB381
> color /B #D7819F
> color /C #B48FE3
> color /D #D7CD85
> color /E salmon
> color /F plum
> color /G #CAC6FD
> color /H navajo white
> color /I medium orchid
> color /J light sky blue
> color /K #E7F981
> show #!2.2 models
> show #!2.3 models
> show #!2.4 models
> show #!2.5 models
> tile #2.1-5
5 models tiled
> tile #2.1-5 columns 3
5 models tiled
> undo
[Repeated 1 time(s)]
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v9-maps-models-color
> assigned.cxs"
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2.1 models
> hide #!2.2 models
> hide #!2.3 models
> hide #!2.5 models
> hide #!2.4 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.5 models
> color /F navajo white
> color /I plum
> undo
> color /H plum
> show #!2.1 models
> hide #!2.5 models
> view v1
> hide #!2.1 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> view v1
> turn y 1 90
[Repeated 1 time(s)]
> turn y 1 180
> hide #!2.1 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.5 models
> turn y 1 180
> hide #!2.5 models
> show #!2.1 models
> turn y 1 180
[Repeated 2 time(s)]
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.3 models
> show #!2.4 models
> hide #!2.3 models
> hide #!2.4 models
> show #!2.5 models
> turn y 1 180
[Repeated 1 time(s)]
> hide #!2.5 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v10-maps-models-color
> assigned.cxs"
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.5 models
> select /F:119-124
245 atoms, 240 bonds, 30 residues, 5 models selected
> select /F:118-124
285 atoms, 280 bonds, 35 residues, 5 models selected
> select /F:1-7,118-124
570 atoms, 560 bonds, 70 residues, 5 models selected
> select /F:1-7,79-84,118-124
810 atoms, 800 bonds, 100 residues, 5 models selected
> select /F:2-7,79-84,118-124
770 atoms, 760 bonds, 95 residues, 5 models selected
> select /F:2-7,79-84,91-94,118-124
930 atoms, 915 bonds, 115 residues, 5 models selected
> select /F:2-7,68-72,79-84,91-94,118-124
1145 atoms, 1135 bonds, 140 residues, 5 models selected
> select /F:2-7,68-72,79-84,91-94,118-124,462-467
1410 atoms, 1405 bonds, 170 residues, 5 models selected
> select /F:2-7,68-72,79-84,91-94,118-124,407-410,462-467
1570 atoms, 1560 bonds, 190 residues, 5 models selected
> select /F:2-7,68-72,79-84,91-94,118-124,406-410,462-467
1620 atoms, 1615 bonds, 195 residues, 5 models selected
> select /F:2-7,68-72,79-84,91-94,118-124,262-266,406-410,462-467
1810 atoms, 1805 bonds, 220 residues, 5 models selected
> select /F:2-7,68-72,79-84,91-94,118-124,262-266,281-286,406-410,462-467
2050 atoms, 2040 bonds, 250 residues, 5 models selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 250 items
> setattr sel res ss_id 88
Assigning ss_id attribute to 250 items
> select clear
> select /H:320-325
255 atoms, 255 bonds, 30 residues, 5 models selected
> select /H:252,256,320-325
330 atoms, 320 bonds, 40 residues, 5 models selected
> select /H:252-256,320-325
460 atoms, 455 bonds, 55 residues, 5 models selected
> select /H:251-256,320-325
505 atoms, 500 bonds, 60 residues, 5 models selected
> select /H:251-256,262-266,320-325
690 atoms, 685 bonds, 85 residues, 5 models selected
> select /H:251-256,261-266,320-325
730 atoms, 725 bonds, 90 residues, 5 models selected
> select /H:251-256,261-266,283-288,320-325
945 atoms, 935 bonds, 1 pseudobond, 120 residues, 6 models selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 120 items
> setattr sel res ss_id 88
Assigning ss_id attribute to 120 items
> select clear
> hide #!2.5 models
> show #!2.1 models
> select /E:83-89
265 atoms, 260 bonds, 35 residues, 5 models selected
> select /E:83-89,69-75
580 atoms, 575 bonds, 70 residues, 5 models selected
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.5 models
> select /E:82-89,69-75
625 atoms, 620 bonds, 75 residues, 5 models selected
> select /E:82-89,69-76
660 atoms, 655 bonds, 80 residues, 5 models selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 80 items
> setattr sel res ss_id 88
Assigning ss_id attribute to 80 items
> select clear
> hide #!2.5 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> select /A:162-173
466 atoms, 471 bonds, 59 residues, 5 models selected
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.2 models
> select /A:162-174
521 atoms, 526 bonds, 64 residues, 5 models selected
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.5 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> hide #!2.5 models
> show #!2.2 models
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v11-M-M-color-SS
> assigned.cxs"
——— End of log from Mon May 23 12:04:10 2022 ———
opened ChimeraX session
> color bfactor #!2.2
21450 atoms, 2597 residues, atom bfactor range 1.74 to 269
> undo
> hide #!2.2 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.1 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v12-M-M-color-SS
> assigned.cxs"
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_1/Fig1-v1.cxs"
——— End of log from Mon May 23 15:10:58 2022 ———
opened ChimeraX session
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.3 models
> show #!1.3 models
> hide #!1.5 models
> volume #1.3 level 0.175
> color zone #1.3 near #2.3 distance 9
> hide #!1.3 models
> undo
> hide #!2.3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_1/Fig1b-3.cxs"
——— End of log from Mon May 23 16:17:23 2022 ———
opened ChimeraX session
> hide #!1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_2/Fig2-1.cxs"
——— End of log from Tue May 24 12:29:31 2022 ———
opened ChimeraX session
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-v1.cxs"
——— End of log from Thu May 26 14:32:30 2022 ———
opened ChimeraX session
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> hide #!2.2 models
> show #!2.5 models
> view name v1
> view v1
> show #!2.3 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.4 models
> hide #!2.4 models
> view v1
[Repeated 1 time(s)]
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/ScRPD/Deposite/J100-ScRFC-PCNA-2DNA-wBRCT-
> Rsf090-v11.pdb"
Chain information for J100-ScRFC-PCNA-2DNA-wBRCT-Rsf090-v11.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
> open 3GLF
Summary of feedback from opening 3GLF fetched from pdb
---
notes | Fetching compressed mmCIF 3glf from
http://files.rcsb.org/download/3glf.cif
Fetching CCD ADP from http://ligand-expo.rcsb.org/reports/A/ADP/ADP.cif
Fetching CCD BEF from http://ligand-expo.rcsb.org/reports/B/BEF/BEF.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif
3glf title:
Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template DNA [more
info...]
Chain information for 3glf #4
---
Chain | Description | UniProt
A F | DNA polymerase III subunit δ | HOLA_ECOLI
B C D G H I | DNA polymerase III subunit τ | DPO3X_ECOLI
E J | DNA polymerase III subunit delta' | HOLB_ECOLI
K M | DNA (5'-D(*TP*TP*TP*TP*TP*TP*ap*TP*ap*GP*GP*CP*CP*ap*G)-3') |
L N | DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*ap*TP*A)-3') |
Non-standard residues in 3glf #4
---
ADP — adenosine-5'-diphosphate
BEF — beryllium trifluoride ion
MG — magnesium ion
ZN — zinc ion
3glf mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide #!3 models
> hide #!2.5 models
> show #!3 models
> hide #!4 models
> show #!4 models
> open 3U5Z
Summary of feedback from opening 3U5Z fetched from pdb
---
notes | Fetching compressed mmCIF 3u5z from
http://files.rcsb.org/download/3u5z.cif
Fetching CCD 08T from http://ligand-expo.rcsb.org/reports/0/08T/08T.cif
3u5z title:
Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-
template DNA, and ATP analog [more info...]
Chain information for 3u5z #5
---
Chain | Description | UniProt
A K | DNA polymerase accessory protein 62 | DPA62_BPT4
B C D E L M N O | DNA polymerase accessory protein 44 | DPA44_BPT4
F G H P Q R | DNA polymerase processivity component | DPA5_BPT4
I S | Template DNA strand |
J T | Primer DNA strand |
Non-standard residues in 3u5z #5
---
08T —
[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium
ADP — adenosine-5'-diphosphate
MG — magnesium ion
3u5z mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide #3-5
> show #3-5 cartoons
> mmaker #3 to #2.5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain E (#3), sequence alignment score = 1658
RMSD between 332 pruned atom pairs is 0.602 angstroms; (across all 338 pairs:
0.694)
> mmaker #3 to #2.5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain E (#3), sequence alignment score = 1658
RMSD between 332 pruned atom pairs is 0.602 angstroms; (across all 338 pairs:
0.694)
> mmaker #4 to #2.5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain I (#4),
sequence alignment score = 531.7
RMSD between 146 pruned atom pairs is 1.105 angstroms; (across all 312 pairs:
9.621)
> mmaker #5 to #2.5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3u5z, chain B (#5),
sequence alignment score = 465.7
RMSD between 141 pruned atom pairs is 1.038 angstroms; (across all 293 pairs:
13.080)
> hide #!4 models
> hide #!5 models
> show #!2.5 models
> hide #!2.5 models
> mmaker #3/A-H to #2.5/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain A (#3), sequence alignment score = 362.9
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain B (#3), sequence alignment score = 1555.9
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain C (#3), sequence alignment score = 1652.7
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain D (#3), sequence alignment score = 1650.9
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain E (#3), sequence alignment score = 1658
Matchmaker Stat5-ref59-v3.pdb, chain F (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain F (#3), sequence alignment score = 201.1
Matchmaker Stat5-ref59-v3.pdb, chain G (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain G (#3), sequence alignment score = 216.7
Matchmaker Stat5-ref59-v3.pdb, chain H (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain H (#3), sequence alignment score = 177.6
RMSD between 1467 pruned atom pairs is 0.714 angstroms; (across all 2392
pairs: 6.053)
> dssp #3
> undo
> dssp #3/A
> undo
> hide #!3 models
> show #!4 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> mmaker #4/A-E to #2.5/A-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4),
sequence alignment score = 176.6
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain B (#4),
sequence alignment score = 462.2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 454 pruned atom pairs is 1.226 angstroms; (across all 1515 pairs:
13.805)
> show #!2.5 models
> view v1
> mmaker #4/F-J to #2.5/A-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain F (#4),
sequence alignment score = 175.7
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain G (#4),
sequence alignment score = 469.4
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain H (#4),
sequence alignment score = 511.1
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain I (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain J (#4),
sequence alignment score = 267.9
RMSD between 449 pruned atom pairs is 1.205 angstroms; (across all 1521 pairs:
13.864)
> mmaker #4/A-E to #2.5/A-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4),
sequence alignment score = 176.6
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain B (#4),
sequence alignment score = 462.2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 454 pruned atom pairs is 1.226 angstroms; (across all 1515 pairs:
13.805)
> select #4/F-J
13948 atoms, 14199 bonds, 23 pseudobonds, 1785 residues, 2 models selected
> delete sel
> delete #4/M-N
> view v1
> hide #!2.5 models
> hide #!4 models
> show #!4 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> mmaker #4 to #2.5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain D (#4),
sequence alignment score = 525.7
RMSD between 144 pruned atom pairs is 1.091 angstroms; (across all 312 pairs:
9.612)
> mmaker #4/A to #2.5/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4),
sequence alignment score = 176.6
RMSD between 19 pruned atom pairs is 1.035 angstroms; (across all 307 pairs:
25.477)
> hide #!2.5 models
> show #!2.5 models
> mmaker #4/E to #2.5/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 76 pruned atom pairs is 1.137 angstroms; (across all 281 pairs:
12.269)
> mmaker #4/C-E to #2.5/C-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs:
10.786)
> mmaker #4/C-E to #2.5/C-E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain D (#4),
sequence alignment score = 525.7
RMSD between 144 pruned atom pairs is 1.091 angstroms; (across all 312 pairs:
9.612)
> mmaker #4/C-E to #2.5/C-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs:
10.786)
> mmaker #4/E to #2.5/E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 76 pruned atom pairs is 1.137 angstroms; (across all 281 pairs:
12.269)
> mmaker #4/D-E to #2.5/D-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 188 pruned atom pairs is 1.174 angstroms; (across all 593 pairs:
11.216)
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!3 models
> hide #!4 models
> show #!2.5 models
> mmaker #3/A-H to #2.5/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain A (#3), sequence alignment score = 362.9
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain B (#3), sequence alignment score = 1555.9
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain C (#3), sequence alignment score = 1652.7
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain D (#3), sequence alignment score = 1650.9
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain E (#3), sequence alignment score = 1658
Matchmaker Stat5-ref59-v3.pdb, chain F (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain F (#3), sequence alignment score = 201.1
Matchmaker Stat5-ref59-v3.pdb, chain G (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain G (#3), sequence alignment score = 216.7
Matchmaker Stat5-ref59-v3.pdb, chain H (#2.5) with J100-ScRFC-PCNA-2DNA-wBRCT-
Rsf090-v11.pdb, chain H (#3), sequence alignment score = 177.6
RMSD between 1467 pruned atom pairs is 0.714 angstroms; (across all 2392
pairs: 6.053)
> hide #!3 models
> show #!4 models
> mmaker #4/B-E to #2.5/B-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain B (#4),
sequence alignment score = 462.2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 454 pruned atom pairs is 1.226 angstroms; (across all 1208 pairs:
10.605)
> hide #!2.5 models
> show #!2.5 models
> mmaker #4/E to #2.5/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 76 pruned atom pairs is 1.137 angstroms; (across all 281 pairs:
12.269)
> mmaker #4/E to #2.5/E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 76 pruned atom pairs is 1.137 angstroms; (across all 281 pairs:
12.269)
> mmaker #4/E to #2.5/E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 76 pruned atom pairs is 1.137 angstroms; (across all 281 pairs:
12.269)
> mmaker #4/C-E to #2.5/C-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs:
10.786)
> hide #!2.5 models
> hide #!1.3 models
> show #!1.5 models
> fitmap #4 inMap #1.5
Fit molecule 3glf (#4) to map polish-stat5-cs_P24_J261_sharp.mrc (#1.5) using
14323 atoms
average map value = 0.1428, steps = 80
shifted from previous position = 0.269
rotated from previous position = 1.09 degrees
atoms outside contour = 10008, contour level = 0.2
Position of 3glf (#4) relative to polish-stat5-cs_P24_J261_sharp.mrc (#1.5)
coordinates:
Matrix rotation and translation
-0.79349866 -0.60576978 0.05833393 208.05381819
-0.43311966 0.49479544 -0.75338227 232.74167460
0.42751285 -0.62307339 -0.65499032 198.11036122
Axis 0.30454517 -0.86280889 0.40350099
Axis point 131.22228743 0.00000000 167.62379289
Rotation angle (degrees) 167.64664469
Shift along axis -57.51207455
> ui mousemode right "translate selected models"
> select #4
14323 atoms, 14626 bonds, 46 pseudobonds, 1795 residues, 3 models selected
> view matrix models
> #4,-0.7935,-0.60577,0.058334,210.2,-0.43312,0.4948,-0.75338,232.2,0.42751,-0.62307,-0.65499,199.53
Drag select of 1.5 polish-stat5-cs_P24_J261_sharp.mrc , 10 residues
> select clear
> select #4
14323 atoms, 14626 bonds, 46 pseudobonds, 1795 residues, 3 models selected
> select clear
> select #4
14323 atoms, 14626 bonds, 46 pseudobonds, 1795 residues, 3 models selected
> view matrix models
> #4,-0.7935,-0.60577,0.058334,209.26,-0.43312,0.4948,-0.75338,231.89,0.42751,-0.62307,-0.65499,199.67
> view matrix models
> #4,-0.7935,-0.60577,0.058334,210.12,-0.43312,0.4948,-0.75338,232.09,0.42751,-0.62307,-0.65499,199.65
> select clear
> select #4
14323 atoms, 14626 bonds, 46 pseudobonds, 1795 residues, 3 models selected
> view matrix models
> #4,-0.7935,-0.60577,0.058334,208.96,-0.43312,0.4948,-0.75338,230.66,0.42751,-0.62307,-0.65499,193.64
> view matrix models
> #4,-0.7935,-0.60577,0.058334,210.09,-0.43312,0.4948,-0.75338,229.74,0.42751,-0.62307,-0.65499,195.04
> fitmap #4 inMap #1.5
Fit molecule 3glf (#4) to map polish-stat5-cs_P24_J261_sharp.mrc (#1.5) using
14323 atoms
average map value = 0.08317, steps = 72
shifted from previous position = 1.87
rotated from previous position = 1.5 degrees
atoms outside contour = 10998, contour level = 0.2
Position of 3glf (#4) relative to polish-stat5-cs_P24_J261_sharp.mrc (#1.5)
coordinates:
Matrix rotation and translation
-0.79699414 -0.60310036 0.03271555 210.44525036
-0.41423841 0.50638850 -0.75629176 227.30908388
0.43955305 -0.61631214 -0.65341600 195.03082143
Axis 0.29791000 -0.86584715 0.40194322
Axis point 129.36888139 0.00000000 165.89627059
Rotation angle (degrees) 166.41214410
Shift along axis -55.72986120
> select clear
> hide #!1.5 models
> show #!2.5 models
> mmaker #4/C-E to #2.5/C-E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain D (#4),
sequence alignment score = 525.7
RMSD between 144 pruned atom pairs is 1.091 angstroms; (across all 312 pairs:
9.612)
> mmaker #4/C-E to #2.5/C-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs:
10.786)
> mmaker #4/C to #2.5/C pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
RMSD between 153 pruned atom pairs is 1.180 angstroms; (across all 310 pairs:
8.065)
> mmaker #4/D to #2.5/D pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
RMSD between 140 pruned atom pairs is 1.150 angstroms; (across all 312 pairs:
10.303)
> mmaker #4/E to #2.5/E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 76 pruned atom pairs is 1.137 angstroms; (across all 281 pairs:
12.269)
> mmaker #4/A-E to #2.5/A-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4),
sequence alignment score = 176.6
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain B (#4),
sequence alignment score = 462.2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 454 pruned atom pairs is 1.226 angstroms; (across all 1515 pairs:
13.805)
> mmaker #4/A-B to #2.5/A-B pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4),
sequence alignment score = 176.6
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain B (#4),
sequence alignment score = 462.2
RMSD between 160 pruned atom pairs is 1.140 angstroms; (across all 612 pairs:
17.477)
> hide #!2.5 models
> show #!2.5 models
> hide #!4 models
> show #!4 models
> mmaker #4/A:1-204 to #2.5/A:63-303 pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4),
sequence alignment score = 74
RMSD between 23 pruned atom pairs is 0.868 angstroms; (across all 163 pairs:
12.128)
> mmaker #4/A:1-204 to #2.5/A:63-303
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4),
sequence alignment score = 74
RMSD between 23 pruned atom pairs is 0.868 angstroms; (across all 163 pairs:
12.128)
> mmaker #4/C-E to #2.5/C-E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain D (#4),
sequence alignment score = 525.7
RMSD between 144 pruned atom pairs is 1.091 angstroms; (across all 312 pairs:
9.612)
> mmaker #4/C-E to #2.5/C-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs:
10.786)
> select #4
14323 atoms, 14626 bonds, 46 pseudobonds, 1795 residues, 3 models selected
> view matrix models
> #4,-0.79798,-0.5982,0.073302,205.84,-0.43439,0.48658,-0.75799,227.51,0.41776,-0.6367,-0.64814,194.31
> mmaker #4/C-E to #2.5/C-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs:
10.786)
> view matrix models
> #4,-0.79798,-0.5982,0.073302,205.45,-0.43439,0.48658,-0.75799,226.22,0.41776,-0.6367,-0.64814,191.98
> view matrix models
> #4,-0.79798,-0.5982,0.073302,209.93,-0.43439,0.48658,-0.75799,227.2,0.41776,-0.6367,-0.64814,192.41
> fitmap #4 inMap #1.5
Fit molecule 3glf (#4) to map polish-stat5-cs_P24_J261_sharp.mrc (#1.5) using
14323 atoms
average map value = 0.07625, steps = 56
shifted from previous position = 1.91
rotated from previous position = 2.48 degrees
atoms outside contour = 11210, contour level = 0.2
Position of 3glf (#4) relative to polish-stat5-cs_P24_J261_sharp.mrc (#1.5)
coordinates:
Matrix rotation and translation
-0.78474199 -0.61127299 0.10259313 209.87320078
-0.47212854 0.48226270 -0.73791418 227.94133822
0.40159016 -0.62750938 -0.66705121 194.81853846
Axis 0.31745756 -0.85973503 0.40009546
Axis point 136.04597759 0.00000000 161.97288425
Rotation angle (degrees) 169.98598502
Shift along axis -51.39730412
> fitmap #4 inMap #1.5
Fit molecule 3glf (#4) to map polish-stat5-cs_P24_J261_sharp.mrc (#1.5) using
14323 atoms
average map value = 0.07625, steps = 64
shifted from previous position = 0.00132
rotated from previous position = 0.0023 degrees
atoms outside contour = 11209, contour level = 0.2
Position of 3glf (#4) relative to polish-stat5-cs_P24_J261_sharp.mrc (#1.5)
coordinates:
Matrix rotation and translation
-0.78473683 -0.61128584 0.10255597 209.87514322
-0.47211620 0.48227795 -0.73791210 227.93970756
0.40161474 -0.62748514 -0.66705922 194.81680740
Axis 0.31745723 -0.85973902 0.40008714
Axis point 136.04429405 0.00000000 161.97271727
Rotation angle (degrees) 169.98394312
Shift along axis -51.39857903
> hide #!2.5 models
> show #!1.5 models
> fitmap #4 inMap #1.5
Fit molecule 3glf (#4) to map polish-stat5-cs_P24_J261_sharp.mrc (#1.5) using
14323 atoms
average map value = 0.07626, steps = 44
shifted from previous position = 0.012
rotated from previous position = 0.00626 degrees
atoms outside contour = 11205, contour level = 0.2
Position of 3glf (#4) relative to polish-stat5-cs_P24_J261_sharp.mrc (#1.5)
coordinates:
Matrix rotation and translation
-0.78471421 -0.61130779 0.10259825 209.88442579
-0.47211893 0.48218581 -0.73797057 227.94307476
0.40165574 -0.62753457 -0.66698803 194.81451864
Axis 0.31747459 -0.85971196 0.40013152
Axis point 136.05289318 0.00000000 161.98082407
Rotation angle (degrees) 169.98366802
Shift along axis -51.38098601
> view matrix models
> #4,-0.78471,-0.61131,0.1026,212.73,-0.47212,0.48219,-0.73797,223.43,0.40166,-0.62753,-0.66699,199.43
> view matrix models
> #4,-0.78471,-0.61131,0.1026,214.46,-0.47212,0.48219,-0.73797,230.2,0.40166,-0.62753,-0.66699,198.56
> view matrix models
> #4,-0.78471,-0.61131,0.1026,209.59,-0.47212,0.48219,-0.73797,230.98,0.40166,-0.62753,-0.66699,193.11
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.80188,-0.57899,0.14748,208.53,-0.52884,0.57293,-0.62616,228.87,0.27805,-0.5801,-0.76562,201.45
> fitmap #4 inMap #1.5
Fit molecule 3glf (#4) to map polish-stat5-cs_P24_J261_sharp.mrc (#1.5) using
14323 atoms
average map value = 0.07399, steps = 56
shifted from previous position = 0.632
rotated from previous position = 3.13 degrees
atoms outside contour = 11308, contour level = 0.2
Position of 3glf (#4) relative to polish-stat5-cs_P24_J261_sharp.mrc (#1.5)
coordinates:
Matrix rotation and translation
-0.79223731 -0.58148948 0.18501356 206.95607859
-0.54247696 0.53230593 -0.64989933 230.84620856
0.27942581 -0.61524010 -0.73715727 199.98606046
Axis 0.32129214 -0.87520434 0.36164723
Axis point 142.41452013 0.00000000 151.19162562
Rotation angle (degrees) 176.90812245
Shift along axis -63.21983717
> hide #!1.5 models
> show #!2.5 models
> view matrix models
> #4,-0.79223,-0.58171,0.18435,206.98,-0.54159,0.53107,-0.65165,230.88,0.28117,-0.6161,-0.73578,199.87
> select clear
> mmaker #4/C-E to #2.5/C-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs:
10.786)
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!2.5 models
> hide #!2.5 models
> show #!4 models
> mmaker #4/C-E to #3/C-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J100-ScRFC-PCNA-2DNA-wBRCT-Rsf090-v11.pdb, chain C (#3) with 3glf,
chain C (#4), sequence alignment score = 513.1
Matchmaker J100-ScRFC-PCNA-2DNA-wBRCT-Rsf090-v11.pdb, chain D (#3) with 3glf,
chain D (#4), sequence alignment score = 484.7
Matchmaker J100-ScRFC-PCNA-2DNA-wBRCT-Rsf090-v11.pdb, chain E (#3) with 3glf,
chain E (#4), sequence alignment score = 300
RMSD between 303 pruned atom pairs is 1.218 angstroms; (across all 919 pairs:
10.954)
> mmaker #4/C-E to #2.5/C-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 299 pruned atom pairs is 1.218 angstroms; (across all 903 pairs:
10.786)
> mmaker #4/A-E to #2.5/A-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3glf, chain A (#4),
sequence alignment score = 176.6
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3glf, chain B (#4),
sequence alignment score = 462.2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3glf, chain C (#4),
sequence alignment score = 507.5
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3glf, chain D (#4),
sequence alignment score = 497.7
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3glf, chain E (#4),
sequence alignment score = 285.9
RMSD between 454 pruned atom pairs is 1.226 angstroms; (across all 1515 pairs:
13.805)
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!2.5 models
> show #!5 models
> view v1
> hide #!2.5 models
> mmaker #5/A-E to #2.5/A-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3u5z, chain B (#5),
sequence alignment score = 259.6
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3u5z, chain C (#5),
sequence alignment score = 428.2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3u5z, chain D (#5),
sequence alignment score = 465.2
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3u5z, chain E (#5),
sequence alignment score = 445.3
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3u5z, chain A (#5),
sequence alignment score = 105.3
RMSD between 389 pruned atom pairs is 1.180 angstroms; (across all 1350 pairs:
20.754)
> show #!2.5 models
> hide #!2.5 models
> select #5/K-R
16812 atoms, 17103 bonds, 14 pseudobonds, 2143 residues, 3 models selected
> delete sel
> delete #5/S-T
> view v1
> show #!2.5 models
> hide #!2.5 models
> hide #!5 models
> show #!2.5 models
> show #!3 models
> hide #!2.5 models
> show #!2.5 models
> hide #!3 models
> hide #!2.5 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #4/F
Nothing selected
> show #!2.5 models
> hide #!2.5 models
> hide #!4 models
> show #!2.5 models
> hide #!2.5 models
> show #!3 models
> hide #!3 models
> show #!4 models
> setattr #4/K c chain_id I
Assigning chain_id attribute to 1 item
> setattr #4/L c chain_id J
Assigning chain_id attribute to 1 item
> hide #!4 models
> show #!5 models
> view v1
> show #!2.5 models
> hide #!5 models
> hide #!2.5 models
> show #!5 models
> show #!2.5 models
> hide #!2.5 models
> setattr #5/F c chain_id Q
Assigning chain_id attribute to 1 item
> setattr #5/H c chain_id F
Assigning chain_id attribute to 1 item
> setattr #5/Q c chain_id H
Assigning chain_id attribute to 1 item
> show #!2.5 models
> mmaker #5/A-H to #2.5/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3u5z, chain B (#5),
sequence alignment score = 259.6
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3u5z, chain C (#5),
sequence alignment score = 428.2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3u5z, chain D (#5),
sequence alignment score = 465.2
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3u5z, chain E (#5),
sequence alignment score = 445.3
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3u5z, chain A (#5),
sequence alignment score = 105.3
Matchmaker Stat5-ref59-v3.pdb, chain F (#2.5) with 3u5z, chain G (#5),
sequence alignment score = 85.8
Matchmaker Stat5-ref59-v3.pdb, chain G (#2.5) with 3u5z, chain F (#5),
sequence alignment score = 162.6
Matchmaker Stat5-ref59-v3.pdb, chain H (#2.5) with 3u5z, chain H (#5),
sequence alignment score = 121.6
RMSD between 390 pruned atom pairs is 1.184 angstroms; (across all 1959 pairs:
30.640)
> hide #!2.5 models
> show #!2.5 models
> cartoon style nucleic xsection oval width 2.5 thickness 2.5
> cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true
> xsection oval width 2.75 thickness 1 arrowScale 1.5
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> kssp #3-5
Unknown command: kssp #3-5
> hide #!2.5 models
> show #!2.5 models
> kssp #3
Unknown command: kssp #3
> dssp #3
> hide #!2.5 models
> show #!2.5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!2.5 models
> dssp #4
> undo
> dssp #4
> undo
> hide #!4 models
> show #!5 models
> dssp #5
> undo
> show #!2.5 models
> view v1
[Repeated 1 time(s)]
> ui mousemode right select
> windowsize 1100 609
> view v1
> windowsize 1100 609
[Repeated 1 time(s)]
> windowsize 1108 609
> windowsize 1100 609
> windowsize 1100 616
> windowsize 1100 609
> 00
Unknown command: 00
> windowsize 1100 609
[Repeated 2 time(s)]
> view v1
[Repeated 1 time(s)]
> windowsize 1100 609
[Repeated 1 time(s)]
> view v1
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-v2.cxs"
> color /A #FFB381
> color /B #D7819F
> color /C #B48FE3
> color /D #D7CD85
> color /E salmon
> color /F navajo white
> color /G #CAC6FD
> color /H plum
> color /I medium orchid
> color /J light sky blue
> color /K #E7F981
> hide #!5 models
> hide #!2.5 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!2.5 models
> mmaker #5/A-H to #2.5/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 3u5z, chain B (#5),
sequence alignment score = 259.6
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 3u5z, chain C (#5),
sequence alignment score = 428.2
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 3u5z, chain D (#5),
sequence alignment score = 465.2
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 3u5z, chain E (#5),
sequence alignment score = 445.3
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 3u5z, chain A (#5),
sequence alignment score = 105.3
Matchmaker Stat5-ref59-v3.pdb, chain F (#2.5) with 3u5z, chain G (#5),
sequence alignment score = 85.8
Matchmaker Stat5-ref59-v3.pdb, chain G (#2.5) with 3u5z, chain F (#5),
sequence alignment score = 162.6
Matchmaker Stat5-ref59-v3.pdb, chain H (#2.5) with 3u5z, chain H (#5),
sequence alignment score = 121.6
RMSD between 390 pruned atom pairs is 1.184 angstroms; (across all 1959 pairs:
30.640)
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> view v1
> hide #!5 models
> show #!5 models
> hide #!2.5 models
> show #!3 models
> select #3-5/I-L
2677 atoms, 2991 bonds, 61 pseudobonds, 131 residues, 5 models selected
> show sel & #!3,5 atoms
> nucleotides sel & #!3,5 stubs
> select clear
> hide #!3 models
> show #!4 models
> hide #!5 models
> select #4/I-L
487 atoms, 543 bonds, 22 pseudobonds, 24 residues, 2 models selected
> nucleotides sel stubs
> show sel atoms
> select clear
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-v2.cxs"
> hide #!4 models
> hide #!2.5 models
> show #!3 models
> view v1
[Repeated 1 time(s)]
> select #3/F:87-94
59 atoms, 58 bonds, 8 residues, 1 model selected
> select #3/F:1-5,87-94
98 atoms, 96 bonds, 13 residues, 1 model selected
> select #3/F:1-5,59-64,87-94
154 atoms, 153 bonds, 19 residues, 1 model selected
> select #3/F:1-5,59-64,87-94/H:157-162
200 atoms, 198 bonds, 25 residues, 1 model selected
> select
> #3/H:1-6,58-63,87-92,110-117,176-181,168-173,157-161,196-199,203-207/F:87-93,2-6,58-62,46-52,34-40,111-117,196-199/G:3-6,59-62,157-162,167-172,176-182,203-207
989 atoms, 979 bonds, 126 residues, 1 model selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 126 items
> setattr sel res ss_id 88
Assigning ss_id attribute to 126 items
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> view v1
> hide #!5 models
> show #!4 models
> select #4/A:61-69
75 atoms, 77 bonds, 9 residues, 1 model selected
> setattr sel res ss_type 1
Assigning ss_type attribute to 9 items
> setattr sel res ss_id 88
Assigning ss_id attribute to 9 items
> select clear
> view v1
> show #!2.5 models
> hide #!4 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-v2.cxs"
> rename #3 ScRFC-PCNA-2DNA-wBRCT #3.1
Expected a keyword
> rename #3 ScRFC-PCNA-2DNA-wBRCT id #3.1
> rename #4 EcLoader-DNA-3GLF id #3.2
> rename #5 T4-Clamp-Loader-DNA-3U5Z id #3.3
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-v2.cxs"
> hide #!3 models
> show #!1.5 models
> volume #1.5 level 0.15
> volume #1.5 level 0.12
> volume #1.5 level 0.2
> view v1
> hide #!1 models
> view v1
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> view v1
> select #2.5/I:27-45/J
699 atoms, 780 bonds, 35 residues, 1 model selected
> ui tool show H-Bonds
Invalid H-bond GUI 'slop_color' attrbute value, using default: Invalid color
name or specifier
[Repeated 1 time(s)]
> hbonds sel color #00fdff showDist true restrict cross interModel false
> distSlop 0.5 intraMol false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2.5 Stat5-ref59-v3.pdb
14 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
Stat5-ref59-v3.pdb #2.5/A MET 163 N Stat5-ref59-v3.pdb #2.5/I DT 34 OP1 no hydrogen 2.652 N/A
Stat5-ref59-v3.pdb #2.5/A ARG 199 NH2 Stat5-ref59-v3.pdb #2.5/J DG 20 O3' no hydrogen 2.742 N/A
Stat5-ref59-v3.pdb #2.5/B ARG 90 NH2 Stat5-ref59-v3.pdb #2.5/I DG 33 OP1 no hydrogen 3.214 N/A
Stat5-ref59-v3.pdb #2.5/C ILE 90 N Stat5-ref59-v3.pdb #2.5/I DT 30 OP1 no hydrogen 2.729 N/A
Stat5-ref59-v3.pdb #2.5/C ARG 94 NH1 Stat5-ref59-v3.pdb #2.5/I DC 31 OP2 no hydrogen 3.513 N/A
Stat5-ref59-v3.pdb #2.5/C ARG 94 NH2 Stat5-ref59-v3.pdb #2.5/I DC 31 OP2 no hydrogen 3.164 N/A
Stat5-ref59-v3.pdb #2.5/C THR 123 OG1 Stat5-ref59-v3.pdb #2.5/I DT 30 OP1 no hydrogen 3.454 N/A
Stat5-ref59-v3.pdb #2.5/D ILE 103 N Stat5-ref59-v3.pdb #2.5/I DT 28 OP1 no hydrogen 2.787 N/A
Stat5-ref59-v3.pdb #2.5/D ARG 107 NH1 Stat5-ref59-v3.pdb #2.5/I DT 29 OP1 no hydrogen 3.397 N/A
Stat5-ref59-v3.pdb #2.5/D ARG 107 NH2 Stat5-ref59-v3.pdb #2.5/I DT 29 OP1 no hydrogen 3.384 N/A
Stat5-ref59-v3.pdb #2.5/D ARG 107 NH2 Stat5-ref59-v3.pdb #2.5/I DT 29 OP2 no hydrogen 3.185 N/A
Stat5-ref59-v3.pdb #2.5/E ASN 80 ND2 Stat5-ref59-v3.pdb #2.5/J DG 20 OP2 no hydrogen 2.915 N/A
Stat5-ref59-v3.pdb #2.5/E ARG 106 NH2 Stat5-ref59-v3.pdb #2.5/I DT 27 OP1 no hydrogen 3.474 N/A
Stat5-ref59-v3.pdb #2.5/G LYS 34 NZ Stat5-ref59-v3.pdb #2.5/J DA 17 OP1 no hydrogen 3.049 N/A
14 hydrogen bonds found
> select up
287 atoms, 293 bonds, 20 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 287 atom styles
> color sel byhetero
> hide #!3 models
> hide #!2 models
> show #!3.1 models
> hide #!3.1 models
> show #!2 models
> view v1
> select #2.5/A:162-164
26 atoms, 25 bonds, 3 residues, 1 model selected
> select #2.5/A:162-164,195-199
71 atoms, 69 bonds, 8 residues, 1 model selected
> select #2.5/A:162-164,195-199/B:86-90
112 atoms, 109 bonds, 13 residues, 1 model selected
> select #2.5/A:162-164,195-199/B:86-90,121-126
149 atoms, 145 bonds, 19 residues, 1 model selected
> select #2.5/A:162-164,195-199/B:86-90,121-125
144 atoms, 140 bonds, 18 residues, 1 model selected
> select #2.5/A:162-164,195-199/B:86-90,121-125/C:90-94
185 atoms, 180 bonds, 23 residues, 1 model selected
> select #2.5/A:162-164,195-199/B:86-90,121-125/C:90-94,123-126
210 atoms, 204 bonds, 27 residues, 1 model selected
> select #2.5/A:162-164,195-199/B:86-90,121-125/C:90-94,123-126/D:103-107
250 atoms, 243 bonds, 32 residues, 1 model selected
> select
> #2.5/A:162-164,195-199/B:86-90,121-125/C:90-94,123-126/D:103-107,147-152
288 atoms, 280 bonds, 38 residues, 1 model selected
> select
> #2.5/A:162-164,195-199/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151
283 atoms, 275 bonds, 37 residues, 1 model selected
> show #!3.1 models
> hide #!3.1 models
> select
> #2.5/A:162-164,195-199,228-243/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151
421 atoms, 416 bonds, 53 residues, 1 model selected
> select
> #2.5/A:162-164,195-199,228-243/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151/E:106-109
455 atoms, 449 bonds, 57 residues, 1 model selected
> select
> #2.5/A:162-164,195-199,228-243/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151/E:106-109,149-152
482 atoms, 475 bonds, 61 residues, 1 model selected
> view v1
[Repeated 1 time(s)]
> hide #2.5 & (~sel | /I:27-45/J) cartoons
> undo
> hide #2.5 & ~(sel | /I:27-45/J) cartoons
> hide #2.5/I:1-27/K
> select clear
> view v1
> select
> #2.5/A:162-164,195-199,228-243/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151/E:76-84,106-109,149-152
552 atoms, 544 bonds, 70 residues, 1 model selected
> show sel cartoons
> select
> #2.5/A:162-164,195-199,228-243/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151/E:74-84,106-109,149-152
572 atoms, 565 bonds, 72 residues, 1 model selected
> show sel cartoons
> select clear
> select #2.5/A:194
10 atoms, 10 bonds, 1 residue, 1 model selected
> view v1
> show #!3.1 models
> hide #!3.1 models
> view v1
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v4.cxs"
> view v1
> select
> #2.5/A:162-164,195-199,226-245/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151/E:74-84,106-109,149-152
604 atoms, 598 bonds, 76 residues, 1 model selected
> show sel cartoons
> select
> #2.5/A:162-164,195-199,223-248/B:86-90,121-125/C:90-94,123-126/D:103-107,147-151/E:74-84,106-109,149-152
649 atoms, 643 bonds, 82 residues, 1 model selected
> show sel cartoons
> select clear
> show #!3.1 models
> view v1
> hide #!3.1 models
> view v1
> hide #!3 models
> show #!3.1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> select #3.1/I-J
860 atoms, 962 bonds, 42 residues, 1 model selected
> ui tool show H-Bonds
Invalid H-bond GUI 'slop_color' attrbute value, using default: Invalid color
name or specifier
[Repeated 1 time(s)]
> hbonds sel color #00fdff showDist true restrict cross interModel false
> distSlop 0.5 intraMol false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3.1 ScRFC-PCNA-2DNA-wBRCT
11 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
ScRFC-PCNA-2DNA-wBRCT #3.1/A SER 384 OG ScRFC-PCNA-2DNA-wBRCT #3.1/I DG 20 OP1 no hydrogen 2.975 N/A
ScRFC-PCNA-2DNA-wBRCT #3.1/A ARG 434 NH1 ScRFC-PCNA-2DNA-wBRCT #3.1/J DG 14 N3 no hydrogen 3.579 N/A
ScRFC-PCNA-2DNA-wBRCT #3.1/A ARG 434 NH2 ScRFC-PCNA-2DNA-wBRCT #3.1/J DA 13 N3 no hydrogen 3.306 N/A
ScRFC-PCNA-2DNA-wBRCT #3.1/A GLN 636 NE2 ScRFC-PCNA-2DNA-wBRCT #3.1/I DA 12 N3 no hydrogen 2.550 N/A
ScRFC-PCNA-2DNA-wBRCT #3.1/C ILE 90 N ScRFC-PCNA-2DNA-wBRCT #3.1/I DA 16 OP1 no hydrogen 3.009 N/A
ScRFC-PCNA-2DNA-wBRCT #3.1/C ARG 94 NH1 ScRFC-PCNA-2DNA-wBRCT #3.1/I DC 17 OP1 no hydrogen 3.400 N/A
ScRFC-PCNA-2DNA-wBRCT #3.1/C ARG 94 NH2 ScRFC-PCNA-2DNA-wBRCT #3.1/I DC 17 OP2 no hydrogen 3.025 N/A
ScRFC-PCNA-2DNA-wBRCT #3.1/C THR 123 OG1 ScRFC-PCNA-2DNA-wBRCT #3.1/I DA 16 OP1 no hydrogen 3.383 N/A
ScRFC-PCNA-2DNA-wBRCT #3.1/D ILE 103 N ScRFC-PCNA-2DNA-wBRCT #3.1/I DG 14 OP1 no hydrogen 3.178 N/A
ScRFC-PCNA-2DNA-wBRCT #3.1/E ASN 80 ND2 ScRFC-PCNA-2DNA-wBRCT #3.1/J DG 14 OP2 no hydrogen 3.382 N/A
ScRFC-PCNA-2DNA-wBRCT #3.1/I DT 9 N3 ScRFC-PCNA-2DNA-wBRCT #3.1/A SER 674 OG no hydrogen 3.284 N/A
11 hydrogen bonds found
> select up
242 atoms, 249 bonds, 17 residues, 1 model selected
> style sel stick
Changed 242 atom styles
> color sel byhetero
> select #3.1/A:384-387
30 atoms, 29 bonds, 4 residues, 1 model selected
> select #3.1/A:384-387,431-440
93 atoms, 91 bonds, 14 residues, 1 model selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #3.1/A:384-387,431-440,454-466
204 atoms, 204 bonds, 27 residues, 1 model selected
> hide #!2 models
> select #3.1/A:384-387,431-440,454-466/B:87-90
237 atoms, 236 bonds, 31 residues, 1 model selected
> select #3.1/A:384-387,431-440,454-466/B:87-90,121-124
260 atoms, 258 bonds, 35 residues, 1 model selected
> select #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94
301 atoms, 298 bonds, 40 residues, 1 model selected
> select #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128
336 atoms, 332 bonds, 45 residues, 1 model selected
> select
> #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128/D:103-106
365 atoms, 360 bonds, 49 residues, 1 model selected
> select
> #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128/D:103-106,147-150
392 atoms, 386 bonds, 53 residues, 1 model selected
> select
> #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128/D:103-106,147-150/E:74-84
482 atoms, 476 bonds, 64 residues, 1 model selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select
> #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128/D:103-106,147-150/E:74-84,101-108
544 atoms, 537 bonds, 72 residues, 1 model selected
> select
> #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128/D:103-106,147-150/E:74-84,101-108,150-154
576 atoms, 568 bonds, 77 residues, 1 model selected
> hide #3.1 & protein cartoons
> select
> #3.1/A:384-387,431-440,454-466/B:87-90,121-124/C:90-94,124-128/D:103-106,147-150/E:74-84,101-108,150-154
576 atoms, 568 bonds, 77 residues, 1 model selected
> show sel cartoons
> select #3.1/K-L
430 atoms, 480 bonds, 21 residues, 1 model selected
> hide sel models
> undo
> hide sel & models
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel cartoons | atom
Expected ',' or a keyword
> hide sel cartoons, atoms
> view v1
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select
> #3.1/A:384-387,431-440,454-466,582,638/B:87-90,121-124/C:90-94,124-128/D:103-106,147-150/E:74-84,101-108,150-154
601 atoms, 594 bonds, 79 residues, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 601 atom styles
> color sel byhetero
> undo
[Repeated 2 time(s)]
> select #3.1/A:582,638
25 atoms, 26 bonds, 2 residues, 1 model selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 25 atom styles
> color sel byhetero
> view v1
> select clear
> view v1
> show #!2 models
> hide #!2 models
> show #!2 models
> view v1
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v5.cxs"
——— End of log from Fri May 27 10:46:01 2022 ———
opened ChimeraX session
> view v1
[Repeated 1 time(s)]
> hide #!2 models
> show #!2 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!2.5 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.4 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!2.4 models
> show #!2.4 models
> hide #!2.4 models
> view v1
> show #!2.5 models
> select #2.5/A:410-413
25 atoms, 24 bonds, 4 residues, 1 model selected
> show #2.5/A:410-413 cartoons
> show #2.5/A:410-414 cartoons
> select clear
> hide #!2.5 models
> show #3.1/A:636-638 cartoons
> show #3.1/A:636-639 cartoons
> select #3.1/A:582
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> undo
[Repeated 1 time(s)]
> color sel byhetero
> select clear
> select #3.1/A:674@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> select #3.1/A:582
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select clear
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> select #2.5/A:233
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> hide #3.1/A:674
> view v1
> hide #!3.1 models
> view v1
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!2.5 models
> show #!2.4 models
> hide #!3 models
> hide #!2.4 models
> show #!3 models
> select #3.2/A:61-63
27 atoms, 28 bonds, 3 residues, 1 model selected
> select #3.2/A:61-63,92-94
48 atoms, 48 bonds, 6 residues, 1 model selected
> select #3.2/A:61-64,92-94
56 atoms, 56 bonds, 7 residues, 1 model selected
> select #3.2/A:61-64,92-95
65 atoms, 65 bonds, 8 residues, 1 model selected
> show #!2.5 models
> select #3.2/A:61-64,22-95
571 atoms, 582 bonds, 74 residues, 1 model selected
> select #3.2/A:61-64,82-95
137 atoms, 139 bonds, 18 residues, 1 model selected
> hide #!2.5 models
> select #3.2/A:61-64,82-95/B:133-136
175 atoms, 178 bonds, 22 residues, 1 model selected
> select #3.2/A:61-64,82-95/B:132-136
181 atoms, 184 bonds, 23 residues, 1 model selected
> select #3.2/A:61-64,82-95/B:100-103,132-136
214 atoms, 216 bonds, 27 residues, 1 model selected
> select #3.2/A:61-64,82-95/B:100-103,132-136/C:132-136
258 atoms, 261 bonds, 32 residues, 1 model selected
> select #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136
298 atoms, 300 bonds, 37 residues, 1 model selected
> select #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104
338 atoms, 339 bonds, 42 residues, 1 model selected
> select
> #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104,133-136
376 atoms, 378 bonds, 46 residues, 1 model selected
> select
> #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104,132-136
382 atoms, 384 bonds, 47 residues, 1 model selected
> show #!2.5 models
> hide #!2.5 models
> select
> #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104,132-136/E:89-94
424 atoms, 425 bonds, 53 residues, 1 model selected
> select
> #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104,132-136/E:89-93
413 atoms, 414 bonds, 52 residues, 1 model selected
> select
> #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104,132-136/E:89-93,121-125
443 atoms, 443 bonds, 57 residues, 1 model selected
> hide #3.2 & protein cartoons
> select
> #3.2/A:61-64,82-95/B:100-103,132-136/C:100-104,132-136/D:100-104,132-136/E:89-93,121-125
443 atoms, 443 bonds, 57 residues, 1 model selected
> show sel cartoons
> show #3.2/A:316
> style sel stick
Changed 443 atom styles
> style sel stick
Changed 443 atom styles
> select #3.2/A:316
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 12 atom styles
> color sel byhetero
> show #3.2/A:313-319 cartoons
> show #!3.1 models
> hide #!3 models
> show #!3 models
> hide #!3.2 models
> show #3.1/A:632-638 cartoons
> view v1
> show #3.1/A:631-638 cartoons
> hide #!3.1 models
> show #!3.2 models
> select clear
> show #!2.5 models
> hide #!2.5 models
> view v1
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> hide #!3.2 models
> show #!3.3 models
> select #3.3/A:15-20
53 atoms, 55 bonds, 6 residues, 1 model selected
> select #3.3/A:15-19
44 atoms, 46 bonds, 5 residues, 1 model selected
> select #3.3/A:15-20
53 atoms, 55 bonds, 6 residues, 1 model selected
> select #3.3/A:16-20
46 atoms, 48 bonds, 5 residues, 1 model selected
> select #3.3/A:16-24
80 atoms, 84 bonds, 9 residues, 1 model selected
> select #3.3/A:16-24/B:80-85
134 atoms, 138 bonds, 15 residues, 1 model selected
> select #3.3/A:16-24/B:80-85,114-118
171 atoms, 174 bonds, 20 residues, 1 model selected
> select #3.3/A:16-24/B:80-84,114-118
160 atoms, 163 bonds, 19 residues, 1 model selected
> select #3.3/A:16-24/B:80-84,114-118/C:80-83
196 atoms, 199 bonds, 23 residues, 1 model selected
> select #3.3/A:16-24/B:80-84,114-118/C:80-84
203 atoms, 206 bonds, 24 residues, 1 model selected
> select #3.3/A:16-24/B:80-84,114-118/C:80-84,114-118
240 atoms, 242 bonds, 29 residues, 1 model selected
> select #3.3/A:16-24/B:80-84,114-118/C:80-84,114-118/D:114-118
277 atoms, 278 bonds, 34 residues, 1 model selected
> select #3.3/A:16-24/B:80-84,114-118/C:80-84,114-118/D:80-84,114-118
320 atoms, 321 bonds, 39 residues, 1 model selected
> select #3.3/A:16-24/B:80-84,114-118/C:80-84,114-118/D:80-84,114-118/E:80-84
363 atoms, 364 bonds, 44 residues, 1 model selected
> select
> #3.3/A:16-24/B:80-84,114-118/C:80-84,114-118/D:80-84,114-118/E:80-84,113-117
395 atoms, 395 bonds, 49 residues, 1 model selected
> view v1
> hide #3.3 & protein & ~sel cartoons
> view v1
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v7.cxs"
> hide #!3.3 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> select @@display & #3.1
916 atoms, 1011 bonds, 10 pseudobonds, 51 residues, 2 models selected
> select @@display & #3.1 & protein
56 atoms, 49 bonds, 9 residues, 1 model selected
> hide sel atoms
> select clear
> select #3.1/A:638
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> view v1
> hide #!3.1.2 models
> show #!2.5 models
> hide #!3.1 models
> hide pseduobond
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide psedobond
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide psedobonds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~psedobonds
Unknown command: ~psedobonds
> hide psedobonds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pbonds
> hide #2.5/G:34
> view v1
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v7.cxs"
> show #!3.1 models
> hide #!2.5 models
> show #!2.5 models
> hide #!3 models
> show #!3 models
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> view v1
> show #!3.1 models
> show #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3.2 models
> hide #!3.1 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v8.cxs"
> view v1
> show #!3.3 models
> hide #!3.3 models
> select #2.5/A:225-244
173 atoms, 177 bonds, 20 residues, 1 model selected
> color sel yellow green
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v8.cxs"
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-1.jpg" width 1100
> height 609 supersample 3
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!3.1 models
> select #3.1/I:12
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #3.1/I:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3.1/I:9-12
81 atoms, 89 bonds, 4 residues, 1 model selected
> transparency sel 80 cartoons
> select clear
> show #!2 models
> hide #!3 models
> select #2.5/A:196
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2.5/A:195
16 atoms, 14 bonds, 2 residues, 1 model selected
> transparency sel 80 cartoons
> select clear
> select add #2.5/I:31
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #2.5/I:33
41 atoms, 44 bonds, 2 residues, 1 model selected
> select #2.5/I:33
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2.5/I:31
19 atoms, 20 bonds, 1 residue, 1 model selected
> select clear
> show #!3.2 models
> hide #!3.1 models
> hide #!2 models
> select #3.2/I:7
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #3.2/I:6
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #3.2/I:5
61 atoms, 65 bonds, 3 residues, 1 model selected
> transparency sel 80 cartoons
> select clear
> hide #!3.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.3 models
> select #3.3/I:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3.3/I:9
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #3.3/I:7
60 atoms, 63 bonds, 3 residues, 1 model selected
> select add #3.3/I:8
80 atoms, 84 bonds, 4 residues, 1 model selected
> transparency sel 80 cartoons
> select clear
> hide #!3.3 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!2 models
> hide #!2 models
> show #!3.1 models
> select #3.1/J:14
22 atoms, 24 bonds, 1 residue, 1 model selected
> transparency sel 80 cartoons
> select clear
> select #3.1/I:12
21 atoms, 23 bonds, 1 residue, 1 model selected
> transparency sel 80
> select clear
> view name v2
> show #!2 models
> hide #!3 models
> hide #!3.1 models
> show #!3.1 models
> hide #!2 models
> view v2
> select #3.1/I:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3.1/I:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3.1/I:9
40 atoms, 42 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!2 models
> hide #!2 models
> show #!3.1 models
> hide #!3.1 models
> show #!2 models
> hide #!2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.3 models
> view v2
> hide #!3.3 models
> show #!3.1 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-2.jpg" width 1100
> height 609 supersample 3
> hide #!3.1 models
> show #!3.2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-3.jpg" width 1100
> height 609 supersample 3
> hide #!3.2 models
> show #!3.3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-4.jpg" width 1100
> height 609 supersample 3
> hide #!3.3 models
> show #!3.1 models
> combine #3.1 id #3.4
Expected a keyword
> combine #3.1 modelId id #3.4
Invalid "modelId" argument: Expected an integer
> combine #3.1 Id #3.4
Expected a keyword
> combine #3.1 modelId #3.4
> select #3.4
22831 atoms, 23321 bonds, 15 pseudobonds, 2789 residues, 3 models selected
> nucleotides sel stubs
> hide #!3.1 models
> close #3.4
> show #!3.1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v9.cxs"
——— End of log from Tue May 31 15:25:24 2022 ———
opened ChimeraX session
> select #2.5/A:225-245
179 atoms, 183 bonds, 21 residues, 1 model selected
> color sel yellow green
> view v2
> show #!2 models
> select clear
> hide #2.5
> hide #2.5 cartoons
> select #2.5/A:225-245
179 atoms, 183 bonds, 21 residues, 1 model selected
> show sel cartoons
> select clear
> select #2.5/A:225-245
179 atoms, 183 bonds, 21 residues, 1 model selected
> color sel grey
> select clear
> view v2
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs"
——— End of log from Mon Jun 6 14:52:02 2022 ———
opened ChimeraX session
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel cyan target
Missing "target" keyword's argument
> color sel cyan target a
> style sel sphere
Changed 14 atom styles
> color sel byhetero
> style sel ball
Changed 14 atom styles
> style sel stick
Changed 14 atom styles
> style sel ball
Changed 14 atom styles
> color sel byhetero
> select clear
> select #3.1/A:638@CZ3
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> select clear
> view v2
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel green target a
> select clear
> select #3.1/A:638
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel lime target a
> color sel byhetero
> color sel yellow green target a
> color sel green yellow target a
> color sel lime target a
> color sel byhetero
> select clear
> view v2
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-2_1.jpg" width
> 1100 height 609 supersample 3
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs"
——— End of log from Mon Jun 6 16:50:44 2022 ———
opened ChimeraX session
> hide #!2 models
> hide #!3.1 models
> show #!3.2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel lime target a
> color sel byhetero
> select clear
> hide #!3.2 models
> show #!3.3 models
> show #3.3/A:61-63 cartoons
> view v2
> select #3.3/A:63
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel green yellow target a
> color sel byhetero
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-4.jpg" width 1100
> height 609 supersample 3
> select #3.3/I:9
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-4.jpg" width 1100
> height 609 supersample 3
> hide #!3.3 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> show #!3.1 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs"
> hide #!2 models
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.3 models
> select #3.3/A:63
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel lime target a
> color sel byhetero
> select clear
> view v2
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-4.jpg" width 1100
> height 609 supersample 3
> hide #!3.3 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> show #!2 models
> select #2.5/A:225-245
179 atoms, 183 bonds, 21 residues, 1 model selected
> transparency sel 80 cartoons
> transparency sel 60 cartoons
> transparency sel 50 cartoons
> select clear
> select #2.5/A:225-245
179 atoms, 183 bonds, 21 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs"
> hide #!3.1 models
> show #!3.2 models
> hide #!2 models
> hide #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> ui windowfill toggle
[Repeated 3 time(s)]
> show #!2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs"
> hide #!3 models
> hide #!2 models
> show #!3.2 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!2 models
> hide #!3.1 models
> show #!3.1 models
> select #3.1/A:431
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.1/A:435
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #3.1/A:431
8 atoms, 6 bonds, 2 residues, 1 model selected
> select up
49 atoms, 48 bonds, 8 residues, 1 model selected
> select clear
> select #3.1/A:435
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #3.1/A:434
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #3.1/A:433
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #3.1/A:432
27 atoms, 23 bonds, 4 residues, 1 model selected
> select add #3.1/A:431
31 atoms, 26 bonds, 5 residues, 1 model selected
> view v2
> select add #3.1/A:436
35 atoms, 29 bonds, 6 residues, 1 model selected
> view v2
> hide sel cartoons
> select #3.1/A:384
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs"
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-2_1.jpg" width
> 1100 height 609 supersample 3
> select #3.1/A:455-462
66 atoms, 66 bonds, 8 residues, 1 model selected
> select #3.1/A:456-462
60 atoms, 60 bonds, 7 residues, 1 model selected
> color sel yellow green
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-2_1.jpg" width
> 1100 height 609 supersample 3
> hide #!2 models
> hide #!3.1 models
> show #!3.2 models
> view v2
> select #3.2/A:83
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.2/A:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.2/A:91
5 atoms, 4 bonds, 1 residue, 1 model selected
> view v2
> select #3.2/A:84-91
56 atoms, 57 bonds, 8 residues, 1 model selected
> color sel yellow green
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3b-3.jpg" width 1100
> height 609 supersample 3
> hide #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!2 models
> show #!3.1 models
> view v2
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/Fig_3/Fig3-focusDNA-v11.cxs"
——— End of log from Mon Jun 6 17:25:34 2022 ———
opened ChimeraX session
> hide #!2.5 models
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.1 models
> view v1
> show #3.1 & protein cartoons
> undo
> show #3.1 & protein cartoons
> hide #!3.1 models
> show #!3.2 models
> show #3.2 & protein cartoons
> hide #!3.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.3 models
> show #3.3 & protein cartoons
> hide #!3 models
> show #!2.5 models
> show #!2.5 cartoons
> select nucleo
Expected an objects specifier or a keyword
> select nucleotide
Expected an objects specifier or a keyword
> nucleotides stubs
> hide #!2.5 models
> show #!3 models
> hide #!3 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.5 models
> nucleotides #2.5 stubs
> select #2.5 & nucleotides
Expected a keyword
> select #2.5/I-K
1166 atoms, 1301 bonds, 1 pseudobond, 58 residues, 2 models selected
> nucleotides sel stubs
> show sel atoms
> select clear
> select #2.5/A:225-245
179 atoms, 183 bonds, 21 residues, 1 model selected
> color sel yellow green
> select clear
> hide #!2.5 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v13-Models-Compare.cxs"
——— End of log from Wed Jun 29 10:57:53 2022 ———
opened ChimeraX session
> select #2.2/I:35-37/J:14-18
163 atoms, 181 bonds, 8 residues, 1 model selected
> delete sel
> view name v3
> view v1
> view v2
> view v3
> view v1
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v14-Models-Compare.cxs"
——— End of log from Wed Jun 29 11:25:52 2022 ———
opened ChimeraX session
> hide #!2.2 models
> show #!2.5 models
> show #!3 models
> hide #!3.3 models
> show #!3.3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> mmaker #3.3/B-H to #2.5/B-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with T4-Clamp-Loader-DNA-3U5Z,
chain B (#3.3), sequence alignment score = 442.4
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with T4-Clamp-Loader-DNA-3U5Z,
chain C (#3.3), sequence alignment score = 461.6
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with T4-Clamp-Loader-DNA-3U5Z,
chain D (#3.3), sequence alignment score = 438.2
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with T4-Clamp-Loader-DNA-3U5Z,
chain E (#3.3), sequence alignment score = 375.3
Matchmaker Stat5-ref59-v3.pdb, chain F (#2.5) with T4-Clamp-Loader-DNA-3U5Z,
chain G (#3.3), sequence alignment score = 85.8
Matchmaker Stat5-ref59-v3.pdb, chain G (#2.5) with T4-Clamp-Loader-DNA-3U5Z,
chain F (#3.3), sequence alignment score = 162.6
Matchmaker Stat5-ref59-v3.pdb, chain H (#2.5) with T4-Clamp-Loader-DNA-3U5Z,
chain H (#3.3), sequence alignment score = 121.6
RMSD between 438 pruned atom pairs is 1.185 angstroms; (across all 1759 pairs:
28.127)
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.3 models
> hide #!2 models
> show #!2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v13-Models-Compare.cxs"
——— End of log from Wed Jun 29 11:45:15 2022 ———
opened ChimeraX session
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!3.3 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.3 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3.3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/S4-v1.cxs"
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/Step5-v1.jpg" width
> 1100 height 609 supersample 3
> hide #!2 models
> show #!3.1 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/RFC-v1.jpg" width 1100
> height 609 supersample 3
> hide #!3.1 models
> show #!3.2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/Ecoli-v1.jpg" width
> 1100 height 609 supersample 3
> hide #!3.2 models
> show #!3.3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/T4-v1.jpg" width 1100
> height 609 supersample 3
> transparency #2-3 0 cartoons
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/S4-v2.cxs"
——— End of log from Fri Jul 1 16:33:56 2022 ———
opened ChimeraX session
> hide #!3.3 models
> show #!3.1 models
> show #3.1/I-L target ca
> color #3.1/K plum cartoons
> color #3.1/L #E7F981 cartoons
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/RFC-v2.jpg" width 1100
> height 609 supersample 3
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/S4-v3.cxs"
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!2 models
> hide #!3 models
> show #!3.1 models
> hide #!2 models
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.3 models
> select #3.3/I:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3.3/I:11
40 atoms, 42 bonds, 2 residues, 1 model selected
> transparency sel 80 cartoons
> select clear
> hide #!3.3 models
> show #!3.2 models
> select #3.2/I:6
20 atoms, 21 bonds, 1 residue, 1 model selected
> transparency sel 80 cartoons
> select clear
> hide #!3.2 models
> show #!3.1 models
> select #3.1/I:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3.1/I:9
40 atoms, 42 bonds, 2 residues, 1 model selected
> select #3.1/I:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3.1/I:9
20 atoms, 21 bonds, 1 residue, 1 model selected
> transparency sel 80 cartoons
> select clear
> select #3.1/I:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> transparency sel 80 cartoons
> select clear
> select add #3.1/I:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3.1/I:9
40 atoms, 42 bonds, 2 residues, 1 model selected
> transparency sel 80 target ca
> transparency sel 100 target ca
> select clear
> select #3.1/I:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3.1/I:9
40 atoms, 42 bonds, 2 residues, 1 model selected
> transparency sel 80 target ca
> transparency sel 80 target atoms
Invalid "target" argument: Character 't' is not an allowed target, must be one
of acrsbmpfl
> transparency sel 80 target atom
Invalid "target" argument: Character 't' is not an allowed target, must be one
of acrsbmpfl
> transparency sel 80 atoms
> transparency sel 100 atoms
> transparency sel 80 atoms
> transparency sel 80 cartoons
> transparency sel 50 cartoons
> transparency sel 70 cartoons
> select clear
> select #3.1/I:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3.1/I:9
40 atoms, 42 bonds, 2 residues, 1 model selected
> transparency sel 80 cartoons
> select clear
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.3 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!3.3 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.3 models
> hide #!3.3 models
> show #!2 models
> hide #!3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/S4-v3.cxs"
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/Step5-v3.jpg" width
> 1100 height 609 supersample 3
> hide #!2 models
> show #!3 models
> show #!3.1 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/RFC-v3.jpg" width 1100
> height 609 supersample 3
> hide #!3.1 models
> show #!3.2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/Ecoli-v3.jpg" width
> 1100 height 609 supersample 3
> hide #!3.2 models
> show #!3.3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/T4-v3.jpg" width 1100
> height 609 supersample 3
> hide #!3.3 models
> show #!3.1 models
> color #3.1/L light sky blue cartoons
[Repeated 1 time(s)]
> color #3.1/L light sky blue target ca
> color #3.1/L light sky blue target a
> color #3.1/L light sky blue a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #3.1/L light sky blue atoms
> color #3.1/L light sky blue
> color #3.1/K plum
> color #3.1/L light blue
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/RFC-v3.jpg" width 1100
> height 609 supersample 3
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S4/S4-v3.cxs"
——— End of log from Mon Jul 4 15:09:05 2022 ———
opened ChimeraX session
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> open 7ti8
Summary of feedback from opening 7ti8 fetched from pdb
---
notes | Fetching compressed mmCIF 7ti8 from
http://files.rcsb.org/download/7ti8.cif
Fetching CCD AGS from http://ligand-expo.rcsb.org/reports/A/AGS/AGS.cif
7ti8 title:
Structure of the yeast clamp loader (Replication Factor C RFC) bound to the
open sliding clamp (Proliferating Cell Nuclear Antigen PCNA) [more info...]
Chain information for 7ti8 #4
---
Chain | Description | UniProt
A | Replication factor C subunit 1 | RFC1_YEAST
B | Replication factor C subunit 4 | RFC4_YEAST
C | Replication factor C subunit 3 | RFC3_YEAST
D | Replication factor C subunit 2 | RFC2_YEAST
E | Replication factor C subunit 5 | RFC5_YEAST
F G H | Proliferating cell nuclear antigen | PCNA_YEAST
Non-standard residues in 7ti8 #4
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> hide #4
> show #4 cartoons
> rename #4 Id #3.4 name Sc-CL-Open-7TI8
Expected a keyword
> rename #4 model Id #3.4 name Sc-CL-Open-7TI8
Expected a keyword
> rename #4 Sc-CL-Open-7TI8 Id #3.4 name
Expected a keyword
> rename #4 Sc-CL-Open-7TI8 Id #3.4
Expected a keyword
> rename #4 Sc-CL-Open-7TI8 id #3.4
> show #!2 models
> hide #!3.1 models
Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'M' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b5' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c2' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b5' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c2' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide #!2.5 models
> show #!2.1 models
> mmaker #3.4 to #2.1 pair ss
Different number of reference/match chains (10 ref, 8 match)
> mmaker #3.4/A-E to #2.1/A-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat1-Rsr115-Ct4.pdb, chain A (#2.1) with Sc-CL-Open-7TI8, chain A
(#3.4), sequence alignment score = 330.6
Matchmaker Stat1-Rsr115-Ct4.pdb, chain B (#2.1) with Sc-CL-Open-7TI8, chain B
(#3.4), sequence alignment score = 1592.5
Matchmaker Stat1-Rsr115-Ct4.pdb, chain C (#2.1) with Sc-CL-Open-7TI8, chain C
(#3.4), sequence alignment score = 1603.5
Matchmaker Stat1-Rsr115-Ct4.pdb, chain D (#2.1) with Sc-CL-Open-7TI8, chain D
(#3.4), sequence alignment score = 1649.7
Matchmaker Stat1-Rsr115-Ct4.pdb, chain E (#2.1) with Sc-CL-Open-7TI8, chain E
(#3.4), sequence alignment score = 1684.7
RMSD between 1352 pruned atom pairs is 0.690 angstroms; (across all 1692
pairs: 3.677)
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> setattr #3.4/F chain_id X
Missing or invalid "attrValue" argument: Expected a text string
> setattr #3.4/F c chain_id X
Assigning chain_id attribute to 1 item
> setattr #3.4/H c chain_id F
Assigning chain_id attribute to 1 item
> setattr #3.4/G c chain_id H
Assigning chain_id attribute to 1 item
> setattr #3.4/X c chain_id G
Assigning chain_id attribute to 1 item
> show #!2.1 models
> mmaker #3.4/A-H to #2.1/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat1-Rsr115-Ct4.pdb, chain A (#2.1) with Sc-CL-Open-7TI8, chain A
(#3.4), sequence alignment score = 330.6
Matchmaker Stat1-Rsr115-Ct4.pdb, chain B (#2.1) with Sc-CL-Open-7TI8, chain B
(#3.4), sequence alignment score = 1592.5
Matchmaker Stat1-Rsr115-Ct4.pdb, chain C (#2.1) with Sc-CL-Open-7TI8, chain C
(#3.4), sequence alignment score = 1603.5
Matchmaker Stat1-Rsr115-Ct4.pdb, chain D (#2.1) with Sc-CL-Open-7TI8, chain D
(#3.4), sequence alignment score = 1649.7
Matchmaker Stat1-Rsr115-Ct4.pdb, chain E (#2.1) with Sc-CL-Open-7TI8, chain E
(#3.4), sequence alignment score = 1684.7
Matchmaker Stat1-Rsr115-Ct4.pdb, chain F (#2.1) with Sc-CL-Open-7TI8, chain G
(#3.4), sequence alignment score = 199.6
Matchmaker Stat1-Rsr115-Ct4.pdb, chain G (#2.1) with Sc-CL-Open-7TI8, chain H
(#3.4), sequence alignment score = 221.2
Matchmaker Stat1-Rsr115-Ct4.pdb, chain H (#2.1) with Sc-CL-Open-7TI8, chain F
(#3.4), sequence alignment score = 208
RMSD between 1352 pruned atom pairs is 0.690 angstroms; (across all 2382
pairs: 32.054)
> hide #!2 models
> show #!2 models
> cartoon style nucleic xsection oval width 2.5 thickness 2.5
> cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true
> xsection oval width 2.75 thickness 1 arrowScale 1.5
> color /A #FFB381
> color /B #D7819F
> color /C #B48FE3
> color /D #D7CD85
> color /E salmon
> color /F navajo white
> color /G #CAC6FD
> color /H plum
> hide #!3 models
Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'U' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> show #!3 models
> hide #!3 models
> show #!3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v14-Models-Compare.cxs"
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> view name v4
> view v1
> hide #!3.4 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> hide #!3 models
> show #!3.1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!3 models
> coulombic #!2.1
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
Stat1-Rsr115-Ct4.pdb #2.1/A ASP 396 OD1
Stat1-Rsr115-Ct4.pdb #2.1/A ASP 396 CG
Stat1-Rsr115-Ct4.pdb #2.1/A ASP 396 OD2
Stat1-Rsr115-Ct4.pdb #2.1/A LEU 413 CD2
Stat1-Rsr115-Ct4.pdb #2.1/A LEU 413 CG
Stat1-Rsr115-Ct4.pdb #2.1/A LEU 413 CD1
Deleting 5' phosphates from: copy of Stat1-Rsr115-Ct4.pdb #/I DT 29, copy of
Stat1-Rsr115-Ct4.pdb #/I DG 11
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of Stat1-Rsr115-Ct4.pdb #/F ARG 470 H bonded to atom that should
not have hydrogens (copy of Stat1-Rsr115-Ct4.pdb #/F ARG 470 C)
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> open 7tiB
Summary of feedback from opening 7tiB fetched from pdb
---
note | Fetching compressed mmCIF 7tib from
http://files.rcsb.org/download/7tib.cif
7tib title:
Structure of the yeast clamp loader (Replication Factor C RFC) bound to the
open sliding clamp (Proliferating Cell Nuclear Antigen PCNA) and primer-
template DNA [more info...]
Chain information for 7tib #4
---
Chain | Description | UniProt
A | Replication factor C subunit 1 | RFC1_YEAST
B | Replication factor C subunit 4 | RFC4_YEAST
C | Replication factor C subunit 3 | RFC3_YEAST
D | Replication factor C subunit 2 | RFC2_YEAST
E | Replication factor C subunit 5 | RFC5_YEAST
F G H | Proliferating cell nuclear antigen | PCNA_YEAST
I | DNA
(5'-D(P*TP*TP*TP*TP*TP*TP*TP*ap*TP*GP*TP*ap*CP*TP*CP*GP*TP*ap*GP*TP*GP*TP*CP*T)-3')
|
J | DNA (5'-D(*ap*GP*ap*CP*ap*CP*TP*ap*CP*GP*ap*GP*TP*ap*CP*ap*TP*A)-3') |
Non-standard residues in 7tib #4
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> hide #4
> show #4 cartoons
> rename #4 Sc-CL-OpenDNA-7TIB id #3.5
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> hide #!3.5 models
> show #!3.5 models
> mmaker #3.4 to #2.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat3-Ref88-Ct3.pdb, chain E (#2.3) with Sc-CL-Open-7TI8, chain E
(#3.4), sequence alignment score = 1707.5
RMSD between 336 pruned atom pairs is 0.625 angstroms; (across all 348 pairs:
1.807)
> undo
> hide #!3.5 models
> show #!3.4 models
> undo
[Repeated 9 time(s)]
> redo
[Repeated 1 time(s)]
> hide #!3.1 models
> hide #!3 models
> show #!3 models
> hide #!3.5 models
> show #!3.5 models
> show #3.5 cartoons
> hide #!3.5 models
> show #!3.4 models
> mmaker #3.4/A-H to #2.1/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat1-Rsr115-Ct4.pdb, chain A (#2.1) with Sc-CL-Open-7TI8, chain A
(#3.4), sequence alignment score = 330.6
Matchmaker Stat1-Rsr115-Ct4.pdb, chain B (#2.1) with Sc-CL-Open-7TI8, chain B
(#3.4), sequence alignment score = 1592.5
Matchmaker Stat1-Rsr115-Ct4.pdb, chain C (#2.1) with Sc-CL-Open-7TI8, chain C
(#3.4), sequence alignment score = 1603.5
Matchmaker Stat1-Rsr115-Ct4.pdb, chain D (#2.1) with Sc-CL-Open-7TI8, chain D
(#3.4), sequence alignment score = 1649.7
Matchmaker Stat1-Rsr115-Ct4.pdb, chain E (#2.1) with Sc-CL-Open-7TI8, chain E
(#3.4), sequence alignment score = 1684.7
Matchmaker Stat1-Rsr115-Ct4.pdb, chain F (#2.1) with Sc-CL-Open-7TI8, chain G
(#3.4), sequence alignment score = 199.6
Matchmaker Stat1-Rsr115-Ct4.pdb, chain G (#2.1) with Sc-CL-Open-7TI8, chain H
(#3.4), sequence alignment score = 221.2
Matchmaker Stat1-Rsr115-Ct4.pdb, chain H (#2.1) with Sc-CL-Open-7TI8, chain F
(#3.4), sequence alignment score = 208
RMSD between 1352 pruned atom pairs is 0.690 angstroms; (across all 2382
pairs: 32.054)
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.5 models
> hide #!2.1 models
> show #!2.3 models
> mmaker #3.5 to #2.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat3-Ref88-Ct3.pdb, chain E (#2.3) with Sc-CL-OpenDNA-7TIB, chain
E (#3.5), sequence alignment score = 1691.9
RMSD between 336 pruned atom pairs is 0.661 angstroms; (across all 343 pairs:
1.225)
> hide #!2.3 models
> show #!2.4 models
> mmaker #3.5 to #2.4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat4-Ref80-Ct6.pdb, chain D (#2.4) with Sc-CL-OpenDNA-7TIB, chain
D (#3.5), sequence alignment score = 1642.5
RMSD between 329 pruned atom pairs is 0.462 angstroms; (across all 330 pairs:
0.497)
> hide #!2.4 models
> show #!2.4 models
> hide #!2.4 models
Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'O' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00f8' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d8' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00f8' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d8' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> open 7SH2
Summary of feedback from opening 7SH2 fetched from pdb
---
note | Fetching compressed mmCIF 7sh2 from
http://files.rcsb.org/download/7sh2.cif
7sh2 title:
Structure of the yeast Rad24-RFC loader bound to DNA and the open 9-1-1 clamp
[more info...]
Chain information for 7sh2 #4
---
Chain | Description | UniProt
A | Checkpoint protein RAD24 | RAD24_YEAST
B | Replication factor C subunit 4 | RFC4_YEAST
C | Replication factor C subunit 3 | RFC3_YEAST
D | Replication factor C subunit 2 | RFC2_YEAST
E | Replication factor C subunit 5 | RFC5_YEAST
F | Mitosis Entry Checkpoint protein MEC3 | A0A6A5PTK1_YEASX
G | DNA damage checkpoint control protein RAD17 | RAD17_YEAST
H | DNA damage checkpoint protein DDC1 | DDC1_YEAST
P | Watson strand |
T | Crick strand |
Non-standard residues in 7sh2 #4
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'H' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02d9' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d3' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02d9' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d3' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide #4
> show #4 cartoons
> mmaker #4 to #2.4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat4-Ref80-Ct6.pdb, chain A (#2.4) with 7sh2, chain A (#4),
sequence alignment score = 2049.6
RMSD between 397 pruned atom pairs is 0.760 angstroms; (across all 404 pairs:
0.876)
> hide #!3 models
> mmaker #4 to #2.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat1-Rsr115-Ct4.pdb, chain A (#2.1) with 7sh2, chain A (#4),
sequence alignment score = 2071.6
RMSD between 394 pruned atom pairs is 0.767 angstroms; (across all 404 pairs:
0.914)
> mmaker #4/A-H to #2.1/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat1-Rsr115-Ct4.pdb, chain A (#2.1) with 7sh2, chain A (#4),
sequence alignment score = 2071.6
Matchmaker Stat1-Rsr115-Ct4.pdb, chain B (#2.1) with 7sh2, chain B (#4),
sequence alignment score = 1549.3
Matchmaker Stat1-Rsr115-Ct4.pdb, chain C (#2.1) with 7sh2, chain C (#4),
sequence alignment score = 1601.1
Matchmaker Stat1-Rsr115-Ct4.pdb, chain D (#2.1) with 7sh2, chain D (#4),
sequence alignment score = 1653.9
Matchmaker Stat1-Rsr115-Ct4.pdb, chain E (#2.1) with 7sh2, chain E (#4),
sequence alignment score = 1670.9
Matchmaker Stat1-Rsr115-Ct4.pdb, chain F (#2.1) with 7sh2, chain F (#4),
sequence alignment score = 947.7
Matchmaker Stat1-Rsr115-Ct4.pdb, chain G (#2.1) with 7sh2, chain G (#4),
sequence alignment score = 1277.2
Matchmaker Stat1-Rsr115-Ct4.pdb, chain H (#2.1) with 7sh2, chain H (#4),
sequence alignment score = 988.1
RMSD between 2240 pruned atom pairs is 0.786 angstroms; (across all 2492
pairs: 1.429)
> rename #4 Sc-911-OpenDNA-7SH2 id #3.6
> show #!3 models
> hide #!3.5 models
> mmaker #3.6/A-H to #2.1/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat1-Rsr115-Ct4.pdb, chain A (#2.1) with Sc-911-OpenDNA-7SH2,
chain A (#3.6), sequence alignment score = 2071.6
Matchmaker Stat1-Rsr115-Ct4.pdb, chain B (#2.1) with Sc-911-OpenDNA-7SH2,
chain B (#3.6), sequence alignment score = 1549.3
Matchmaker Stat1-Rsr115-Ct4.pdb, chain C (#2.1) with Sc-911-OpenDNA-7SH2,
chain C (#3.6), sequence alignment score = 1601.1
Matchmaker Stat1-Rsr115-Ct4.pdb, chain D (#2.1) with Sc-911-OpenDNA-7SH2,
chain D (#3.6), sequence alignment score = 1653.9
Matchmaker Stat1-Rsr115-Ct4.pdb, chain E (#2.1) with Sc-911-OpenDNA-7SH2,
chain E (#3.6), sequence alignment score = 1670.9
Matchmaker Stat1-Rsr115-Ct4.pdb, chain F (#2.1) with Sc-911-OpenDNA-7SH2,
chain F (#3.6), sequence alignment score = 947.7
Matchmaker Stat1-Rsr115-Ct4.pdb, chain G (#2.1) with Sc-911-OpenDNA-7SH2,
chain G (#3.6), sequence alignment score = 1277.2
Matchmaker Stat1-Rsr115-Ct4.pdb, chain H (#2.1) with Sc-911-OpenDNA-7SH2,
chain H (#3.6), sequence alignment score = 988.1
RMSD between 2240 pruned atom pairs is 0.786 angstroms; (across all 2492
pairs: 1.429)
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/ScRPD/Deposite/eLife-77469_maps-models_Michael E.
> O'Donnell/RFC−DNA1−DNA2.pdb"
Chain information for RFC−DNA1−DNA2.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
I | No description available
J | No description available
K | No description available
L | No description available
> hide #4
> show #4 cartoons
> hide #!3 models
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> mmaker #4/A-H to #2.4/A-H pair ss
Different number of reference/match chains (8 ref, 5 match)
> mmaker #4/A- to #2.4/A-E pair ss
> matchmaker #4/A- to #2.4/A-E pair ss
Missing or invalid "matchAtoms" argument: only initial part "#4/A" of atom
specifier valid
> mmaker #4/A-E to #2.4/A-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat4-Ref80-Ct6.pdb, chain A (#2.4) with RFC−DNA1−DNA2.pdb, chain A
(#4), sequence alignment score = 303.5
Matchmaker Stat4-Ref80-Ct6.pdb, chain B (#2.4) with RFC−DNA1−DNA2.pdb, chain B
(#4), sequence alignment score = 1535.5
Matchmaker Stat4-Ref80-Ct6.pdb, chain C (#2.4) with RFC−DNA1−DNA2.pdb, chain C
(#4), sequence alignment score = 1581.3
Matchmaker Stat4-Ref80-Ct6.pdb, chain D (#2.4) with RFC−DNA1−DNA2.pdb, chain D
(#4), sequence alignment score = 1624.5
Matchmaker Stat4-Ref80-Ct6.pdb, chain E (#2.4) with RFC−DNA1−DNA2.pdb, chain E
(#4), sequence alignment score = 1576.3
RMSD between 1337 pruned atom pairs is 0.871 angstroms; (across all 1631
pairs: 3.361)
> close #4
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/ScRPD/Deposite/eLife-77469_maps-models_Michael E.
> O'Donnell/RFC−closed PCNA−DNA1.pdb"
Chain information for RFC−closed PCNA−DNA1.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
> hide #4
> show #4 cartoons
> mmaker #4/A-H to #2.4/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat4-Ref80-Ct6.pdb, chain A (#2.4) with RFC−closed PCNA−DNA1.pdb,
chain A (#4), sequence alignment score = 342.7
Matchmaker Stat4-Ref80-Ct6.pdb, chain B (#2.4) with RFC−closed PCNA−DNA1.pdb,
chain B (#4), sequence alignment score = 1559.5
Matchmaker Stat4-Ref80-Ct6.pdb, chain C (#2.4) with RFC−closed PCNA−DNA1.pdb,
chain C (#4), sequence alignment score = 1578.9
Matchmaker Stat4-Ref80-Ct6.pdb, chain D (#2.4) with RFC−closed PCNA−DNA1.pdb,
chain D (#4), sequence alignment score = 1611.9
Matchmaker Stat4-Ref80-Ct6.pdb, chain E (#2.4) with RFC−closed PCNA−DNA1.pdb,
chain E (#4), sequence alignment score = 1612.3
Matchmaker Stat4-Ref80-Ct6.pdb, chain F (#2.4) with RFC−closed PCNA−DNA1.pdb,
chain F (#4), sequence alignment score = 202.5
Matchmaker Stat4-Ref80-Ct6.pdb, chain G (#2.4) with RFC−closed PCNA−DNA1.pdb,
chain G (#4), sequence alignment score = 210.2
Matchmaker Stat4-Ref80-Ct6.pdb, chain H (#2.4) with RFC−closed PCNA−DNA1.pdb,
chain H (#4), sequence alignment score = 199.5
RMSD between 1347 pruned atom pairs is 0.830 angstroms; (across all 2380
pairs: 30.360)
> close #4
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/ScRPD/Deposite/eLife-77469_maps-models_Michael E.
> O'Donnell/RFC−open PCNA−DNA1.pdb"
Chain information for RFC−open PCNA−DNA1.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
> hide #4
> show #4 cartoons
> mmaker #4/A-H to #2.4/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat4-Ref80-Ct6.pdb, chain A (#2.4) with RFC−open PCNA−DNA1.pdb,
chain A (#4), sequence alignment score = 345
Matchmaker Stat4-Ref80-Ct6.pdb, chain B (#2.4) with RFC−open PCNA−DNA1.pdb,
chain B (#4), sequence alignment score = 1561.9
Matchmaker Stat4-Ref80-Ct6.pdb, chain C (#2.4) with RFC−open PCNA−DNA1.pdb,
chain C (#4), sequence alignment score = 1577.7
Matchmaker Stat4-Ref80-Ct6.pdb, chain D (#2.4) with RFC−open PCNA−DNA1.pdb,
chain D (#4), sequence alignment score = 1613.1
Matchmaker Stat4-Ref80-Ct6.pdb, chain E (#2.4) with RFC−open PCNA−DNA1.pdb,
chain E (#4), sequence alignment score = 1620.7
Matchmaker Stat4-Ref80-Ct6.pdb, chain F (#2.4) with RFC−open PCNA−DNA1.pdb,
chain F (#4), sequence alignment score = 205.6
Matchmaker Stat4-Ref80-Ct6.pdb, chain G (#2.4) with RFC−open PCNA−DNA1.pdb,
chain G (#4), sequence alignment score = 203
Matchmaker Stat4-Ref80-Ct6.pdb, chain H (#2.4) with RFC−open PCNA−DNA1.pdb,
chain H (#4), sequence alignment score = 207.2
RMSD between 1477 pruned atom pairs is 0.760 angstroms; (across all 2390
pairs: 5.815)
> hide #!2 models
> show #!3 models
> hide #!3.6 models
> show #!3.5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3.5 models
> show #!3.5 models
> hide #!3.5 models
> show #!3.5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3.5 models
> close #4
> show #!3.5 models
> hide #!3.5 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.5 models
> show #!3.6 models
> cartoon style nucleic xsection oval width 2.5 thickness 2.5
> cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true
> xsection oval width 2.75 thickness 1 arrowScale 1.5
> color /A #FFB381
> color /B #D7819F
> color /C #B48FE3
> color /D #D7CD85
> color /E salmon
> color /F navajo white
> color /G #CAC6FD
> color /H plum
> hide #!3.6 models
> hide #!3.5 models
> show #!3.6 models
> hide #!3.6 models
> show #!3.5 models
> setattr #3.5/F c chain_id X
Assigning chain_id attribute to 1 item
> setattr #3.5/H c chain_id F
Assigning chain_id attribute to 1 item
> setattr #3.5/G c chain_id H
Assigning chain_id attribute to 1 item
> setattr #3.5/X c chain_id G
Assigning chain_id attribute to 1 item
> hide #!3.5 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> select #3.1/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/A:638@CD2
1 atom, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> color sel lime
> undo
> color sel lime atoms
> color sel byhetero
> select clear
> show #!2 models
> show #!2.5 models
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #2/A:225-245
895 atoms, 915 bonds, 105 residues, 5 models selected
> color sel yellow green cartoons
> show #!2.1 models
> hide #!2 models
> show #!2.2 models
> show #!2.3 models
> show #!2.4 models
> hide #!2.5 models
> hide #!2.4 models
> hide #!2.3 models
> hide #!2.2 models
> hide #!2.1 models
> show #!2.1 models
> select clear
> select #2.1/A:239
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #2.1/A:240
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #2.1/A:241
20 atoms, 17 bonds, 3 residues, 1 model selected
> select add #2.1/A:242
32 atoms, 29 bonds, 4 residues, 1 model selected
> setattribute sel res ss_type 0
Unknown command: setattribute sel res ss_type 0
> setattri sel res ss_type 0
Unknown command: setattri sel res ss_type 0
> setattr sel res ss_type 0
Assigning ss_type attribute to 4 items
> select clear
> hide #!2 models
> hide #!2.1 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> ui tool show "Side View"
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> select #3.1/A:455
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.1/A:456
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.1/A:463
16 atoms, 14 bonds, 2 residues, 1 model selected
> select up
68 atoms, 68 bonds, 8 residues, 1 model selected
> color sel yellow green cartoons
> select clear
> show #!2.5 models
> hide #!2.5 models
> hide #!3.1 models
> show #!3.2 models
> select #3.2/A:316@CE2
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel lime atoms
> color sel byhetero
> select clear
> hide #!3.2 models
> show #!3.3 models
> select #3.3/C:175
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.3/C:173
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel yellow green cartoons
> undo
> color sel lime atoms
> color sel byhetero
> select clear
> hide #!3.3 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.4 models
> show #!3.1 models
> hide #!3.4 models
> hide #!3.1 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.4 models
> select #3.4/A:638
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel lime atoms
> color sel byhetero
> select clear
> hide #!3.4 models
> show #!3.4 models
> show #!3.1 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.1 models
> select #3.4/A:455
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.4/A:456
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.4/A:459
16 atoms, 14 bonds, 2 residues, 1 model selected
> hide #!3.4 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.4 models
> select add #3.4/A:458
27 atoms, 24 bonds, 3 residues, 1 model selected
> select add #3.4/A:457
36 atoms, 32 bonds, 4 residues, 1 model selected
> hide #!3.4 models
> show #!3.1 models
> select #3.1/A:463
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.4 models
> select #3.4/A:459
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.4/A:458
19 atoms, 17 bonds, 2 residues, 1 model selected
> select add #3.4/A:457
28 atoms, 25 bonds, 3 residues, 1 model selected
> select add #3.4/A:456
36 atoms, 32 bonds, 4 residues, 1 model selected
> color sel yellow green cartoons
> select clear
> show #!3.1 models
> hide #!3.1 models
> show #!3.5 models
> hide #!3.4 models
> select #3.5/A:638
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel lime atoms
> color sel byhetero
> select clear
> select #3.5/A:455
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.5/A:456-461
51 atoms, 51 bonds, 6 residues, 1 model selected
> select #3.5/A:456-462
60 atoms, 60 bonds, 7 residues, 1 model selected
> color sel yellow green cartoons
> select clear
> select #3.5/F:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.5/F:116
16 atoms, 14 bonds, 2 residues, 1 model selected
> select up
245 atoms, 247 bonds, 29 residues, 1 model selected
> select clear
> select #3.5/F:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.5/F:115
14 atoms, 12 bonds, 2 residues, 1 model selected
> setattri #3.5/F:111-115 res ss_type 2
Unknown command: setattri #3.5/F:111-115 res ss_type 2
> setattr #3.5/F:111-115 res ss_type 2
Assigning ss_type attribute to 5 items
> select clear
> hide #!3.5 models
> show #!3.6 models
> select #3.6/H:283
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.6/H:287
7 atoms, 6 bonds, 1 residue, 1 model selected
> setattr #3.6/H:283-287 res ss_type 2
Assigning ss_type attribute to 5 items
> setattr #3.6/H:283-287 res ss_id 88
Assigning ss_id attribute to 5 items
> select clear
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> view v2
> view v3
> hide #!3.6 models
> hide #!3 models
> show #!2.5 models
> view v3
> show #!2.4 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.4 models
> hide #!2.5 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> select #3.2/A:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.2/A:83
16 atoms, 14 bonds, 2 residues, 1 model selected
> color #3.2/A:84-90 yellow green cartoons
> select clear
> hide #!3.2 models
> show #!2.5 models
> hide #!2.5 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.2 models
Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'U' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'u' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a8' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x15' for virtual key 32 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> undo
[Repeated 1 time(s)]
> hide #!3.1 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.2 models
> select #3.2/B:135
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3.2/A:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.2/A:84
16 atoms, 14 bonds, 2 residues, 1 model selected
> color #3.2/A:84-90 #FFB381 cartoons
> select clear
> hide #!3.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.2 models
> select #3.2/A:117
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.2/A:116
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #3.2/A:115
25 atoms, 22 bonds, 3 residues, 1 model selected
> color sel yellow green cartoons
> select clear
> hide #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.5 models
> hide #!3.5 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.5 models
> select #3.5/I-J
855 atoms, 955 bonds, 26 pseudobonds, 42 residues, 2 models selected
> show sel atoms
> nucleotides sel stubs
> color #3.5/I medium orchid target ca
> color #3.5/I medium orchid
> color #3.5/J light sky blue
> select clear
> hide #!3.5 models
> show #!3.6 models
> show #3.6/t,p
> nucleotides #3.6/t,p slubs
Missing or invalid "representation" argument: Should be one of 'atoms',
'fill', 'ladder', 'slab', 'stubs', or 'tube/slab'
> nucleotides #3.6/t,p stubs
> color #3.6/t plum
> color #3.6/p light blue
> select clear
> select #3.6/A:225-245
132 atoms, 134 bonds, 1 pseudobond, 16 residues, 2 models selected
> select #3.6/A:225-244
126 atoms, 128 bonds, 1 pseudobond, 15 residues, 2 models selected
> color sel yellow green cartoons
> select clear
> view v3
> hide #!3.6 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.6 models
Mismatch between Cocoa '\x0' and Carbon 't' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'T' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 't' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 't' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2020' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02c7' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2020' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02c7' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> color #3.6/t thistle
> hide #!3.6 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> color #3.1/k thistle
> view v3
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v15-Models-Compare.cxs"
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.5 models
> hide #!3.5 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> show #!2.5 models
> view v3
[Repeated 1 time(s)]
> hide #!3 models
> show #!3 models
> hide #!3 models
> view v3
> hide #!2 models
> show #!2 models
> hide #!2.5 models
> show #!2.1 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/SI-5-multi-comparison.cxs"
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S5/SI5-Stat1.jpg" width
> 1100 height 609 supersample 3
> hide #!2.1 models
> show #!3 models
> hide #!3.2 models
> open 3U60
Summary of feedback from opening 3U60 fetched from pdb
---
note | Fetching compressed mmCIF 3u60 from
http://files.rcsb.org/download/3u60.cif
3u60 title:
Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP
Analog [more info...]
Chain information for 3u60 #4
---
Chain | Description | UniProt
A | DNA polymerase accessory protein 62 | DPA62_BPT4
B C D E | DNA polymerase accessory protein 44 | DPA44_BPT4
F G H | DNA polymerase processivity component | DPA5_BPT4
I | Template DNA strand |
J | Primer DNA strand |
Non-standard residues in 3u60 #4
---
08T —
[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium
ADP — adenosine-5'-diphosphate
MG — magnesium ion
> mmaker #4 to #2.4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat4-Ref80-Ct6.pdb, chain B (#2.4) with 3u60, chain C (#4),
sequence alignment score = 474.3
RMSD between 146 pruned atom pairs is 1.106 angstroms; (across all 299 pairs:
8.323)
> hide #4
> show #4 cartoons
> cartoon style nucleic xsection oval width 2.5 thickness 2.5
> cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true
> xsection oval width 2.75 thickness 1 arrowScale 1.5
> color #4/A #FFB381
> color #4/B #D7819F
> color #4/C #B48FE3
> color #4/D #D7CD85
> color #/E salmon
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #4/E salmon
> color #4/F navajo white
> setattr #4/F c chain_id X
Assigning chain_id attribute to 1 item
> setattr #4/H c chain_id F
Assigning chain_id attribute to 1 item
> setattr #4/X c chain_id H
Assigning chain_id attribute to 1 item
> color /F navajo white
> color /G #CAC6FD
> color /H plum
> select #4/I-J
897 atoms, 1003 bonds, 38 pseudobonds, 44 residues, 2 models selected
> show sel
> nucleotides sel stubs
> color #4/I medium orchid
> color #4/J light sky blue
> select clear
> rename #4 T4-partially-closed-3U60 id #3.7
> mmaker #3.7/A-H to #2.4/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat4-Ref80-Ct6.pdb, chain A (#2.4) with T4-partially-closed-3U60,
chain B (#3.7), sequence alignment score = 249.7
Matchmaker Stat4-Ref80-Ct6.pdb, chain B (#2.4) with T4-partially-closed-3U60,
chain C (#3.7), sequence alignment score = 474.3
Matchmaker Stat4-Ref80-Ct6.pdb, chain C (#2.4) with T4-partially-closed-3U60,
chain D (#3.7), sequence alignment score = 446.7
Matchmaker Stat4-Ref80-Ct6.pdb, chain D (#2.4) with T4-partially-closed-3U60,
chain E (#3.7), sequence alignment score = 411.7
Matchmaker Stat4-Ref80-Ct6.pdb, chain E (#2.4) with T4-partially-closed-3U60,
chain A (#3.7), sequence alignment score = 121.1
Matchmaker Stat4-Ref80-Ct6.pdb, chain F (#2.4) with T4-partially-closed-3U60,
chain G (#3.7), sequence alignment score = 106.8
Matchmaker Stat4-Ref80-Ct6.pdb, chain G (#2.4) with T4-partially-closed-3U60,
chain F (#3.7), sequence alignment score = 104.3
Matchmaker Stat4-Ref80-Ct6.pdb, chain H (#2.4) with T4-partially-closed-3U60,
chain H (#3.7), sequence alignment score = 115.5
RMSD between 394 pruned atom pairs is 1.188 angstroms; (across all 2000 pairs:
31.824)
> show #!2.4 models
> mmaker #3.7/B-H to #2.4/B-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat4-Ref80-Ct6.pdb, chain B (#2.4) with T4-partially-closed-3U60,
chain B (#3.7), sequence alignment score = 469.2
Matchmaker Stat4-Ref80-Ct6.pdb, chain C (#2.4) with T4-partially-closed-3U60,
chain C (#3.7), sequence alignment score = 453.9
Matchmaker Stat4-Ref80-Ct6.pdb, chain D (#2.4) with T4-partially-closed-3U60,
chain D (#3.7), sequence alignment score = 406.4
Matchmaker Stat4-Ref80-Ct6.pdb, chain E (#2.4) with T4-partially-closed-3U60,
chain E (#3.7), sequence alignment score = 375.1
Matchmaker Stat4-Ref80-Ct6.pdb, chain F (#2.4) with T4-partially-closed-3U60,
chain G (#3.7), sequence alignment score = 106.8
Matchmaker Stat4-Ref80-Ct6.pdb, chain G (#2.4) with T4-partially-closed-3U60,
chain F (#3.7), sequence alignment score = 104.3
Matchmaker Stat4-Ref80-Ct6.pdb, chain H (#2.4) with T4-partially-closed-3U60,
chain H (#3.7), sequence alignment score = 115.5
RMSD between 424 pruned atom pairs is 1.235 angstroms; (across all 1810 pairs:
28.258)
> hide #!3 models
> show #!3 models
> hide #!3 models
> view v3
> hide #!2 models
> show #!3 models
> show #!3.4 models
> hide #!3.7 models
> hide #!3.4 models
> show #!3.3 models
> select #3.7/A:63
11 atoms, 11 bonds, 1 residue, 1 model selected
> show #!3.7 models
> hide #!3.3 models
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel lime atoms
> color sel byhetero
> select clear
> view v3
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S5/Si5-multi-
> comparison-v2.cxs"
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/1_Figs/SI/S5/SI-5-multi-
> comparison-v2.cxs"
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v15-Models-Compare.cxs"
——— End of log from Tue Jul 5 16:32:16 2022 ———
opened ChimeraX session
> hide #!3 models
> hide #!2.4 models
> show #!2.5 models
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/0_MM/polish_5ntGap_P43_J266_sharp.mrc"
Opened polish_5ntGap_P43_J266_sharp.mrc as #4, grid size 420,420,420, pixel
0.828, shown at level 0.0553, step 2, values float32
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/0_MM/5ntGap-Rsr132-Ct1.pdb"
Chain information for 5ntGap-Rsr132-Ct1.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
> surface dust #5 size 10
No surfaces specified
> surface dust #5 size 10
No surfaces specified
> surface dust #5 size 10
No surfaces specified
> hide #!5 models
> show #!5 models
> surface dust #4 size 10
> hide #5
> show #5 cartoons
> show ligand & #5
> hide #!2 models
> show #!2 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> mmaker #5 #2.5
> matchmaker #5 #2.5
Missing required "to" argument
> mmaker #5 to #2.5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 5ntGap-Rsr132-Ct1.pdb,
chain A (#5), sequence alignment score = 2053.5
RMSD between 414 pruned atom pairs is 0.678 angstroms; (across all 426 pairs:
0.922)
> mmaker #5/A-H to #2.5/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stat5-ref59-v3.pdb, chain A (#2.5) with 5ntGap-Rsr132-Ct1.pdb,
chain A (#5), sequence alignment score = 2053.5
Matchmaker Stat5-ref59-v3.pdb, chain B (#2.5) with 5ntGap-Rsr132-Ct1.pdb,
chain B (#5), sequence alignment score = 1565.5
Matchmaker Stat5-ref59-v3.pdb, chain C (#2.5) with 5ntGap-Rsr132-Ct1.pdb,
chain C (#5), sequence alignment score = 1613.7
Matchmaker Stat5-ref59-v3.pdb, chain D (#2.5) with 5ntGap-Rsr132-Ct1.pdb,
chain D (#5), sequence alignment score = 1677.3
Matchmaker Stat5-ref59-v3.pdb, chain E (#2.5) with 5ntGap-Rsr132-Ct1.pdb,
chain E (#5), sequence alignment score = 1627.1
Matchmaker Stat5-ref59-v3.pdb, chain F (#2.5) with 5ntGap-Rsr132-Ct1.pdb,
chain F (#5), sequence alignment score = 1258.7
Matchmaker Stat5-ref59-v3.pdb, chain G (#2.5) with 5ntGap-Rsr132-Ct1.pdb,
chain G (#5), sequence alignment score = 1329.4
Matchmaker Stat5-ref59-v3.pdb, chain H (#2.5) with 5ntGap-Rsr132-Ct1.pdb,
chain H (#5), sequence alignment score = 1376
RMSD between 2539 pruned atom pairs is 0.887 angstroms; (across all 2572
pairs: 0.979)
> hide #!2 models
> show #!2 models
> color /A #FFB381
> undo
> color #4/A #FFB381
> color #4/A #FFB381 cartoons
> color #5/A #FFB381 cartoons
> color #5/A #D7819F cartoons
> undo
> color #5/B #D7819F cartoons
> color #5/A #D7819F
> color #5/B #D7819F
> color #5/A #FFB381
> color #5/C #B48FE3
> color #5/C #D7CD85
> color #5/C #B48FE3
> color #5/D #D7CD85
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> color #5/E salmon
> color #5/F navajo white
> color #5/G #CAC6FD
> color #5/H plum
> color #5/I medium orchid
> color #5/J light sky blue
> color #5/K #E7F981
> select #5/A:225-245
179 atoms, 183 bonds, 21 residues, 1 model selected
> color sel yellow green
> color #5 & ions green yellow
> cartoon style nucleic xsection oval width 2.5 thickness 2.5
> cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true
> xsection oval width 2.75 thickness 1 arrowScale 1.5
[Repeated 1 time(s)]
> hide #!2 models
> show #!4 models
> volume #4 level 0.2
> hide #!4 models
> rename #4 id #1.6
> hide #!1.5 models
> show #!1.6 models
> hide #!1.6 models
> rename #5 id #2.6
> show #!2 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> select /E:69-76,82-89
1684 atoms, 1677 bonds, 1 pseudobond, 208 residues, 14 models selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 208 items
> setattr sel res ss_id 88
Assigning ss_id attribute to 208 items
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> select clear
> show #!2.5 models
> hide #!2.5 models
> sho3 #2.6/I-K
Unknown command: sho3 #2.6/I-K
> show #2.6/I-K
> nucleotides #!2.6 stubs
> hide #!2.6 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.6 models
> select ligands
Expected an objects specifier or a keyword
> select ligand
1898 atoms, 2011 bonds, 9 pseudobonds, 69 residues, 16 models selected
> color sel & #!2.6 byhetero
> show sel
> hide #!2.6 models
> show #!2.5 models
> color sel by hetero
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color sel by hetero
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color sel by heter
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color sel byhetero
> hide #!2.5 models
> show #!2.4 models
> show #!2.6 models
> select clear
> hide #!2.4 models
> show #!2.5 models
> hide #!2.5 models
> select /E:69-76,82-89
1684 atoms, 1677 bonds, 1 pseudobond, 208 residues, 14 models selected
> select /F:2-7,68-72,79-84,91-94,118-124,262-266,281-286,406-410,462-467
3470 atoms, 3444 bonds, 428 residues, 10 models selected
> select /H:251-256,261-266,283-288,320-325
1434 atoms, 1423 bonds, 2 pseudobonds, 182 residues, 12 models selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 182 items
> setattr sel res ss_id 88
Assigning ss_id attribute to 182 items
> select /F:2-7,68-72,79-84,91-94,118-124,262-266,281-286,406-410,462-467
3470 atoms, 3444 bonds, 428 residues, 10 models selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 428 items
> setattr sel res ss_id 88
Assigning ss_id attribute to 428 items
> select /H:251-256,261-266,283-288,320-325
1434 atoms, 1423 bonds, 2 pseudobonds, 182 residues, 12 models selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 182 items
> setattr sel res ss_id 88
Assigning ss_id attribute to 182 items
> select clear
> select #8/A:542-551
Nothing selected
> select #2.6/A:542-551
Nothing selected
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v16-Models-Compare.cxs"
——— End of log from Mon Nov 14 16:29:22 2022 ———
opened ChimeraX session
> windowsize 1100 609
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> scene a
Unknown command: scene a
> scene
Unknown command: scene
> view name a
> view a
> hide #!2 models
> show #!1.5 models
> show #!1.6 models
> select #1.6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1.6,-0.22141,-0.65568,-0.72185,456.14,0.65793,0.44593,-0.60685,79.739,0.71979,-0.60929,0.33266,88.355
> view matrix models
> #1.6,-0.82155,0.31994,-0.47191,354.07,0.54784,0.21373,-0.80882,173.93,-0.15792,-0.92302,-0.35086,417.05
> view matrix models
> #1.6,0.2326,0.87708,-0.42028,59.036,0.72056,-0.44564,-0.53122,209.05,-0.65321,-0.17928,-0.73564,443.87
> view matrix models
> #1.6,0.70108,0.12899,-0.70132,150.99,0.22706,-0.97269,0.048074,290.41,-0.67597,-0.19295,-0.71122,446.18
> view matrix models
> #1.6,0.60047,-0.51721,-0.60985,264.85,-0.16538,-0.82649,0.53811,252.8,-0.78236,-0.22226,-0.58182,448.44
> view matrix models
> #1.6,0.57011,-0.73495,-0.36719,266.56,-0.36389,-0.62659,0.68918,228.56,-0.73659,-0.25929,-0.62467,453.83
> view matrix models
> #1.6,0.94044,-0.052853,-0.33581,76.94,0.08167,-0.92378,0.37411,252.82,-0.32999,-0.37925,-0.86445,441.82
> view matrix models
> #1.6,0.85393,-0.51064,0.10029,97.231,-0.50456,-0.76526,0.39974,327.03,-0.12737,-0.39195,-0.91113,415.36
> view matrix models
> #1.6,0.58674,-0.80823,-0.049953,222.25,-0.71053,-0.54344,0.447,318.01,-0.38843,-0.22678,-0.89314,431.01
> view matrix models
> #1.6,0.90943,-0.40959,-0.071959,99.096,-0.37535,-0.88295,0.28196,343.98,-0.17902,-0.22941,-0.95672,404.46
> view matrix models
> #1.6,0.90303,-0.42331,-0.073067,102.8,-0.38805,-0.87682,0.28392,344.89,-0.18425,-0.22803,-0.95606,405.05
> ui mousemode right "translate selected models"
> view matrix models
> #1.6,0.90303,-0.42331,-0.073067,102.34,-0.38805,-0.87682,0.28392,342.46,-0.18425,-0.22803,-0.95606,409.64
Drag select of 1.5 polish-stat5-cs_P24_J261_sharp.mrc , 1.6
polish_5ntGap_P43_J266_sharp.mrc
> fitmap #1.6 into #1.5
Expected a keyword
> fitmap #1.6 inMap #1.5
Fit map polish_5ntGap_P43_J266_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 18449 points
correlation = 0.3556, correlation about mean = 0.09213, overlap = 778.8
steps = 124, shift = 4.9, angle = 6.7 degrees
Position of polish_5ntGap_P43_J266_sharp.mrc (#1.6) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#1.5) coordinates:
Matrix rotation and translation
0.87352274 -0.45623470 -0.16972896 125.07705210
-0.41255062 -0.87892728 0.23935084 354.13160520
-0.25837957 -0.13905661 -0.95598287 408.84027559
Axis -0.96754585 0.22666977 0.11169533
Axis point 0.00000000 212.54782761 193.62884215
Rotation angle (degrees) 168.72313703
Shift along axis 4.91869518
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> select #1.6
2 models selected
> view matrix models
> #1.6,0.87352,-0.45623,-0.16973,125.95,-0.41255,-0.87893,0.23935,358.3,-0.25838,-0.13906,-0.95598,410.76
> fitmap #1.6 inMap #1.5
Fit map polish_5ntGap_P43_J266_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 18449 points
correlation = 0.8771, correlation about mean = 0.5704, overlap = 3014
steps = 52, shift = 1.94, angle = 0.441 degrees
Position of polish_5ntGap_P43_J266_sharp.mrc (#1.6) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#1.5) coordinates:
Matrix rotation and translation
0.87170089 -0.46143907 -0.16495923 125.42444601
-0.41755781 -0.87560736 0.24281108 358.94595186
-0.25648204 -0.14277861 -0.95594520 409.63204578
Axis -0.96705741 0.22953883 0.11005401
Axis point 0.00000000 215.64863841 193.33966149
Rotation angle (degrees) 168.50032611
Shift along axis 6.18104297
> select clear
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> view a
> undo
> fitmap #1.6 inMap #1.5
Fit map polish_5ntGap_P43_J266_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 18449 points
correlation = 0.8772, correlation about mean = 0.5706, overlap = 3014
steps = 44, shift = 0.0164, angle = 0.00928 degrees
Position of polish_5ntGap_P43_J266_sharp.mrc (#1.6) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#1.5) coordinates:
Matrix rotation and translation
0.87176732 -0.46134892 -0.16486031 125.39301972
-0.41746972 -0.87563656 0.24285724 358.93687422
-0.25639964 -0.14289082 -0.95595054 409.64287180
Axis -0.96707449 0.22949008 0.11000561
Axis point 0.00000000 215.64574697 193.33322266
Rotation angle (degrees) 168.49574430
Shift along axis 6.17107225
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1.5 models
> volume #1.6 level 0.15
> show #!1.5 models
> hide #!1.5 models
> view name b
> volume #1.6 level 0.125
> volume #1.6 level 0.1
> volume #1.6 level 0.09
> fitmap #1.6 inMap #1.5
Fit map polish_5ntGap_P43_J266_sharp.mrc in map polish-
stat5-cs_P24_J261_sharp.mrc using 43198 points
correlation = 0.8254, correlation about mean = 0.6664, overlap = 3446
steps = 36, shift = 0.0184, angle = 0.0274 degrees
Position of polish_5ntGap_P43_J266_sharp.mrc (#1.6) relative to polish-
stat5-cs_P24_J261_sharp.mrc (#1.5) coordinates:
Matrix rotation and translation
0.87164345 -0.46144439 -0.16524759 125.49552069
-0.41744562 -0.87558413 0.24308762 358.88898373
-0.25685959 -0.14290385 -0.95582511 409.68868322
Axis -0.96704169 0.22951963 0.11023209
Axis point 0.00000000 215.65386308 193.36616354
Rotation angle (degrees) 168.48799029
Shift along axis 6.17350609
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.5 models
> view b
> hide #!1.6 models
> show #!2 models
> show #!1.6 models
> hide #!1.6 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/3_ScRR91-10nt/Overall-v17-Models-Compare.cxs"
[Repeated 1 time(s)]
——— End of log from Mon Nov 14 16:55:53 2022 ———
opened ChimeraX session
> hide #!2 models
> show #!3 models
> hide #!3.7 models
> show #!3.6 models
> show #!3.5 models
> hide #!3.6 models
> hide #!3.5 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> show #!2.5 models
> hide #!2.6 models
> hide #!3 models
> show #!3 models
> hide #!2.5 models
> hide #!3 models
> show #!2.5 models
> open /Users/fengwei.zheng/Documents/Phenix/4_Elg1_RFC-
> PCNA/2_Coot/0-Apo/Elg1-RFC-AF5-v2_Rsr02-Ct1.pdb
Chain information for Elg1-RFC-AF5-v2_Rsr02-Ct1.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> open /Users/fengwei.zheng/Documents/Phenix/4_Elg1_RFC-
> PCNA/2_Coot/1-Cmplx/Elg1_RFC-PCNA-v3_rsr04.pdb
Chain information for Elg1_RFC-PCNA-v3_rsr04.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
> hide #!2 models
> show #!3 models
> rename #4-5 id #4 Elg1_RFC
Expected '.' or a keyword
> rename #4-5 id #4
> rename #4 Elg1_RFC
> hide #4
> show #4 cartoons
> hide #4.2 models
> hide #4.1 models
> show #4.2 models
> mmaker #4.2 to #3.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain E (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain E (#4.2), sequence alignment score = 1645.8
RMSD between 290 pruned atom pairs is 0.912 angstroms; (across all 341 pairs:
1.436)
> hide #4.2 models
> show #4.2 models
> hide #4.2 models
> show #4.2 models
> hide #!3 models
> show #!3 models
> mmaker #4.2/A-H to #3.1/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 7.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain B (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 9.5
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain C (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 4.3
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain D (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain A (#4.2), sequence alignment score = 228.1
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain E (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain B (#4.2), sequence alignment score = 483.9
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain C (#4.2), sequence alignment score = 1.9
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain D (#4.2), sequence alignment score = 8.5
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain E (#4.2), sequence alignment score = 13.7
RMSD between 179 pruned atom pairs is 1.291 angstroms; (across all 861 pairs:
44.247)
> mmaker #4.2/F-H to #3.1/F-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 1242.4
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 1237.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 1161.4
RMSD between 403 pruned atom pairs is 1.252 angstroms; (across all 767 pairs:
3.172)
> mmaker #4.1 to #4.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Elg1-RFC-
AF5-v2_Rsr02-Ct1.pdb, chain A (#4.1), sequence alignment score = 3064.9
RMSD between 606 pruned atom pairs is 0.297 angstroms; (across all 606 pairs:
0.297)
> hide #!3 models
> show #4.1 models
> mmaker #4.1/A-E to #4.2/A-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Elg1-RFC-
AF5-v2_Rsr02-Ct1.pdb, chain A (#4.1), sequence alignment score = 3064.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Elg1-RFC-
AF5-v2_Rsr02-Ct1.pdb, chain B (#4.1), sequence alignment score = 1641.2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Elg1-RFC-
AF5-v2_Rsr02-Ct1.pdb, chain C (#4.1), sequence alignment score = 1739.6
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Elg1-RFC-
AF5-v2_Rsr02-Ct1.pdb, chain D (#4.1), sequence alignment score = 1806.3
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Elg1-RFC-
AF5-v2_Rsr02-Ct1.pdb, chain E (#4.1), sequence alignment score = 1802.2
RMSD between 1976 pruned atom pairs is 0.355 angstroms; (across all 1976
pairs: 0.355)
> hide #4.1 models
> show #!3 models
> hide #!1 models
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Structures/RR911/templates/ystRFC-PCNA_1sxj.pdb"
ystRFC-PCNA_1sxj.pdb title:
Crystal structure of the eukaryotic clamp loader (replication factor C, RFC)
bound to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA)
[more info...]
Chain information for ystRFC-PCNA_1sxj.pdb #5
---
Chain | Description | UniProt
A | activator 1 95 kda subunit | RFC1_YEAST
B | activator 1 37 kda subunit | RFC4_YEAST
C | activator 1 40 kda subunit | RFC3_YEAST
D | activator 1 41 kda subunit | RFC2_YEAST
E | activator 1 40 kda subunit | RFC5_YEAST
F | PCNA | PCNA_YEAST
G | PCNA | PCNA_YEAST
H | PCNA | PCNA_YEAST
Non-standard residues in ystRFC-PCNA_1sxj.pdb #5
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> rename #5 id #4.3
> close #4.3
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Structures/RR911/templates/ystRFC-PCNA_1sxj.pdb"
ystRFC-PCNA_1sxj.pdb title:
Crystal structure of the eukaryotic clamp loader (replication factor C, RFC)
bound to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA)
[more info...]
Chain information for ystRFC-PCNA_1sxj.pdb #5
---
Chain | Description | UniProt
A | activator 1 95 kda subunit | RFC1_YEAST
B | activator 1 37 kda subunit | RFC4_YEAST
C | activator 1 40 kda subunit | RFC3_YEAST
D | activator 1 41 kda subunit | RFC2_YEAST
E | activator 1 40 kda subunit | RFC5_YEAST
F | PCNA | PCNA_YEAST
G | PCNA | PCNA_YEAST
H | PCNA | PCNA_YEAST
Non-standard residues in ystRFC-PCNA_1sxj.pdb #5
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> rename #5 id #4
> hide #4.2 models
> mmaker #4.3/A-H to #3.1/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain A (#4.3), sequence alignment score = 1956.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain B (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain B (#4.3), sequence alignment score = 1541.7
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain C (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain C (#4.3), sequence alignment score = 1606.5
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain D (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain D (#4.3), sequence alignment score = 1617.1
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain E (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain E (#4.3), sequence alignment score = 1471.9
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain F (#4.3), sequence alignment score = 1241.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain G (#4.3), sequence alignment score = 1219.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain H (#4.3), sequence alignment score = 1142.2
RMSD between 606 pruned atom pairs is 0.928 angstroms; (across all 2490 pairs:
35.810)
> hide #4.3
> show #4.3 cartoons
> mmaker #4.3/A to #3.1/A pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain A (#4.3), sequence alignment score = 1956.8
RMSD between 204 pruned atom pairs is 0.730 angstroms; (across all 441 pairs:
18.453)
> mmaker #4.3/A,F-H to #3.1/A,F-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain A (#4.3), sequence alignment score = 1956.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain F (#4.3), sequence alignment score = 1241.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain G (#4.3), sequence alignment score = 1219.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain H (#4.3), sequence alignment score = 1142.2
RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 1208 pairs:
33.241)
> scene name a
Unknown command: scene name a
> view name elg1a
> mmaker #4.3/A to #3.1/A pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain A (#4.3), sequence alignment score = 1956.8
RMSD between 204 pruned atom pairs is 0.730 angstroms; (across all 441 pairs:
18.453)
> hide #!3 models
> setattr #4.3/H c chain_id X
Assigning chain_id attribute to 1 item
> setattr #4.3/F c chain_id G
Assigning chain_id attribute to 1 item
> undo
> hide #!3 models
> undo
> view elg1a
> hide #!3 models
> close #4.3
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Structures/RR911/templates/ystRFC-PCNA_1sxj.pdb"
ystRFC-PCNA_1sxj.pdb title:
Crystal structure of the eukaryotic clamp loader (replication factor C, RFC)
bound to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA)
[more info...]
Chain information for ystRFC-PCNA_1sxj.pdb #5
---
Chain | Description | UniProt
A | activator 1 95 kda subunit | RFC1_YEAST
B | activator 1 37 kda subunit | RFC4_YEAST
C | activator 1 40 kda subunit | RFC3_YEAST
D | activator 1 41 kda subunit | RFC2_YEAST
E | activator 1 40 kda subunit | RFC5_YEAST
F | PCNA | PCNA_YEAST
G | PCNA | PCNA_YEAST
H | PCNA | PCNA_YEAST
Non-standard residues in ystRFC-PCNA_1sxj.pdb #5
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> rename #5 id #4
> show #!3 models
> hide #4.3
> show #4.3 cartoons
> mmaker #4.3/A to #3.1/A pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain A (#4.3), sequence alignment score = 1956.8
RMSD between 204 pruned atom pairs is 0.730 angstroms; (across all 441 pairs:
18.453)
> hide #!3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v1.cxs"
> view name a
> show #!3 models
> hide #!3 models
> setattr #4.3/H c chain_id X
Assigning chain_id attribute to 1 item
> setattr #4.3/G c chain_id H
Assigning chain_id attribute to 1 item
> setattr #4.3/F c chain_id G
Assigning chain_id attribute to 1 item
> setattr #4.3/X c chain_id F
Assigning chain_id attribute to 1 item
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v2.cxs"
> show #!3 models
> mmaker #4.3/A,F-H to #3.1/A,F-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain A (#4.3), sequence alignment score = 1956.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain G (#4.3), sequence alignment score = 1241.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain H (#4.3), sequence alignment score = 1219.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain F (#4.3), sequence alignment score = 1142.2
RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 1208 pairs:
33.241)
> hide #!3 models
> show #!3 models
> hide #!4.3 models
> hide #!3 models
> show #!4.3 models
> mmaker #4.3/F-H to #3.1/F-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain G (#4.3), sequence alignment score = 1241.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain H (#4.3), sequence alignment score = 1219.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain F (#4.3), sequence alignment score = 1142.2
RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 767 pairs:
2.686)
> mmaker #4.3/F to #3.1/F pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain F (#4.3), sequence alignment score = 1172.8
RMSD between 239 pruned atom pairs is 0.861 angstroms; (across all 254 pairs:
1.184)
> hide #!4.3 models
> show #!3 models
> show #!4.3 models
> mmaker #4.3/F-H to #3.1/F-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain G (#4.3), sequence alignment score = 1241.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain H (#4.3), sequence alignment score = 1219.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ystRFC-PCNA_1sxj.pdb,
chain F (#4.3), sequence alignment score = 1142.2
RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 767 pairs:
2.686)
> hide #!4.3 models
> show #!4.3 models
> hide #!3 models
Populating font family aliases took 332 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/ScRFC-PCNA_1SXJ.pdb" models
> #4.3 relModel #3.1
> close #4.3
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/ScRFC-PCNA_1SXJ.pdb"
ScRFC-PCNA_1SXJ.pdb title:
Crystal structure of the eukaryotic clamp loader (replication factor C, RFC)
bound to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA)
[more info...]
Chain information for ScRFC-PCNA_1SXJ.pdb #5
---
Chain | Description | UniProt
A | activator 1 95 kda subunit | RFC1_YEAST
B | activator 1 37 kda subunit | RFC4_YEAST
C | activator 1 40 kda subunit | RFC3_YEAST
D | activator 1 41 kda subunit | RFC2_YEAST
E | activator 1 40 kda subunit | RFC5_YEAST
F | PCNA | PCNA_YEAST
G | PCNA | PCNA_YEAST
H | PCNA | PCNA_YEAST
Non-standard residues in ScRFC-PCNA_1SXJ.pdb #5
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> rename #5 id #4
> hide #4.3
> show #4.3 cartoons
> mmaker #4.3/F-H to #3.1/F-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain G (#4.3), sequence alignment score = 1241.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain H (#4.3), sequence alignment score = 1219.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain F (#4.3), sequence alignment score = 1142.2
RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 767 pairs:
2.686)
> show #!3 models
> hide #!3 models
> close #4.3
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/ScRFC-PCNA_1SXJ.pdb"
Summary of feedback from opening /Users/fengwei.zheng/OneDrive - Van Andel
Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/ScRFC-PCNA_1SXJ.pdb
---
warnings | Cannot find LINK/SSBOND residue MSE (-2 )
Cannot find LINK/SSBOND residue HIS (-3 )
ScRFC-PCNA_1SXJ.pdb title:
Crystal structure of the eukaryotic clamp loader (replication factor C, RFC)
bound to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA)
[more info...]
Chain information for ScRFC-PCNA_1SXJ.pdb #5
---
Chain | Description | UniProt
A | activator 1 95 kda subunit | RFC1_YEAST
B | activator 1 37 kda subunit | RFC4_YEAST
C | activator 1 40 kda subunit | RFC3_YEAST
D | activator 1 41 kda subunit | RFC2_YEAST
E | activator 1 40 kda subunit | RFC5_YEAST
F | PCNA | PCNA_YEAST
G | PCNA | PCNA_YEAST
H | PCNA | PCNA_YEAST
Non-standard residues in ScRFC-PCNA_1SXJ.pdb #5
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> rename #5 id #4
> hide #4.3
> show #4.3 cartoons
> mmaker #4.3/F-H to #3.1/F-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain G (#4.3), sequence alignment score = 1241.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain H (#4.3), sequence alignment score = 1219.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain F (#4.3), sequence alignment score = 1142.2
RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 767 pairs:
2.686)
> lighting soft
> hide #!4.3 models
> show #!3 models
> mmaker #4.3/F,G,H to #3.1/F,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain F (#4.3), sequence alignment score = 1172.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain G (#4.3), sequence alignment score = 1216.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain H (#4.3), sequence alignment score = 1124.2
RMSD between 547 pruned atom pairs is 0.967 angstroms; (across all 765 pairs:
2.525)
> show #!4.3 models
> hide #!3 models
> mmaker #4.3/A,F,G,H to #3.1/A,F,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain A (#4.3), sequence alignment score = 1956.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain F (#4.3), sequence alignment score = 1172.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain G (#4.3), sequence alignment score = 1216.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain H (#4.3), sequence alignment score = 1124.2
RMSD between 580 pruned atom pairs is 1.006 angstroms; (across all 1206 pairs:
13.225)
> mmaker #4.3/A,F-H to #3.1/A,F-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain A (#4.3), sequence alignment score = 1956.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain G (#4.3), sequence alignment score = 1241.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain H (#4.3), sequence alignment score = 1219.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain F (#4.3), sequence alignment score = 1142.2
RMSD between 563 pruned atom pairs is 0.988 angstroms; (across all 1208 pairs:
33.241)
> mmaker #4.3/A,F,G,H to #3.1/A,F,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain A (#4.3), sequence alignment score = 1956.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain F (#4.3), sequence alignment score = 1172.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain G (#4.3), sequence alignment score = 1216.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain H (#4.3), sequence alignment score = 1124.2
RMSD between 580 pruned atom pairs is 1.006 angstroms; (across all 1206 pairs:
13.225)
> hide #!4.3 models
> show #4.2 models
> show #!3 models
> mmaker #4.2/A,F,G,H to #3.1/A,F,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain A (#4.2), sequence alignment score = 349.3
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 1178.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 1237.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 1154.8
RMSD between 567 pruned atom pairs is 1.192 angstroms; (across all 1307 pairs:
25.309)
> hide #!3 models
> hide #4.2 models
> show #4.1 models
> mmaker #4.1/A-E to #4.2/A-E pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Elg1-RFC-
AF5-v2_Rsr02-Ct1.pdb, chain A (#4.1), sequence alignment score = 3064.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Elg1-RFC-
AF5-v2_Rsr02-Ct1.pdb, chain B (#4.1), sequence alignment score = 1641.2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Elg1-RFC-
AF5-v2_Rsr02-Ct1.pdb, chain C (#4.1), sequence alignment score = 1739.6
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Elg1-RFC-
AF5-v2_Rsr02-Ct1.pdb, chain D (#4.1), sequence alignment score = 1806.3
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Elg1-RFC-
AF5-v2_Rsr02-Ct1.pdb, chain E (#4.1), sequence alignment score = 1802.2
RMSD between 1976 pruned atom pairs is 0.355 angstroms; (across all 1976
pairs: 0.355)
> show #4.2 models
> hide #4.2 models
> hide #4.1 models
> show #!4.3 models
> show #!3 models
> mmaker #4.2/A,B,C,D,E,F,G,H to #3.1/A,B,C,D,E,F,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain A (#4.2), sequence alignment score = 349.3
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain B (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain B (#4.2), sequence alignment score = 1567.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain C (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain C (#4.2), sequence alignment score = 1634.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain D (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain D (#4.2), sequence alignment score = 1643.5
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain E (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain E (#4.2), sequence alignment score = 1645.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 1178.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 1237.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 1154.8
RMSD between 291 pruned atom pairs is 0.986 angstroms; (across all 2629 pairs:
21.565)
> show #4.2 models
> hide #!4.3 models
> mmaker #4.2/A,F,G,H to #3.1/A,F,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain A (#4.2), sequence alignment score = 349.3
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 1178.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 1237.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 1154.8
RMSD between 567 pruned atom pairs is 1.192 angstroms; (across all 1307 pairs:
25.309)
> hide #4.2 models
> show #!4.3 models
> mmaker #4.3/A,B,C,D,E,F,G,H to #3.1/A,B,C,D,E,F,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain A (#4.3), sequence alignment score = 1956.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain B (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain B (#4.3), sequence alignment score = 1541.7
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain C (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain C (#4.3), sequence alignment score = 1606.5
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain D (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain D (#4.3), sequence alignment score = 1617.1
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain E (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain E (#4.3), sequence alignment score = 1471.9
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain F (#4.3), sequence alignment score = 1172.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain G (#4.3), sequence alignment score = 1216.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain H (#4.3), sequence alignment score = 1124.2
RMSD between 531 pruned atom pairs is 1.127 angstroms; (across all 2488 pairs:
14.043)
> mmaker #4.2/F,G,H to #3.1/F,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 1178.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 1237.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 1154.8
RMSD between 569 pruned atom pairs is 1.194 angstroms; (across all 765 pairs:
1.944)
> mmaker #4.3/F,G,H to #3.1/F,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain F (#4.3), sequence alignment score = 1172.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain G (#4.3), sequence alignment score = 1216.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain H (#4.3), sequence alignment score = 1124.2
RMSD between 547 pruned atom pairs is 0.967 angstroms; (across all 765 pairs:
2.525)
> mmaker #4.3/A,F,G,H to #3.1/A,F,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain A (#4.3), sequence alignment score = 1956.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain F (#4.3), sequence alignment score = 1172.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain G (#4.3), sequence alignment score = 1216.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain H (#4.3), sequence alignment score = 1124.2
RMSD between 580 pruned atom pairs is 1.006 angstroms; (across all 1206 pairs:
13.225)
> hide #!4.3 models
> show #4.2 models
> mmaker #4.2/F,G,H to #3.1/F,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain F (#4.2), sequence alignment score = 1178.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain G (#4.2), sequence alignment score = 1237.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with Elg1_RFC-
PCNA-v3_rsr04.pdb, chain H (#4.2), sequence alignment score = 1154.8
RMSD between 569 pruned atom pairs is 1.194 angstroms; (across all 765 pairs:
1.944)
> show #!4.3 models
> hide #!4.3 models
> hide #4.2 models
> show #4.1 models
> show #4.2 models
> hide #!3 models
> hide #4.1 models
> show #4.1 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v3.cxs"
> cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true
> xsection oval width 2.75 thickness 1 arrowScale 1.5
> color /A #FFB381
> color /B #D7819F
> color /C #B48FE3
> color /D #D7CD85
> color /E salmon
> color /F navajo white
> color /G #CAC6FD
> color /H plum
> show #!4.3 models
> hide #4.2 models
> hide #4.1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4.3 models
> hide #!3 models
> show #4.1 models
> show #!3 models
> hide #!4 models
> show #!4 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v4.cxs"
——— End of log from Tue Dec 6 11:47:28 2022 ———
opened ChimeraX session
> hide #!3 models
> show #!3 models
> hide #4.1 models
> show #4.2 models
> hide #4.2 models
> show #4.2 models
> view name a
> hide #!3 models
> show #4.1 models
> select #4.1-2/A:278-329
838 atoms, 848 bonds, 104 residues, 2 models selected
> delete sel
> show #!4.3 models
> hide #!4.3 models
> select #4.1-2/B:1-8
122 atoms, 120 bonds, 16 residues, 2 models selected
> delete sel
> select #4.1-2/C:1-9
138 atoms, 136 bonds, 18 residues, 2 models selected
> show #!4.3 models
> hide #!4.3 models
> delete sel
> show #!4.3 models
> hide #!4.2 models
> hide #!4.1 models
> show #!4.2 models
> show #!4.1 models
> hide #!4.3 models
> select #4.1-2/D:1-23
356 atoms, 360 bonds, 46 residues, 2 models selected
> show #!4.3 models
> hide #!4.3 models
> delete sel
> show #!4.3 models
> hide #!4.2 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.3 models
> show #!4.2 models
> select #4.1-2/A:663-696
570 atoms, 578 bonds, 68 residues, 2 models selected
> delete sel
> select #4.1-2/A:734-765
546 atoms, 552 bonds, 64 residues, 2 models selected
> delete sel
> select #4.1-2/A:734-791
440 atoms, 456 bonds, 52 residues, 2 models selected
> delete sel
> view a
> show #!3 models
> hide #!4.2 models
> hide #!4.1 models
> show #!4.1 models
> show #!4.2 models
> hide #!4.1 models
> hide #!3 models
> show #!3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v5.cxs"
> hide #!3 models
> color #4.1-2/A:557-616 magenta
> select #4.1-2/A:515-532
272 atoms, 272 bonds, 36 residues, 2 models selected
> select #4.1-2/A:515-533
280 atoms, 280 bonds, 38 residues, 2 models selected
> select #4.1-2/A:515-534
292 atoms, 292 bonds, 40 residues, 2 models selected
> select #4.1-2/A:515-535
304 atoms, 304 bonds, 42 residues, 2 models selected
> select #4.1-2/A:213-231
280 atoms, 284 bonds, 38 residues, 2 models selected
> select #4.1-2/A:213-232
296 atoms, 300 bonds, 40 residues, 2 models selected
> select #4.1-2/A:213-231
280 atoms, 284 bonds, 38 residues, 2 models selected
> select #4.1-2/A:212-231
296 atoms, 300 bonds, 40 residues, 2 models selected
> select #4.1-2/A:212-231,515-535
600 atoms, 604 bonds, 82 residues, 2 models selected
> show #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> color sel blue cartoons
> view a
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v6.cxs"
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> select #4.1-2/A:1-231,515-535
1028 atoms, 1050 bonds, 134 residues, 2 models selected
> color sel blue cartoons
> hide #!4.2 models
> show #!4.2 models
> view a
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v6.cxs"
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Elg1_RFC-v1.jpg" width 1100
> height 609 supersample 3
> hide #!4.1 models
> show #!4.2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Elg1_RFC-PCNA_v1.jpg" width
> 1100 height 609 supersample 3
> hide #!4.2 models
> hide #!4 models
> show #!4.3 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/RFC-PCNA_v1.jpg" width 1100
> height 609 supersample 3
> hide #!4.3 models
> hide #!4 models
> show #!3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Elg1_RFC-PCNA-2DNA_v1.jpg"
> width 1100 height 609 supersample 3
> hide #!3 models
> show #!2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Rad24_RFC-
> PCNA-10nt_gap_DNA_v1.jpg" width 1100 height 609 supersample 3
> hide #!2 models
> show #!4 models
> show #!4.2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v7.cxs"
——— End of log from Tue Dec 6 12:15:53 2022 ———
opened ChimeraX session
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Downloads/12-Elg1_RFC/0-map/0-CS/Local/0-Elg1RFC/cryosparc_P29_J632_004_volume_map_sharp.mrc"
Opened cryosparc_P29_J632_004_volume_map_sharp.mrc as #5, grid size
420,420,420, pixel 0.828, shown at level 0.1, step 2, values float32
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Downloads/12-Elg1_RFC/0-map/0-CS/Local/1-Elg1RFC-
> PCNA/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/Downloads/12-Elg1_RFC/0-map/0-CS/Local/1-Elg1RFC-
> PCNA/Open/cryosparc_P29_J701_004_volume_map_sharp.mrc"
Opened cryosparc_P29_J701_004_volume_map_sharp.mrc as #7, grid size
420,420,420, pixel 0.828, shown at level 0.0759, step 2, values float32
> surface dust #0-9 size 10
> volume #5-7 step 1 level 0.15
> hide #!4 models
> show #!4 models
> select add #5
2 models selected
> select subtract #5
Nothing selected
> select add #5
2 models selected
> select add #6
4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.36561,0.14267,-0.91977,377.08,0.71938,0.67036,-0.18197,-33.129,0.59061,-0.72819,-0.34773,269.16,#6,-0.36561,0.14267,-0.91977,377.08,0.71938,0.67036,-0.18197,-33.129,0.59061,-0.72819,-0.34773,269.16
> view matrix models
> #5,0.38251,0.71444,0.58589,-123.87,0.90722,-0.41055,-0.091667,108.33,0.17504,0.56659,-0.80519,195.32,#6,0.38251,0.71444,0.58589,-123.87,0.90722,-0.41055,-0.091667,108.33,0.17504,0.56659,-0.80519,195.32
> view matrix models
> #5,0.88522,0.1504,0.44019,-84.089,0.39058,-0.75428,-0.52774,336.56,0.25266,0.63909,-0.72645,154.9,#6,0.88522,0.1504,0.44019,-84.089,0.39058,-0.75428,-0.52774,336.56,0.25266,0.63909,-0.72645,154.9
> view matrix models
> #5,0.89431,0.22573,0.38634,-89.043,0.44658,-0.3965,-0.8021,314.2,-0.027878,0.88985,-0.4554,109.97,#6,0.89431,0.22573,0.38634,-89.043,0.44658,-0.3965,-0.8021,314.2,-0.027878,0.88985,-0.4554,109.97
> view matrix models
> #5,0.90632,0.21245,0.36532,-84.98,0.42181,-0.40187,-0.81276,321.38,-0.025859,0.89071,-0.45383,109.18,#6,0.90632,0.21245,0.36532,-84.98,0.42181,-0.40187,-0.81276,321.38,-0.025859,0.89071,-0.45383,109.18
> select add #7
6 models selected
> view matrix models
> #5,0.90662,0.20218,0.37036,-84.14,0.42188,-0.45113,-0.78645,325.27,0.0080759,0.86925,-0.4943,114.4,#6,0.90662,0.20218,0.37036,-84.14,0.42188,-0.45113,-0.78645,325.27,0.0080759,0.86925,-0.4943,114.4,#7,0.99993,0.00015236,-0.011438,2.0352,-0.00079073,0.99844,-0.055827,10.423,0.011412,0.055833,0.99837,-11.573
> hide #!7 models
> hide #!5 models
> select subtract #7
4 models selected
> view matrix models
> #5,-0.025136,0.96689,0.25395,-29.878,0.9987,0.013002,0.04935,-5.9153,0.044414,0.25486,-0.96596,297.84,#6,-0.025136,0.96689,0.25395,-29.878,0.9987,0.013002,0.04935,-5.9153,0.044414,0.25486,-0.96596,297.84
> view matrix models
> #5,0.83634,-0.074993,-0.54306,139.79,-0.058915,-0.99716,0.04697,353.6,-0.54504,-0.0072879,-0.83838,423.6,#6,0.83634,-0.074993,-0.54306,139.79,-0.058915,-0.99716,0.04697,353.6,-0.54504,-0.0072879,-0.83838,423.6
> view matrix models
> #5,0.040608,-0.99887,0.024519,336,-0.58373,-0.0038,0.81194,138.69,-0.81093,-0.047284,-0.58322,431.43,#6,0.040608,-0.99887,0.024519,336,-0.58373,-0.0038,0.81194,138.69,-0.81093,-0.047284,-0.58322,431.43
> view matrix models
> #5,-0.34757,-0.41118,0.84269,156.84,-0.32076,0.89664,0.3052,29.408,-0.88109,-0.16422,-0.44353,438.68,#6,-0.34757,-0.41118,0.84269,156.84,-0.32076,0.89664,0.3052,29.408,-0.88109,-0.16422,-0.44353,438.68
> view matrix models
> #5,-0.72128,-0.40442,-0.56231,473.99,-0.6819,0.27219,0.67892,132.68,-0.12151,0.87313,-0.4721,132.58,#6,-0.72128,-0.40442,-0.56231,473.99,-0.6819,0.27219,0.67892,132.68,-0.12151,0.87313,-0.4721,132.58
> view matrix models
> #5,0.63823,-0.66341,-0.39057,247.93,-0.76761,-0.50984,-0.38836,473.33,0.058516,0.54767,-0.83464,221.68,#6,0.63823,-0.66341,-0.39057,247.93,-0.76761,-0.50984,-0.38836,473.33,0.058516,0.54767,-0.83464,221.68
> view matrix models
> #5,0.73227,-0.63751,-0.23951,199.79,-0.66536,-0.59476,-0.45117,481.12,0.14518,0.48974,-0.8597,220.82,#6,0.73227,-0.63751,-0.23951,199.79,-0.66536,-0.59476,-0.45117,481.12,0.14518,0.48974,-0.8597,220.82
> view matrix models
> #5,0.56843,-0.71447,-0.40794,272.08,-0.81895,-0.4439,-0.3637,466.66,0.078766,0.54082,-0.83744,219.79,#6,0.56843,-0.71447,-0.40794,272.08,-0.81895,-0.4439,-0.3637,466.66,0.078766,0.54082,-0.83744,219.79
> view matrix models
> #5,0.76854,-0.57763,-0.2751,189.55,-0.63121,-0.61435,-0.47343,482.46,0.10446,0.5375,-0.83677,215.71,#6,0.76854,-0.57763,-0.2751,189.55,-0.63121,-0.61435,-0.47343,482.46,0.10446,0.5375,-0.83677,215.71
> view matrix models
> #5,0.72535,-0.61997,-0.29918,208.73,-0.67932,-0.57436,-0.45677,481.1,0.11135,0.53456,-0.83777,215.18,#6,0.72535,-0.61997,-0.29918,208.73,-0.67932,-0.57436,-0.45677,481.1,0.11135,0.53456,-0.83777,215.18
> select subtract #6
2 models selected
> show #!5 models
> hide #!6 models
> view matrix models
> #5,-0.80566,-0.57504,0.14226,369.37,-0.59084,0.76275,-0.26291,190.14,0.042677,-0.29587,-0.95428,397.4
> view matrix models
> #5,-0.92978,0.33001,0.16309,223.08,0.21293,0.84357,-0.493,86.718,-0.30027,-0.42365,-0.85461,458.03
> view matrix models
> #5,0.17164,0.86776,0.46641,-110.41,0.18657,0.43623,-0.88028,236.27,-0.96733,0.23811,-0.087023,305.61
> view matrix models
> #5,0.74719,-0.043762,0.66317,-77.351,0.3703,0.85601,-0.36073,34.117,-0.55189,0.5151,0.6558,49.671
> view matrix models
> #5,0.64687,-0.30179,-0.70034,238.94,0.41416,0.91015,-0.0096631,-48.062,0.64033,-0.2838,0.71374,-12.728
> view matrix models
> #5,-0.21312,0.41992,-0.88218,283.84,0.37224,0.86973,0.32406,-95.962,0.90334,-0.25932,-0.34167,135.98
> view matrix models
> #5,-0.21634,0.9726,-0.085136,36.819,0.6005,0.20131,0.77387,-96.775,0.7698,0.11629,-0.6276,143.46
> view matrix models
> #5,-0.15506,0.93711,-0.31269,75.462,0.94378,0.04698,-0.32721,79.427,-0.29195,-0.34585,-0.89172,449.57
> view matrix models
> #5,-0.063094,0.99767,-0.025884,-3.805,0.91806,0.047849,-0.39355,95.816,-0.39139,-0.048593,-0.91894,417.47
> volume #5 level 0.25
> volume #5 level 0.3
> view matrix models
> #5,0.92485,-0.32999,0.18913,33.246,0.054759,-0.37655,-0.92478,412.25,0.37638,0.86563,-0.33018,17.895
> view matrix models
> #5,0.84021,-0.40253,0.36333,28.01,0.19614,-0.39907,-0.8957,387.7,0.50554,0.82384,-0.25636,-9.4418
> view matrix models
> #5,0.79692,-0.41261,0.44122,22.54,0.26503,-0.41754,-0.86915,374.8,0.54285,0.80958,-0.22339,-19.095
> view matrix models
> #5,0.2021,0.27397,0.94026,-95.635,0.91547,-0.39395,-0.081984,118.21,0.34795,0.87735,-0.33043,20.499
> view matrix models
> #5,0.11026,0.78859,0.60496,-111.24,0.94572,-0.27046,0.18018,42.54,0.30571,0.55225,-0.7756,168.27
> volume #5 level 0.275
> volume #5 level 0.28
> show #!6 models
> hide #!5 models
> select add #6
4 models selected
> select subtract #5
2 models selected
> ui mousemode right "translate selected models"
> show #!5 models
> select add #5
4 models selected
> view matrix models
> #5,0.11026,0.78859,0.60496,-109.28,0.94572,-0.27046,0.18018,55.78,0.30571,0.55225,-0.7756,163.39,#6,0.72535,-0.61997,-0.29918,210.69,-0.67932,-0.57436,-0.45677,494.34,0.11135,0.53456,-0.83777,210.29
> hide #!5 models
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.39939,0.71253,0.57688,-4.9893,0.88904,0.14739,0.43346,-64.783,0.22382,0.68598,-0.69234,134.9,#6,0.92605,-0.36358,0.1012,59.536,-0.24962,-0.79119,-0.5583,473.97,0.28306,0.49175,-0.82344,184.79
> view matrix models
> #5,-0.38473,0.7224,0.57456,-8.8713,0.91382,0.21039,0.34738,-64.426,0.13007,0.65869,-0.74108,165.09,#6,0.92584,-0.36846,0.084066,63.487,-0.23103,-0.72784,-0.64566,475.56,0.29908,0.57835,-0.75898,155.57
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.38473,0.7224,0.57456,-8.5561,0.91382,0.21039,0.34738,-63.28,0.13007,0.65869,-0.74108,163.55,#6,0.92584,-0.36846,0.084066,63.802,-0.23103,-0.72784,-0.64566,476.71,0.29908,0.57835,-0.75898,154.03
Drag select of 11 residues, 6 cryosparc_P29_J677_003_volume_map_sharp.mrc
> select clear
> rename #5-7 id #5
> hide #!4 models
> show #!5.1 models
> select add #5.1
2 models selected
> view matrix models
> #5.1,-0.38473,0.7224,0.57456,-6.5595,0.91382,0.21039,0.34738,-39.937,0.13007,0.65869,-0.74108,166.22
> ui mousemode right "rotate selected models"
> view matrix models
> #5.1,-0.34188,0.75883,0.55434,-16.39,0.91905,0.39308,0.028727,-14.468,-0.1961,0.51929,-0.8318,261.68
> ui mousemode right "translate selected models"
> view matrix models
> #5.1,-0.34188,0.75883,0.55434,4.1369,0.91905,0.39308,0.028727,-20.715,-0.1961,0.51929,-0.8318,267.79
> ui mousemode right "rotate selected models"
> view matrix models
> #5.1,-0.14347,0.87483,0.4627,-32.283,0.98009,0.060752,0.18903,-0.79165,0.13726,0.48061,-0.86612,226.35
> view matrix models
> #5.1,-0.080913,0.89876,0.43091,-40.956,0.99399,0.040798,0.10155,16.749,0.07369,0.43654,-0.89666,250.38
> fitmap #5.1 inMap #5.2
Fit map cryosparc_P29_J632_004_volume_map_sharp.mrc in map
cryosparc_P29_J677_003_volume_map_sharp.mrc using 158091 points
correlation = 0.9533, correlation about mean = 0.8198, overlap = 3.161e+04
steps = 192, shift = 3.9, angle = 21.1 degrees
Position of cryosparc_P29_J632_004_volume_map_sharp.mrc (#5.1) relative to
cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.2) coordinates:
Matrix rotation and translation
-0.53250380 0.84041401 -0.10071736 138.03273860
-0.59424680 -0.45593109 -0.66256892 467.48309176
-0.60275237 -0.29296951 0.74219838 181.20849958
Axis 0.23627820 0.32094187 -0.91715262
Axis point 213.77740768 230.20734826 0.00000000
Rotation angle (degrees) 128.54420570
Shift along axis 16.45317566
> select clear
> hide #!5.1 models
> show #!5.3 models
> select add #5.3
2 models selected
> view matrix models
> #5.3,0.31714,0.53441,-0.78347,170.13,-0.94116,0.075628,-0.32938,387.12,-0.11677,0.84184,0.52695,-40.035
> view matrix models
> #5.3,-0.11454,-0.59602,-0.79476,445.23,-0.58842,0.68529,-0.42912,236.69,0.8004,0.4185,-0.4292,44.446
> view matrix models
> #5.3,0.31906,-0.94748,0.021986,281.39,0.25949,0.065023,-0.96355,291.21,0.91152,0.31314,0.26661,-83.105
> view matrix models
> #5.3,0.8625,-0.31808,0.39361,8.2688,0.30282,-0.29877,-0.905,336.17,0.40546,0.89976,-0.16137,-17.822
> view matrix models
> #5.3,0.82719,-0.52666,-0.19591,157.7,-0.50038,-0.53175,-0.68327,478.8,0.25568,0.66322,-0.70339,148.14
> view matrix models
> #5.3,0.56647,-0.81097,0.14641,191.26,-0.26656,-0.34842,-0.89864,444.54,0.77978,0.47002,-0.41354,36.301
> view matrix models
> #5.3,0.92616,-0.37016,0.072179,64.333,-0.15623,-0.55078,-0.8199,445.9,0.34325,0.74808,-0.56794,93.305
> view matrix models
> #5.3,0.50968,-0.8593,-0.042875,244.05,-0.57304,-0.30187,-0.7619,465.96,0.64176,0.41289,-0.64627,112.9
> view matrix models
> #5.3,0.66291,-0.70836,0.24244,138.91,-0.16081,-0.45097,-0.87793,439.88,0.73122,0.543,-0.41286,32.092
> view matrix models
> #5.3,0.80243,-0.57884,0.14507,109.32,-0.22841,-0.52251,-0.82147,454.06,0.5513,0.62604,-0.55149,74.676
> view matrix models
> #5.3,0.67169,-0.73577,-0.086441,201.76,-0.5878,-0.45829,-0.66668,478.51,0.45091,0.49861,-0.74031,148.86
> view matrix models
> #5.3,0.80497,-0.59024,0.060255,126.24,-0.33294,-0.53344,-0.77756,466.52,0.49109,0.60585,-0.62592,102.35
> view matrix models
> #5.3,0.60624,-0.79158,0.076619,193.49,-0.45551,-0.42459,-0.78245,470.2,0.65191,0.43945,-0.61798,101.35
> view matrix models
> #5.3,0.84623,-0.52947,0.059717,108.46,-0.30283,-0.57014,-0.7637,465.05,0.4384,0.62818,-0.64281,110.87
> view matrix models
> #5.3,0.54906,-0.83423,0.05094,215.7,-0.52702,-0.39288,-0.75359,472.12,0.64867,0.38692,-0.65537,117.84
> view matrix models
> #5.3,0.55801,-0.81859,0.13614,195.94,-0.54037,-0.48295,-0.68902,478.44,0.62978,0.31091,-0.71184,144.64
> ui mousemode right "translate selected models"
> view matrix models
> #5.3,0.55801,-0.81859,0.13614,207.98,-0.54037,-0.48295,-0.68902,495.07,0.62978,0.31091,-0.71184,141.49
> view matrix models
> #5.3,0.55801,-0.81859,0.13614,210.12,-0.54037,-0.48295,-0.68902,493.2,0.62978,0.31091,-0.71184,137.83
> ui mousemode right "rotate selected models"
> view matrix models
> #5.3,0.78743,-0.6164,0.0020855,158.62,-0.462,-0.59243,-0.65999,493.08,0.40805,0.51873,-0.75127,148.14
> ui mousemode right "translate selected models"
> view matrix models
> #5.3,0.78743,-0.6164,0.0020855,138.41,-0.462,-0.59243,-0.65999,498.92,0.40805,0.51873,-0.75127,139.79
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #5.3,0.78743,-0.6164,0.0020855,143.47,-0.462,-0.59243,-0.65999,505.73,0.40805,0.51873,-0.75127,139.27
> ui mousemode right "rotate selected models"
> view matrix models
> #5.3,0.80165,-0.59211,0.0823,122.19,-0.34711,-0.57313,-0.74232,496.95,0.4867,0.56651,-0.66497,101.37
> fitmap #5.3 inMap #5.2
Fit map cryosparc_P29_J701_004_volume_map_sharp.mrc in map
cryosparc_P29_J677_003_volume_map_sharp.mrc using 347135 points
correlation = 0.8968, correlation about mean = 0.7925, overlap = 2.38e+04
steps = 256, shift = 10.9, angle = 18.1 degrees
Position of cryosparc_P29_J701_004_volume_map_sharp.mrc (#5.3) relative to
cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.2) coordinates:
Matrix rotation and translation
0.99845364 0.05399836 0.01321052 -10.86198174
-0.05443621 0.99788961 0.03539819 3.29465681
-0.01127120 -0.03606258 0.99928597 7.38308998
Axis -0.54074826 0.18525478 -0.82053153
Axis point 51.38380777 198.36045742 0.00000000
Rotation angle (degrees) 3.78862562
Shift along axis 0.42589055
> select clear
> hide #!5.2 models
> volume #5.3 level 0.175
> volume #5.3 level 0.2
> ui mousemode right select
> hide #!5.1 models
> show #!5.2 models
> show #!4 models
> fitmap #4.2 inMap #5.2
Fit molecule Elg1_RFC-PCNA-v3_rsr04.pdb (#4.2) to map
cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.2) using 20380 atoms
average map value = 0.05878, steps = 96
shifted from previous position = 4.63
rotated from previous position = 4.75 degrees
atoms outside contour = 16977, contour level = 0.15
Position of Elg1_RFC-PCNA-v3_rsr04.pdb (#4.2) relative to
cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.2) coordinates:
Matrix rotation and translation
0.99758484 0.05159763 0.04649926 -22.87801885
-0.05283491 0.99827034 0.02578373 10.04697680
-0.04508845 -0.02817823 0.99858550 17.30051962
Axis -0.36211712 0.61460848 -0.70080497
Axis point 148.78669247 433.96861741 0.00000000
Rotation angle (degrees) 4.27301044
Shift along axis 2.33518917
> ui mousemode right "translate selected models"
> select add #4.2
20380 atoms, 20704 bonds, 2 pseudobonds, 2575 residues, 2 models selected
> view matrix models
> #4.2,0.93928,-0.32242,0.1175,45.368,-0.16291,-0.7203,-0.67426,471.11,0.30203,0.61417,-0.72909,143.34
> fitmap #4.2 inMap #5.2
Fit molecule Elg1_RFC-PCNA-v3_rsr04.pdb (#4.2) to map
cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.2) using 20380 atoms
average map value = 0.2398, steps = 116
shifted from previous position = 3.53
rotated from previous position = 4.23 degrees
atoms outside contour = 8754, contour level = 0.15
Position of Elg1_RFC-PCNA-v3_rsr04.pdb (#4.2) relative to
cryosparc_P29_J677_003_volume_map_sharp.mrc (#5.2) coordinates:
Matrix rotation and translation
0.99999878 0.00046628 0.00148852 -0.64945417
-0.00046460 0.99999925 -0.00112811 0.37220285
-0.00148904 0.00112742 0.99999825 0.01258259
Axis 0.58590405 0.77346311 -0.24180832
Axis point -7.55369589 0.00000000 398.64399382
Rotation angle (degrees) 0.11028431
Shift along axis -0.09567522
> hide #!5 models
> show #!4.1 models
> mmaker #4.1 to #4.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Elg1-RFC-
AF5-v2_Rsr02-Ct1.pdb, chain A (#4.1), sequence alignment score = 2856.7
RMSD between 462 pruned atom pairs is 0.300 angstroms; (across all 462 pairs:
0.300)
> hide #!4.1 models
> show #!4.1 models
> select clear
> hide #!4.2 models
> show #!5 models
> show #!5.1 models
> hide #!5.2 models
> mmaker #4.1 to #5.1
No 'to' model specified
> fitmap #4.1 inMap #5.1
Fit molecule Elg1-RFC-AF5-v2_Rsr02-Ct1.pdb (#4.1) to map
cryosparc_P29_J632_004_volume_map_sharp.mrc (#5.1) using 14258 atoms
average map value = 0.5589, steps = 64
shifted from previous position = 0.245
rotated from previous position = 0.684 degrees
atoms outside contour = 4131, contour level = 0.28
Position of Elg1-RFC-AF5-v2_Rsr02-Ct1.pdb (#4.1) relative to
cryosparc_P29_J632_004_volume_map_sharp.mrc (#5.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00001573 0.00012749 -0.01045293
0.00001571 0.99999999 0.00013730 -0.02133687
-0.00012749 -0.00013730 0.99999998 0.05449296
Axis -0.73023040 0.67806417 0.08362147
Axis point 0.00000000 398.26212072 144.18039597
Rotation angle (degrees) 0.01077290
Shift along axis -0.00227793
> color zone #5.1 near #4.1 distance 10
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> show #!4.2 models
> hide #!5.1 models
> show #!5.2 models
> color zone #5.2 near #4.2 distance 10
> hide #!5.2 models
> show #!5.3 models
> color zone #5.3 near #4.2 distance 10
> hide #!4 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> hide #!4 models
> hide #!5 models
> show #!5.1 models
> show #!5.2 models
> hide #!5 models
> show #!5 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v8.cxs"
——— End of log from Thu Jan 12 10:32:45 2023 ———
opened ChimeraX session
> hide #!5.1 models
> hide #!5.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!5 models
> show #!5 models
> open /Users/fengwei.zheng/Documents/Phenix/4_Elg1_RFC-
> PCNA/2_Coot/2-Open/Open-Rsr28.pdb
Chain information for Open-Rsr28.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
> hide #6
> undo
> hide #6 & protein
> show #6 cartoons
> mmaker #6/A-H to #4.2/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb,
chain A (#6), sequence alignment score = 6.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain H (#4.2) with Open-Rsr28.pdb,
chain B (#6), sequence alignment score = 3.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain F (#4.2) with Open-Rsr28.pdb,
chain C (#6), sequence alignment score = 2.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb,
chain D (#6), sequence alignment score = 172.4
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb,
chain E (#6), sequence alignment score = 529.1
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb,
chain F (#6), sequence alignment score = 5.5
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb,
chain H (#6), sequence alignment score = 3.5
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb,
chain G (#6), sequence alignment score = 16.9
RMSD between 168 pruned atom pairs is 1.162 angstroms; (across all 685 pairs:
34.822)
> hide #!5.3 models
> hide #!6 models
> hide #!4.2 models
> show #!4.2 models
> show #!6 models
> hide #!4.2 models
> show #!4.2 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> mmaker #6/A-H to #4.2/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb,
chain A (#6), sequence alignment score = 6.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain H (#4.2) with Open-Rsr28.pdb,
chain B (#6), sequence alignment score = 3.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain F (#4.2) with Open-Rsr28.pdb,
chain C (#6), sequence alignment score = 2.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb,
chain D (#6), sequence alignment score = 172.4
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb,
chain E (#6), sequence alignment score = 529.1
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb,
chain F (#6), sequence alignment score = 5.5
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb,
chain H (#6), sequence alignment score = 3.5
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb,
chain G (#6), sequence alignment score = 16.9
RMSD between 168 pruned atom pairs is 1.162 angstroms; (across all 685 pairs:
34.822)
> hide #!4.2 models
> show #!4.2 models
> view name a
> hide #!6 models
> show #!6 models
> hide #!4 models
> mmaker #6/A-H to #4.2/A-H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb,
chain A (#6), sequence alignment score = 2124.7
RMSD between 376 pruned atom pairs is 0.742 angstroms; (across all 454 pairs:
1.890)
> show #!4 models
> mmaker #6/A-H to #4.2/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb,
chain A (#6), sequence alignment score = 6.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain H (#4.2) with Open-Rsr28.pdb,
chain B (#6), sequence alignment score = 3.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain F (#4.2) with Open-Rsr28.pdb,
chain C (#6), sequence alignment score = 2.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb,
chain D (#6), sequence alignment score = 172.4
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb,
chain E (#6), sequence alignment score = 529.1
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb,
chain F (#6), sequence alignment score = 5.5
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb,
chain H (#6), sequence alignment score = 3.5
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb,
chain G (#6), sequence alignment score = 16.9
RMSD between 168 pruned atom pairs is 1.162 angstroms; (across all 685 pairs:
34.822)
> mmaker #6/A-G to #4.2/A-G pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb,
chain A (#6), sequence alignment score = 6.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain F (#4.2) with Open-Rsr28.pdb,
chain B (#6), sequence alignment score = 4.1
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb,
chain C (#6), sequence alignment score = 229.3
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb,
chain D (#6), sequence alignment score = 651.7
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb,
chain E (#6), sequence alignment score = 521
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb,
chain F (#6), sequence alignment score = 3.5
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb,
chain G (#6), sequence alignment score = 16.9
RMSD between 147 pruned atom pairs is 1.078 angstroms; (across all 1024 pairs:
27.227)
> mmaker #6/A-H to #4.2/A-H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb,
chain A (#6), sequence alignment score = 2124.7
RMSD between 376 pruned atom pairs is 0.742 angstroms; (across all 454 pairs:
1.890)
> mmaker #6/A-E,G,H to #4.2/A-E,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb,
chain A (#6), sequence alignment score = 2124.7
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb,
chain B (#6), sequence alignment score = 1590.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb,
chain C (#6), sequence alignment score = 1640.2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb,
chain D (#6), sequence alignment score = 1564.7
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb,
chain E (#6), sequence alignment score = 1666.3
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb,
chain G (#6), sequence alignment score = 1278.6
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain H (#4.2) with Open-Rsr28.pdb,
chain H (#6), sequence alignment score = 1265.3
RMSD between 1935 pruned atom pairs is 0.751 angstroms; (across all 2279
pairs: 1.563)
> mmaker #6/A-E,G,H to #4.2/A-E,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb,
chain A (#6), sequence alignment score = 2124.7
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb,
chain B (#6), sequence alignment score = 1590.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb,
chain C (#6), sequence alignment score = 1640.2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb,
chain D (#6), sequence alignment score = 1564.7
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb,
chain E (#6), sequence alignment score = 1666.3
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb,
chain G (#6), sequence alignment score = 1278.6
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain H (#4.2) with Open-Rsr28.pdb,
chain H (#6), sequence alignment score = 1265.3
RMSD between 1935 pruned atom pairs is 0.751 angstroms; (across all 2279
pairs: 1.563)
> view a
> mmaker #6/A-E,G,H to #4.2/A-E,G,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain A (#4.2) with Open-Rsr28.pdb,
chain A (#6), sequence alignment score = 2124.7
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain B (#4.2) with Open-Rsr28.pdb,
chain B (#6), sequence alignment score = 1590.9
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain C (#4.2) with Open-Rsr28.pdb,
chain C (#6), sequence alignment score = 1640.2
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain D (#4.2) with Open-Rsr28.pdb,
chain D (#6), sequence alignment score = 1564.7
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain E (#4.2) with Open-Rsr28.pdb,
chain E (#6), sequence alignment score = 1666.3
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain G (#4.2) with Open-Rsr28.pdb,
chain G (#6), sequence alignment score = 1278.6
Matchmaker Elg1_RFC-PCNA-v3_rsr04.pdb, chain H (#4.2) with Open-Rsr28.pdb,
chain H (#6), sequence alignment score = 1265.3
RMSD between 1935 pruned atom pairs is 0.751 angstroms; (across all 2279
pairs: 1.563)
> hide #!6 models
> show #!6 models
> cartoon style nucleic xsection oval width 2.5 thickness 2.5
> cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true
> xsection oval width 2.75 thickness 1 arrowScale
Missing "arrowScale" keyword's argument
> cartoon style nucleic xsection oval width 2.5 thickness 2.5
> cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true
> xsection oval width 2.75 thickness 1 arrowScale 1.5
> color /A #FFB381
> color /B #D7819F
> color /C #B48FE3
> color /D #D7CD85
> color /E salmon
> color /F navajo white
> color /G #CAC6FD
> color /H plum
> hide #!4 models
> show #!4 models
> hide #!6 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!4.1 models
> hide #!4.2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/apo-4.jpg" width 1100 height
> 609 supersample 3
> hide #!4.1 models
> show #!4.2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/complex-4_closed.jpg" width
> 1100 height 609 supersample 3
> hide #!4.2 models
> show #!6 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/complex-open-4.jpg" width
> 1100 height 609 supersample 3
> rename #6 id #4.4
> rename #4.3 id #4.5
> rename #4.4 id #4.3
> rename #4.5 id #4.4
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/1-Fig/Overall-Elg1_RFC-
> PCNA_v9.cxs"
——— End of log from Thu Feb 2 14:25:37 2023 ———
opened ChimeraX session
> close #1.1-6
> rename #5 id #1
> undo
No undo action is available
> undo
No undo action is available
> rename #1.1 id #1.9
> rename #1.1.1 id #1.1
> rename #1.9.1 id #1.1
> rename #1.9.2 id #1.2
> rename #1.9.3 id #1.3
> close #1.9
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> rename #2 id #5
> rename #4 id #2
> rename #5 id #3
> rename #3.8 id #4
> hide #!2 models
> show #!3.7 models
> hide #!3.1 models
> hide #!3.7 models
> show #!3.6 models
> hide #!3.6 models
> show #!3.5 models
> show #!3.7 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3.7 models
> hide #!3.5 models
> show #!3.3 models
> show #!3.7 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3.7 models
> show #!3.7 models
Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'M' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b5' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c2' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b5' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c2' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide #!3.7 models
> hide #!3.3 models
> show #!3.7 models
> mmaker #3.7/A-H to #3.3/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain B (#3.3) with T4-partially-
closed-3U60, chain B (#3.7), sequence alignment score = 1640.1
Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain C (#3.3) with T4-partially-
closed-3U60, chain C (#3.7), sequence alignment score = 1670.1
Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain D (#3.3) with T4-partially-
closed-3U60, chain D (#3.7), sequence alignment score = 1676.1
Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain E (#3.3) with T4-partially-
closed-3U60, chain E (#3.7), sequence alignment score = 1595.7
Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain A (#3.3) with T4-partially-
closed-3U60, chain A (#3.7), sequence alignment score = 970.8
Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain G (#3.3) with T4-partially-
closed-3U60, chain G (#3.7), sequence alignment score = 1121.9
Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain F (#3.3) with T4-partially-
closed-3U60, chain F (#3.7), sequence alignment score = 1072.1
Matchmaker T4-Clamp-Loader-DNA-3U5Z, chain H (#3.3) with T4-partially-
closed-3U60, chain H (#3.7), sequence alignment score = 1072.7
RMSD between 1630 pruned atom pairs is 0.939 angstroms; (across all 2133
pairs: 4.217)
> show #!3.3 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!3.3 models
> hide #!3.7 models
> rename #2.4 id #3
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.1 models
> close #1.1-3
> undo
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Apo_P29_J632_004.mrc"
Opened Apo_P29_J632_004.mrc as #5, grid size 420,420,420, pixel 0.828, shown
at level 0.1, step 2, values float32
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Closed_P29_J651_004.mrc"
Opened Closed_P29_J651_004.mrc as #6, grid size 420,420,420, pixel 0.828,
shown at level 0.112, step 2, values float32
> 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 #7, grid size 420,420,420, pixel 0.828, shown
at level 0.0759, step 2, values float32
> surface dust #0-9 size 10
> volume #0-9 step 1 level 0.2
> rename #5-7 id #1
> close #2.1-3
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Open_Rsr35-Ct2.pdb"
Chain information for Open_Rsr35-Ct2.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Closed_Rsr21-Ct2.pdb"
Chain information for Closed_Rsr21-Ct2.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Apo_Rsr13-Ct1.pdb"
Chain information for Apo_Rsr13-Ct1.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> rename #5-7 id #2
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1.1 models
> volume #1.1 level 0.2427
> volume #1.1 level 0.25
> volume #1.2 level 0.25
> show #!1.2 models
> show #!1.1 models
> hide #!1.1 models
> fitmap #1.3 inMap #1.2
Fit map Open_P29_J701_004.mrc in map Closed_P29_J651_004.mrc using 237652
points
correlation = 0.9163, correlation about mean = 0.7463, overlap = 4.587e+04
steps = 72, shift = 1.2, angle = 3.78 degrees
Position of Open_P29_J701_004.mrc (#1.3) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
0.99846800 0.05408100 0.01170019 -10.30909942
-0.05446551 0.99788392 0.03551333 3.16581617
-0.00975484 -0.03609618 0.99930071 7.19292834
Axis -0.54332972 0.16278780 -0.82358542
Axis point 50.16340237 190.10932176 0.00000000
Rotation angle (degrees) 3.77845856
Shift along axis 0.19260545
> fitmap #1.3 inMap #1.2
Fit map Open_P29_J701_004.mrc in map Closed_P29_J651_004.mrc using 237652
points
correlation = 0.9163, correlation about mean = 0.7463, overlap = 4.587e+04
steps = 44, shift = 0.0047, angle = 0.00319 degrees
Position of Open_P29_J701_004.mrc (#1.3) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
0.99846943 0.05406085 0.01167117 -10.30344284
-0.05444475 0.99788351 0.03555654 3.15145256
-0.00972425 -0.03613755 0.99929951 7.19271566
Axis -0.54396073 0.16233238 -0.82325872
Axis point 49.91498696 190.04300007 0.00000000
Rotation angle (degrees) 3.77853341
Shift along axis 0.19478517
> hide #!1.3 models
> show #!1.1 models
> select add #1.1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1.1,1,0,0,20.005,0,1,0,-52.909,0,0,1,-5.5041
> ui mousemode right "rotate selected models"
> view matrix models
> #1.1,0.96269,0.098534,0.25205,-38.349,0.098856,0.73896,-0.66646,101.45,-0.25192,0.66651,0.70164,-28.454
> view matrix models
> #1.1,0.53825,0.4119,0.73527,-114.61,-0.0030756,0.87339,-0.48702,60.74,-0.84278,0.25988,0.47137,184.39
> view matrix models
> #1.1,0.74584,0.42996,0.50878,-109.91,-0.55244,0.82603,0.11179,48.341,-0.3722,-0.36444,0.85361,148.27
> view matrix models
> #1.1,0.52749,0.25649,0.80992,-98.783,-0.6543,0.73073,0.19472,66.796,-0.54189,-0.63265,0.55328,280.07
> ui mousemode right "translate selected models"
> view matrix models
> #1.1,0.52749,0.25649,0.80992,-106.74,-0.6543,0.73073,0.19472,87.853,-0.54189,-0.63265,0.55328,273.54
> ui mousemode right "rotate selected models"
> view matrix models
> #1.1,0.098208,0.95952,0.26397,-61.158,-0.769,0.24153,-0.59186,340.57,-0.63165,-0.14487,0.7616,162
> ui mousemode right "translate selected models"
> view matrix models
> #1.1,0.098208,0.95952,0.26397,-62.613,-0.769,0.24153,-0.59186,357.57,-0.63165,-0.14487,0.7616,153.86
> view matrix models
> #1.1,0.098208,0.95952,0.26397,-62.007,-0.769,0.24153,-0.59186,354.74,-0.63165,-0.14487,0.7616,153.58
> ui mousemode right "rotate selected models"
> view matrix models
> #1.1,-0.37574,0.92601,-0.036368,77.617,-0.62871,-0.28355,-0.7241,450.56,-0.68084,-0.24921,0.68874,193.92
> ui mousemode right "move picked models"
> view matrix models #1.2,1,0,0,0.60822,0,1,0,-1.1694,0,0,1,-1.7261
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #1.1,-0.37574,0.92601,-0.036368,77.411,-0.62871,-0.28355,-0.7241,451.31,-0.68084,-0.24921,0.68874,194.2
> view matrix models
> #1.1,-0.37574,0.92601,-0.036368,78.093,-0.62871,-0.28355,-0.7241,448.18,-0.68084,-0.24921,0.68874,193.83
> ui mousemode right "rotate selected models"
> view matrix models
> #1.1,-0.47989,0.86818,0.12633,75.389,-0.66869,-0.26874,-0.69328,446.36,-0.56794,-0.41718,0.70951,201.6
> ui mousemode right "translate selected models"
> view matrix models
> #1.1,-0.47989,0.86818,0.12633,74.505,-0.66869,-0.26874,-0.69328,449.25,-0.56794,-0.41718,0.70951,203.09
> fitmap #1.1 inMap #1.2
Fit map Apo_P29_J632_004.mrc in map Closed_P29_J651_004.mrc using 177080
points
correlation = 0.9554, correlation about mean = 0.8333, overlap = 6.544e+04
steps = 136, shift = 10.4, angle = 13.8 degrees
Position of Apo_P29_J632_004.mrc (#1.1) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
-0.53167181 0.84082990 -0.10163741 138.30893277
-0.59440769 -0.45592717 -0.66242729 467.36322207
-0.60332793 -0.29177986 0.74219938 181.16060019
Axis 0.23684727 0.32058507 -0.91713062
Axis point 214.02322176 230.00862665 0.00000000
Rotation angle (degrees) 128.51355729
Shift along axis 16.43983009
> select clear
> fitmap #1.1 inMap #1.2
Fit map Apo_P29_J632_004.mrc in map Closed_P29_J651_004.mrc using 177080
points
correlation = 0.9554, correlation about mean = 0.8332, overlap = 6.544e+04
steps = 40, shift = 0.02, angle = 0.0146 degrees
Position of Apo_P29_J632_004.mrc (#1.1) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
-0.53166894 0.84085996 -0.10140345 138.26555130
-0.59444099 -0.45575618 -0.66251506 467.36512760
-0.60329764 -0.29196031 0.74215304 181.21186663
Axis 0.23677270 0.32069442 -0.91711165
Axis point 214.01750894 230.03589560 0.00000000
Rotation angle (degrees) 128.50888878
Shift along axis 16.42738178
> fitmap #1.1 inMap #1.2
Fit map Apo_P29_J632_004.mrc in map Closed_P29_J651_004.mrc using 177080
points
correlation = 0.9554, correlation about mean = 0.8332, overlap = 6.544e+04
steps = 44, shift = 0.00271, angle = 0.0131 degrees
Position of Apo_P29_J632_004.mrc (#1.1) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
-0.53161955 0.84086495 -0.10162082 138.29770231
-0.59440936 -0.45586428 -0.66246907 467.36981335
-0.60337232 -0.29177714 0.74216436 181.19164725
Axis 0.23686606 0.32061097 -0.91711672
Axis point 214.03623238 230.01983811 0.00000000
Rotation angle (degrees) 128.51062360
Shift along axis 16.42803132
> fitmap #1.1 inMap #1.2
Fit map Apo_P29_J632_004.mrc in map Closed_P29_J651_004.mrc using 177080
points
correlation = 0.9554, correlation about mean = 0.8333, overlap = 6.544e+04
steps = 44, shift = 0.00547, angle = 0.00549 degrees
Position of Apo_P29_J632_004.mrc (#1.1) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
-0.53165206 0.84085176 -0.10155984 138.29032133
-0.59445654 -0.45587056 -0.66242241 467.36761183
-0.60329719 -0.29180533 0.74221436 181.17303227
Axis 0.23681688 0.32060010 -0.91713322
Axis point 214.02327529 230.01586551 0.00000000
Rotation angle (degrees) 128.51021345
Shift along axis 16.42778112
> fitmap #1.1 inMap #1.2
Fit map Apo_P29_J632_004.mrc in map Closed_P29_J651_004.mrc using 177080
points
correlation = 0.9554, correlation about mean = 0.8332, overlap = 6.544e+04
steps = 44, shift = 0.0043, angle = 0.00568 degrees
Position of Apo_P29_J632_004.mrc (#1.1) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
-0.53160795 0.84087318 -0.10161334 138.29147093
-0.59441612 -0.45585042 -0.66247254 467.36956255
-0.60337588 -0.29177506 0.74216229 181.19046957
Axis 0.23686679 0.32061421 -0.91711540
Axis point 214.03536942 230.02087432 0.00000000
Rotation angle (degrees) 128.50976744
Shift along axis 16.42941045
> hide #!1.1 models
> show #!1.3 models
> fitmap #1.3 inMap #1.2
Fit map Open_P29_J701_004.mrc in map Closed_P29_J651_004.mrc using 237652
points
correlation = 0.9163, correlation about mean = 0.7463, overlap = 4.587e+04
steps = 76, shift = 2.18, angle = 0.00673 degrees
Position of Open_P29_J701_004.mrc (#1.3) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
0.99847121 0.05403075 0.01165822 -10.30458864
-0.05441530 0.99788108 0.03566953 3.12065853
-0.00970627 -0.03624939 0.99929564 7.19549858
Axis -0.54538334 0.16201351 -0.82237986
Axis point 49.33029056 190.01227038 0.00000000
Rotation angle (degrees) 3.78049874
Shift along axis 0.20810677
> fitmap #1.3 inMap #1.2
Fit map Open_P29_J701_004.mrc in map Closed_P29_J651_004.mrc using 237652
points
correlation = 0.9163, correlation about mean = 0.7463, overlap = 4.587e+04
steps = 44, shift = 0.017, angle = 0.00916 degrees
Position of Open_P29_J701_004.mrc (#1.3) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
0.99847089 0.05401047 0.01177905 -10.31589801
-0.05439840 0.99788567 0.03556701 3.14237342
-0.00983316 -0.03615339 0.99929787 7.21475146
Axis -0.54428386 0.16401441 -0.82271158
Axis point 49.77722572 190.44719609 0.00000000
Rotation angle (degrees) 3.77767482
Shift along axis 0.19451174
> fitmap #1.3 inMap #1.2
Fit map Open_P29_J701_004.mrc in map Closed_P29_J651_004.mrc using 237652
points
correlation = 0.9163, correlation about mean = 0.7463, overlap = 4.587e+04
steps = 40, shift = 0.00249, angle = 0.00786 degrees
Position of Open_P29_J701_004.mrc (#1.3) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
0.99846855 0.05407941 0.01166090 -10.30495846
-0.05446293 0.99788250 0.03555703 3.15432127
-0.00971331 -0.03613766 0.99929962 7.19127314
Axis -0.54385330 0.16213802 -0.82336799
Axis point 49.94959949 190.00826391 0.00000000
Rotation angle (degrees) 3.77931257
Shift along axis 0.19475696
> hide #!1.2 models
> show #!1.2 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!2 models
> hide #!2.1 models
> hide #!2.3 models
> hide #2
> show #2 cartoons
> hide #!1.2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.3 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.3 models
> show #!2.3 models
> rename #2.1 id #2.4
> rename #2.3 id #2.1
> rename #2.4 id #2.3
> dssp #2.1
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.3 models
> show #!1.2 models
> fitmap #2.2 into #1.2
Expected a keyword
> fitmap #2.2 inMap #1.2
Fit molecule Closed_Rsr21-Ct2.pdb (#2.2) to map Closed_P29_J651_004.mrc (#1.2)
using 20396 atoms
average map value = 0.5299, steps = 96
shifted from previous position = 2.2
rotated from previous position = 0.0243 degrees
atoms outside contour = 5814, contour level = 0.25
Position of Closed_Rsr21-Ct2.pdb (#2.2) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
0.99999994 0.00035092 0.00004122 -0.05675804
-0.00035093 0.99999991 0.00023301 0.01544387
-0.00004114 -0.00023302 0.99999997 0.02603591
Axis -0.55054223 0.09730088 -0.82911748
Axis point 40.87711022 144.23535640 0.00000000
Rotation angle (degrees) 0.02425026
Shift along axis 0.01116357
> fitmap #2.2 inMap #1.2
Fit molecule Closed_Rsr21-Ct2.pdb (#2.2) to map Closed_P29_J651_004.mrc (#1.2)
using 20396 atoms
average map value = 0.5299, steps = 48
shifted from previous position = 0.00321
rotated from previous position = 0.0124 degrees
atoms outside contour = 5821, contour level = 0.25
Position of Closed_Rsr21-Ct2.pdb (#2.2) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
0.99999995 0.00027075 0.00018784 -0.07196012
-0.00027077 0.99999996 0.00009619 0.02685335
-0.00018781 -0.00009624 0.99999998 0.02957657
Axis -0.28026577 0.54714148 -0.78872511
Axis point 75.83157399 253.85711713 0.00000000
Rotation angle (degrees) 0.01966895
Shift along axis 0.01153276
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> hide #!2.2 models
> show #!2.1 models
> show #!1.1 models
> hide #!1.1 models
> fitmap #2.1 inMap #1.1
Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using
14334 atoms
average map value = 0.1059, steps = 256
shifted from previous position = 6.71
rotated from previous position = 12.3 degrees
atoms outside contour = 11693, contour level = 0.25
Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1)
coordinates:
Matrix rotation and translation
-0.34605883 -0.61582784 -0.70781308 452.68197651
0.92660434 -0.34264703 -0.15491101 95.51991162
-0.14713154 -0.70947099 0.68920478 213.89900228
Axis -0.32012214 -0.32365583 0.89037561
Axis point 232.27888694 234.97078197 0.00000000
Rotation angle (degrees) 119.98349746
Shift along axis 14.62135558
> show #!1.1 models
> fitmap #2.1 inMap #1.1
Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using
14334 atoms
average map value = 0.1059, steps = 64
shifted from previous position = 0.00414
rotated from previous position = 0.00474 degrees
atoms outside contour = 11697, contour level = 0.25
Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1)
coordinates:
Matrix rotation and translation
-0.34610474 -0.61584749 -0.70777353 452.68996732
0.92659759 -0.34263541 -0.15497706 95.53219304
-0.14706605 -0.70945954 0.68923054 213.88132249
Axis -0.32007831 -0.32367173 0.89038558
Axis point 232.27069070 234.97487266 0.00000000
Rotation angle (degrees) 119.98377952
Shift along axis 14.61953711
> fitmap #2.1 inMap #1.1
Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using
14334 atoms
average map value = 0.1059, steps = 96
shifted from previous position = 0.0113
rotated from previous position = 0.00502 degrees
atoms outside contour = 11697, contour level = 0.25
Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1)
coordinates:
Matrix rotation and translation
-0.34607756 -0.61591612 -0.70772710 452.69785423
0.92661307 -0.34260447 -0.15495291 95.51375708
-0.14703247 -0.70941491 0.68928364 213.85472149
Axis -0.32005463 -0.32365232 0.89040115
Axis point 232.27102169 234.96820683 0.00000000
Rotation angle (degrees) 119.98010060
Shift along axis 14.61519915
> mmaker #2.1 to #2.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with Apo_Rsr13-Ct1.pdb, chain
A (#2.1), sequence alignment score = 2286.5
RMSD between 463 pruned atom pairs is 0.554 angstroms; (across all 468 pairs:
0.626)
> fitmap #2.1 inMap #1.1
Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using
14334 atoms
average map value = 0.5957, steps = 64
shifted from previous position = 0.157
rotated from previous position = 0.482 degrees
atoms outside contour = 2745, contour level = 0.25
Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1)
coordinates:
Matrix rotation and translation
0.99999992 -0.00036860 0.00015434 0.03360214
0.00036859 0.99999993 0.00000892 -0.05847336
-0.00015434 -0.00000886 0.99999999 0.03317737
Axis -0.02223603 0.38613254 0.92217527
Axis point 166.27122211 91.56510687 0.00000000
Rotation angle (degrees) 0.02290123
Shift along axis 0.00726970
> fitmap #2.1 inMap #1.1
Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using
14334 atoms
average map value = 0.5957, steps = 28
shifted from previous position = 0.00837
rotated from previous position = 0.0162 degrees
atoms outside contour = 2751, contour level = 0.25
Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1)
coordinates:
Matrix rotation and translation
0.99999994 -0.00028578 0.00017460 0.02061477
0.00028583 0.99999993 -0.00026147 0.01061319
-0.00017453 0.00026152 0.99999995 -0.01155826
Axis 0.61543508 0.41083533 0.67264701
Axis point -23.78939691 52.16999953 0.00000000
Rotation angle (degrees) 0.02434492
Shift along axis 0.00927269
> fitmap #2.1 inMap #1.1
Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using
14334 atoms
average map value = 0.5957, steps = 40
shifted from previous position = 0.00369
rotated from previous position = 0.0134 degrees
atoms outside contour = 2748, contour level = 0.25
Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1)
coordinates:
Matrix rotation and translation
0.99999993 -0.00036973 0.00008964 0.05155215
0.00036974 0.99999993 -0.00006076 -0.04294827
-0.00008962 0.00006079 0.99999999 0.00801005
Axis 0.15775307 0.23264623 0.95968208
Axis point 119.85213693 136.92144571 0.00000000
Rotation angle (degrees) 0.02207417
Shift along axis 0.00582786
> hide #!1.1 models
> show #!1.2 models
> hide #!2.1 models
> show #!1.1 models
> hide #!2 models
> show #!2 models
> hide #!1.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> fitmap #2.2 inMap #1.2
Fit molecule Closed_Rsr21-Ct2.pdb (#2.2) to map Closed_P29_J651_004.mrc (#1.2)
using 20396 atoms
average map value = 0.5299, steps = 44
shifted from previous position = 0.0124
rotated from previous position = 0.00518 degrees
atoms outside contour = 5817, contour level = 0.25
Position of Closed_Rsr21-Ct2.pdb (#2.2) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
0.99999992 0.00035879 0.00019546 -0.07845402
-0.00035881 0.99999993 0.00007698 0.04457567
-0.00019544 -0.00007705 0.99999998 0.03459009
Axis -0.18524298 0.47008690 -0.86296196
Axis point 116.80668095 215.77843870 0.00000000
Rotation angle (degrees) 0.02382222
Shift along axis 0.00563756
> hide #!1.2 models
> show #!1.3 models
> hide #!2.2 models
> show #!2.3 models
> hide #!1.3 models
> show #!1.3 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 = 104
shifted from previous position = 3.53
rotated from previous position = 3.76 degrees
atoms outside contour = 7939, contour level = 0.2
Position of Open_Rsr35-Ct2.pdb (#2.3) relative to Open_P29_J701_004.mrc (#1.3)
coordinates:
Matrix rotation and translation
0.99999958 -0.00019051 -0.00089775 0.18621644
0.00019039 0.99999997 -0.00013868 -0.01529551
0.00089778 0.00013851 0.99999959 -0.15553984
Axis 0.14932340 -0.96726299 0.20519462
Axis point 175.78595151 0.00000000 205.56499069
Rotation angle (degrees) 0.05317922
Shift along axis 0.01068532
> 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 = 48
shifted from previous position = 0.0157
rotated from previous position = 0.00798 degrees
atoms outside contour = 7937, contour level = 0.2
Position of Open_Rsr35-Ct2.pdb (#2.3) relative to Open_P29_J701_004.mrc (#1.3)
coordinates:
Matrix rotation and translation
0.99999945 -0.00016289 -0.00103286 0.20092650
0.00016273 0.99999997 -0.00015774 -0.01519499
0.00103289 0.00015757 0.99999945 -0.19544163
Axis 0.14909330 -0.97676325 0.15396343
Axis point 191.51218184 0.00000000 192.30881426
Rotation angle (degrees) 0.06058738
Shift along axis 0.01470784
> 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 = 0.00945
rotated from previous position = 0.01 degrees
atoms outside contour = 7933, contour level = 0.2
Position of Open_Rsr35-Ct2.pdb (#2.3) relative to Open_P29_J701_004.mrc (#1.3)
coordinates:
Matrix rotation and translation
0.99999957 -0.00015733 -0.00091213 0.18403567
0.00015730 0.99999999 -0.00003129 -0.02941522
0.00091214 0.00003115 0.99999958 -0.15351458
Axis 0.03371094 -0.98489011 0.16986772
Axis point 170.08865047 0.00000000 201.34858010
Rotation angle (degrees) 0.05306314
Shift along axis 0.00909760
> hide #!1.3 models
> show #!2.2 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.3 models
> show #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> hide #!2.2 models
> show #!2.1 models
> show #!2.2 models
> hide #!2.1 models
> hide #!2.2 models
> show #!1.2 models
> show #!1.1 models
> fitmap #1.1 inMap #1.2
Fit map Apo_P29_J632_004.mrc in map Closed_P29_J651_004.mrc using 177080
points
correlation = 0.9554, correlation about mean = 0.8333, overlap = 6.544e+04
steps = 40, shift = 0.0132, angle = 0.00323 degrees
Position of Apo_P29_J632_004.mrc (#1.1) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
-0.53165456 0.84084486 -0.10160393 138.29871862
-0.59440409 -0.45588234 -0.66246137 467.36416897
-0.60334667 -0.29180682 0.74217355 181.17850074
Axis 0.23684746 0.32061253 -0.91712098
Axis point 214.02602519 230.01629830 0.00000000
Rotation angle (degrees) 128.51223036
Shift along axis 16.43590525
> hide #!1.1 models
> show #!1.3 models
> fitmap #1.3 inMap #1.2
Fit map Open_P29_J701_004.mrc in map Closed_P29_J651_004.mrc using 237652
points
correlation = 0.9163, correlation about mean = 0.7463, overlap = 4.587e+04
steps = 60, shift = 0.0156, angle = 0.00323 degrees
Position of Open_P29_J701_004.mrc (#1.3) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
0.99847088 0.05404146 0.01163678 -10.30111530
-0.05442446 0.99788338 0.03559124 3.13643466
-0.00968875 -0.03617014 0.99929868 7.17943599
Axis -0.54450170 0.16181110 -0.82300369
Axis point 49.62497877 189.92565671 0.00000000
Rotation angle (degrees) 3.77832215
Shift along axis 0.20778243
> hide #!1.3 models
> show #!2.2 models
> fitmap #2.2 inMap #1.2
Fit molecule Closed_Rsr21-Ct2.pdb (#2.2) to map Closed_P29_J651_004.mrc (#1.2)
using 20396 atoms
average map value = 0.5299, steps = 48
shifted from previous position = 0.0107
rotated from previous position = 0.0141 degrees
atoms outside contour = 5824, contour level = 0.25
Position of Closed_Rsr21-Ct2.pdb (#2.2) relative to Closed_P29_J651_004.mrc
(#1.2) coordinates:
Matrix rotation and translation
0.99999990 0.00045273 -0.00000385 -0.05890733
-0.00045273 0.99999988 0.00018531 0.05191103
0.00000394 -0.00018531 0.99999998 0.02161157
Axis -0.37879465 -0.00796476 -0.92544647
Axis point 114.66064074 128.55070385 0.00000000
Rotation angle (degrees) 0.02802947
Shift along axis 0.00189997
> hide #!2.2 models
> show #!2.1 models
> hide #!1.2 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> fitmap #2.1 inMap #1.1
Fit molecule Apo_Rsr13-Ct1.pdb (#2.1) to map Apo_P29_J632_004.mrc (#1.1) using
14334 atoms
average map value = 0.5957, steps = 40
shifted from previous position = 0.0121
rotated from previous position = 0.00578 degrees
atoms outside contour = 2751, contour level = 0.25
Position of Apo_Rsr13-Ct1.pdb (#2.1) relative to Apo_P29_J632_004.mrc (#1.1)
coordinates:
Matrix rotation and translation
0.99999994 -0.00033528 0.00009045 0.04412438
0.00033528 0.99999994 -0.00001345 -0.04522649
-0.00009045 0.00001348 1.00000000 0.01639942
Axis 0.03875892 0.26026838 0.96475806
Axis point 139.38671802 130.91516584 0.00000000
Rotation angle (degrees) 0.01991165
Shift along axis 0.00576066
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.3 models
> hide #!2.1 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 = 48
shifted from previous position = 0.0181
rotated from previous position = 0.00972 degrees
atoms outside contour = 7939, contour level = 0.2
Position of Open_Rsr35-Ct2.pdb (#2.3) relative to Open_P29_J701_004.mrc (#1.3)
coordinates:
Matrix rotation and translation
0.99999947 -0.00009973 -0.00102301 0.19106219
0.00009977 0.99999999 0.00003409 -0.03701575
0.00102301 -0.00003419 0.99999948 -0.15971900
Axis -0.03319861 -0.99473147 0.09699052
Axis point 157.64348455 0.00000000 187.16936061
Rotation angle (degrees) 0.05892461
Shift along axis 0.01498650
> hide #!1.3 models
> hide #!2.3 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.1 models
> show #!2.1 models
> show #!2.2 models
> color #1.1 #b2b2b24d models
> color #1.1 #b2b2b200 models
> color #1.1 #b2b2b280 models
> color #1.1 #b2b2b24d models
> color #1.1 #b2b2b2ff models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-PCNA_v10.cxs"
> show #!3.1 models
> cartoon style nucleic xsection oval width 2.5 thickness 2.5
> cartoon style protein modeHelix tube radius 1.75 sides 10 arrows true
> xsection oval width 2.75 thickness 1 arrowScale 1.5
> hide #!3.1 models
> hide #!3 models
> hide #!2.1 models
> show #!2.1 models
> mmaker #2.1/A-H to #2.2/A-H pais ss bring #1.1
> matchmaker #2.1/A-H to #2.2/A-H pais ss bring #1.1
Expected a keyword
> mmaker #2.1/A-H to #2.2/A-H pair ss bring #1.1
Different number of reference/match chains (8 ref, 5 match)
> mmaker #2.1/A-E to #2.2/A-E pair ss bring #1.1
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with Apo_Rsr13-Ct1.pdb, chain
A (#2.1), sequence alignment score = 2286.5
Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with Apo_Rsr13-Ct1.pdb, chain
B (#2.1), sequence alignment score = 1631.1
Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with Apo_Rsr13-Ct1.pdb, chain
C (#2.1), sequence alignment score = 1685.8
Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with Apo_Rsr13-Ct1.pdb, chain
D (#2.1), sequence alignment score = 1702.7
Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with Apo_Rsr13-Ct1.pdb, chain
E (#2.1), sequence alignment score = 1740.3
RMSD between 1753 pruned atom pairs is 0.557 angstroms; (across all 1782
pairs: 0.653)
> mmaker #2.1/A-E to #2.2/A-E pair ss bring #1.1
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with Apo_Rsr13-Ct1.pdb, chain
A (#2.1), sequence alignment score = 2286.5
Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with Apo_Rsr13-Ct1.pdb, chain
B (#2.1), sequence alignment score = 1631.1
Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with Apo_Rsr13-Ct1.pdb, chain
C (#2.1), sequence alignment score = 1685.8
Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with Apo_Rsr13-Ct1.pdb, chain
D (#2.1), sequence alignment score = 1702.7
Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with Apo_Rsr13-Ct1.pdb, chain
E (#2.1), sequence alignment score = 1740.3
RMSD between 1753 pruned atom pairs is 0.557 angstroms; (across all 1782
pairs: 0.653)
> hide #!1.1 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!2.3 models
> hide #!2.1 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.3 models
> show #!1.3 models
> mmaker #2.3/A-H to #2.2/A-H pair ss bring #1.3
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with Open_Rsr35-Ct2.pdb, chain
A (#2.3), sequence alignment score = 2326.1
Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with Open_Rsr35-Ct2.pdb, chain
B (#2.3), sequence alignment score = 1631.1
Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with Open_Rsr35-Ct2.pdb, chain
C (#2.3), sequence alignment score = 1685.8
Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with Open_Rsr35-Ct2.pdb, chain
D (#2.3), sequence alignment score = 1702.7
Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with Open_Rsr35-Ct2.pdb, chain
E (#2.3), sequence alignment score = 1740.3
Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with Open_Rsr35-Ct2.pdb, chain
F (#2.3), sequence alignment score = 1283.2
Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with Open_Rsr35-Ct2.pdb, chain
G (#2.3), sequence alignment score = 1301.2
Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with Open_Rsr35-Ct2.pdb, chain
H (#2.3), sequence alignment score = 1292.2
RMSD between 2118 pruned atom pairs is 0.609 angstroms; (across all 2550
pairs: 4.762)
> mmaker #2.3/A-H to #2.2/A-H pair ss bring #1.3
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with Open_Rsr35-Ct2.pdb, chain
A (#2.3), sequence alignment score = 2326.1
Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with Open_Rsr35-Ct2.pdb, chain
B (#2.3), sequence alignment score = 1631.1
Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with Open_Rsr35-Ct2.pdb, chain
C (#2.3), sequence alignment score = 1685.8
Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with Open_Rsr35-Ct2.pdb, chain
D (#2.3), sequence alignment score = 1702.7
Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with Open_Rsr35-Ct2.pdb, chain
E (#2.3), sequence alignment score = 1740.3
Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with Open_Rsr35-Ct2.pdb, chain
F (#2.3), sequence alignment score = 1283.2
Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with Open_Rsr35-Ct2.pdb, chain
G (#2.3), sequence alignment score = 1301.2
Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with Open_Rsr35-Ct2.pdb, chain
H (#2.3), sequence alignment score = 1292.2
RMSD between 2118 pruned atom pairs is 0.609 angstroms; (across all 2550
pairs: 4.762)
> 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 = 84
shifted from previous position = 0.00231
rotated from previous position = 0.00928 degrees
atoms outside contour = 7941, contour level = 0.2
Position of Open_Rsr35-Ct2.pdb (#2.3) relative to Open_P29_J701_004.mrc (#1.3)
coordinates:
Matrix rotation and translation
0.99999961 -0.00012946 -0.00086989 0.16857509
0.00012945 0.99999999 -0.00000951 -0.03224247
0.00086989 0.00000939 0.99999962 -0.13983225
Axis 0.01074383 -0.98904979 0.14719066
Axis point 163.05133459 0.00000000 193.55515090
Rotation angle (degrees) 0.05039270
Shift along axis 0.01311855
> mmaker #2.3/A-H to #2.2/A-H pair ss bring #1.3
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with Open_Rsr35-Ct2.pdb, chain
A (#2.3), sequence alignment score = 2326.1
Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with Open_Rsr35-Ct2.pdb, chain
B (#2.3), sequence alignment score = 1631.1
Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with Open_Rsr35-Ct2.pdb, chain
C (#2.3), sequence alignment score = 1685.8
Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with Open_Rsr35-Ct2.pdb, chain
D (#2.3), sequence alignment score = 1702.7
Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with Open_Rsr35-Ct2.pdb, chain
E (#2.3), sequence alignment score = 1740.3
Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with Open_Rsr35-Ct2.pdb, chain
F (#2.3), sequence alignment score = 1283.2
Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with Open_Rsr35-Ct2.pdb, chain
G (#2.3), sequence alignment score = 1301.2
Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with Open_Rsr35-Ct2.pdb, chain
H (#2.3), sequence alignment score = 1292.2
RMSD between 2118 pruned atom pairs is 0.609 angstroms; (across all 2550
pairs: 4.762)
> hide #!2.3 models
> hide #!1 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-PCNA_v11.cxs"
> hide #!2 models
> show #!3.8 models
> hide #!3 models
> show #!2 models
> hide #!2.2 models
> show #!2.1 models
> show #!2.2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.2 models
> select #2.1/B:68
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2.1/B:67
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.1/B:68
4 atoms, 3 bonds, 1 residue, 1 model selected
> show #!2.3 models
> hide #!2.1 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> select #2/B:68
12 atoms, 9 bonds, 3 residues, 3 models selected
> show #!2.2 models
> hide #!2.1 models
> hide #!2.2 models
> show #!2.3 models
> show #!2.2 models
> hide #!2.3 models
> show #!2.3 models
> setattr sel res ss_type 0
Assigning ss_type attribute to 3 items
> hide #!2.3 models
> hide #!2.2 models
> show #!2.3 models
> select clear
> hide #!2.3 models
> show #!2.2 models
> show #!2.3 models
> hide #!2.2 models
> setattr #2/A:357-359 res ss_type 1
Assigning ss_type attribute to 9 items
> select #2.3/B:68
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2.3/A:356
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2.3/A:357
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.3/A:355
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2.3/A:356
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2.3/A:355
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2.3/B:69
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2.3/B:74
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2.3/B:69
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2.3/B:74
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.3 models
> show #!2.2 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.1 models
> hide #!2.3 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> select #2.2/A:580
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!2.2 models
> show #!2.1 models
> show #!2.2 models
> setattr #2/A:573-380 res ss_type 1
Assigning ss_type attribute to 0 items
> undo
> show #!2.2 models
> setattr #2/A:573-580 res ss_type 1
Assigning ss_type attribute to 24 items
> select #2/A:573-580
201 atoms, 204 bonds, 24 residues, 3 models selected
> show #!2.3 models
> hide #!2.2 models
> show #!2.2 models
> setattr sel res ss_type 1
Assigning ss_type attribute to 24 items
> setattr sel res ss_id 88
Assigning ss_id attribute to 24 items
> hide #!2.3 models
> hide #!2.2 models
> show #!2.2 models
> show #!2.3 models
> select #2/A:586-592
186 atoms, 186 bonds, 21 residues, 3 models selected
> setattr sel res ss_type 1
Assigning ss_type attribute to 21 items
> setattr sel res ss_id 88
Assigning ss_id attribute to 21 items
> hide #!2.2 models
> hide #!2.3 models
> show #!2.2 models
> show #!2.3 models
> hide #!2.3 models
> hide #!2.2 models
> select clear
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> show #!2.3 models
> show #!2.1 models
> hide #!2.2 models
> select #2.1/C:71
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2.1/C:72
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide #!2.1 models
> show #!2.1 models
> select #2/C:72
12 atoms, 9 bonds, 3 residues, 3 models selected
> show #!2.2 models
> hide #!2.2 models
> hide #!2.3 models
> show #!2.2 models
> show #!2.3 models
> setattr sel res ss_type 0
Assigning ss_type attribute to 3 items
> hide #!2.2 models
> hide #!2.1 models
> show #!2.2 models
> hide #!2.3 models
> select clear
> show #!2.3 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.3 models
> hide #!2.2 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.2 models
> select #2/F:2-6
84 atoms, 84 bonds, 10 residues, 2 models selected
> show #!2.3 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.3 models
> setattr sel res ss_type 2
Assigning ss_type attribute to 10 items
> show #!2.3 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.3 models
> select clear
> show #!2.3 models
> hide #!2.2 models
> show #!2.2 models
> show #!2.1 models
> hide #!2.2 models
> hide #!2.3 models
> show #!2.2 models
> hide #!2.1 models
> show #!2.3 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-PCNA_v12.cxs"
> select #2/A:334-338
114 atoms, 114 bonds, 15 residues, 3 models selected
> select #2/B:75-78
96 atoms, 93 bonds, 12 residues, 3 models selected
> show #!2.1 models
> show #!2.3 models
> setattr sel res ss_type 2
Assigning ss_type attribute to 12 items
> hide #!2.1 models
> hide #!2.3 models
> select clear
> hide #!2.2 models
> show #!2.1 models
> select #2/A:334-338
114 atoms, 114 bonds, 15 residues, 3 models selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 15 items
> select clear
> select #2.1/A:338
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #2/D:187-188
66 atoms, 66 bonds, 6 residues, 3 models selected
> select #2/D:63-64,187-188
135 atoms, 138 bonds, 12 residues, 3 models selected
> select #2/D:62-64,187-188
159 atoms, 162 bonds, 15 residues, 3 models selected
> select #2/D:62-64,94-95,187-188
210 atoms, 210 bonds, 21 residues, 3 models selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 21 items
> select clear
> hide #!2.1 models
> show #!2.2 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-PCNA_v12.cxs"
> select #2/A:600-601
54 atoms, 54 bonds, 6 residues, 3 models selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 6 items
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-
> PCNA_dssp_v13.cxs"
> select #2.2/F:61
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2.2/F:171
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2.2/F:62
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/F:58-61
82 atoms, 82 bonds, 8 residues, 2 models selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 8 items
> show #!2.3 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.3 models
> show #!2.3 models
> select #2/F:58-61
82 atoms, 82 bonds, 8 residues, 2 models selected
> setattr sel res ss_type 2
Assigning ss_type attribute to 8 items
> setattr sel res ss_id 88
Assigning ss_id attribute to 8 items
> hide #!2.3 models
> select clear
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-
> PCNA_dssp_v13.cxs"
——— End of log from Fri Feb 10 12:12:25 2023 ———
opened ChimeraX session
> show #!2.1 models
> hide #!2.2 models
> hide #!2.1 models
> show #!2.2 models
> combine #2.2 modelId #2.4
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> close #2.4
> show #!2.2 models
> combine #2.2/B modelId #2.4
> hide #!2.2 models
> delete #2.4 & ~/B
> show #!2.2 models
> hide #!2.2 models
> hide #!2.4 models
> show #!2.4 models
> undo
[Repeated 2 time(s)]
> hide #!2.2 models
> undo
[Repeated 6 time(s)]
> hide #!2.4 models
> show #!2.4 models
> close #2.4
> combine #2.2 modelId #2.4
> hide #!2.2 models
> delete #2.4 & ~/C
> hide #!2.4 models
> show #!2.4 models
> close #2.4
> combine #2.2 modelId #2.4
> delete #2.4 & ~/D
> hide #!2.4 models
> show #!2.4 models
> close #2.4
> combine #2.2 modelId #2.4
> delete #2.4 & ~/E
> hide #!2.4 models
> show #!2.4 models
> close #2.4
> combine #2.2 modelId #2.4
> delete #2.4 & ~/F
> hide #!2.4 models
> show #!2.4 models
> close #2.4
> combine #2.2 modelId #2.4
> delete #2.4 & ~/G
> hide #!2.4 models
> show #!2.4 models
> close #2.4
> combine #2.2 modelId #2.4
> delete #2.4 & ~/H
> hide #!2.4 models
> show #!2.4 models
> close #2.4
> show #!2.2 models
> rename #4 Rad24-gappedDNA
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-
> PCNA_dssp_v14.cxs"
> color /A #A8B98A
> color /B #BCAAC2
> color /C #F3929D
> color /D #E3FB90
> color /E #C5BAE5
> color /F #AEDFE2
> color /G #DF8DD7
> color /H #B5F9A0
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.2 models
> show #!3 models
> hide #!2 models
> hide #!3.8 models
> show #!3.1 models
> show #!3.2 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.2 models
> hide #!3 models
> show #!2 models
> mmaker #3.1/A-H to #2.2/A-H pair ss bring #3.2-8
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with ScRFC-PCNA-2DNA-wBRCT,
chain A (#3.1), sequence alignment score = 332.6
Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with ScRFC-PCNA-2DNA-wBRCT,
chain B (#3.1), sequence alignment score = 1577.7
Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with ScRFC-PCNA-2DNA-wBRCT,
chain C (#3.1), sequence alignment score = 1640.2
Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with ScRFC-PCNA-2DNA-wBRCT,
chain D (#3.1), sequence alignment score = 1543.9
Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with ScRFC-PCNA-2DNA-wBRCT,
chain E (#3.1), sequence alignment score = 1656.5
Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with ScRFC-PCNA-2DNA-wBRCT,
chain F (#3.1), sequence alignment score = 1122.1
Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with ScRFC-PCNA-2DNA-wBRCT,
chain G (#3.1), sequence alignment score = 1214.2
Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with ScRFC-PCNA-2DNA-wBRCT,
chain H (#3.1), sequence alignment score = 1193.2
RMSD between 354 pruned atom pairs is 1.089 angstroms; (across all 2504 pairs:
19.089)
> show #!3 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!2 models
> show #!3.8 models
> hide #!3.1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> mmaker #3.8/A-H to #2.2/A-H pair ss bring #3.1-7
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain A (#3.8), sequence alignment score = 379.8
Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain B (#3.8), sequence alignment score = 1486.5
Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain C (#3.8), sequence alignment score = 1525.5
Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain D (#3.8), sequence alignment score = 1468.3
Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain E (#3.8), sequence alignment score = 1400.7
Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain G (#3.8), sequence alignment score = 1144
Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain H (#3.8), sequence alignment score = 1202.2
Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain F (#3.8), sequence alignment score = 1187.8
RMSD between 439 pruned atom pairs is 1.189 angstroms; (across all 2426 pairs:
32.359)
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> mmaker #3.8/A-H to #3.1/A-H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain A (#3.8), sequence alignment score = 1956.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain B (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain B (#3.8), sequence alignment score = 1484.1
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain C (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain C (#3.8), sequence alignment score = 1539.9
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain D (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain D (#3.8), sequence alignment score = 1540.3
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain E (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain E (#3.8), sequence alignment score = 1431.7
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain F (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain G (#3.8), sequence alignment score = 1166.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain G (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain H (#3.8), sequence alignment score = 1234.2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain F (#3.8), sequence alignment score = 1166.8
RMSD between 606 pruned atom pairs is 0.928 angstroms; (across all 2490 pairs:
35.810)
> undo
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.1 models
> mmaker #3.8/A,H to #3.1/A,H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain A (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain A (#3.8), sequence alignment score = 1956.8
Matchmaker ScRFC-PCNA-2DNA-wBRCT, chain H (#3.1) with ScRFC-PCNA_1SXJ.pdb,
chain H (#3.8), sequence alignment score = 1174
RMSD between 416 pruned atom pairs is 0.967 angstroms; (across all 695 pairs:
14.894)
> show #!3.1 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> mmaker #3.8/A-H to #2.2/A-H pair ss bring #3.1-7
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain A (#3.8), sequence alignment score = 379.8
Matchmaker Closed_Rsr21-Ct2.pdb, chain B (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain B (#3.8), sequence alignment score = 1486.5
Matchmaker Closed_Rsr21-Ct2.pdb, chain C (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain C (#3.8), sequence alignment score = 1525.5
Matchmaker Closed_Rsr21-Ct2.pdb, chain D (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain D (#3.8), sequence alignment score = 1468.3
Matchmaker Closed_Rsr21-Ct2.pdb, chain E (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain E (#3.8), sequence alignment score = 1400.7
Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain G (#3.8), sequence alignment score = 1144
Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain H (#3.8), sequence alignment score = 1202.2
Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain F (#3.8), sequence alignment score = 1187.8
RMSD between 439 pruned atom pairs is 1.189 angstroms; (across all 2426 pairs:
32.359)
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> mmaker #3.8/A,H to #2.2/A,H pair ss bring #3.1-7
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain A (#3.8), sequence alignment score = 379.8
Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain H (#3.8), sequence alignment score = 1233.4
RMSD between 224 pruned atom pairs is 0.661 angstroms; (across all 637 pairs:
16.331)
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> mmaker #3.8/A,F-H to #2.2/A,F-H pair ss bring #3.1-7
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain A (#3.8), sequence alignment score = 379.8
Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain G (#3.8), sequence alignment score = 1144
Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain H (#3.8), sequence alignment score = 1202.2
Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain F (#3.8), sequence alignment score = 1187.8
RMSD between 573 pruned atom pairs is 0.990 angstroms; (across all 1145 pairs:
32.103)
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> mmaker #3.8/A,F,G,H to #2.2/A,F,G,H pair ss bring #3.1-7
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Closed_Rsr21-Ct2.pdb, chain A (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain A (#3.8), sequence alignment score = 379.8
Matchmaker Closed_Rsr21-Ct2.pdb, chain F (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain F (#3.8), sequence alignment score = 1181.2
Matchmaker Closed_Rsr21-Ct2.pdb, chain G (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain G (#3.8), sequence alignment score = 1207
Matchmaker Closed_Rsr21-Ct2.pdb, chain H (#2.2) with ScRFC-PCNA_1SXJ.pdb,
chain H (#3.8), sequence alignment score = 1233.4
RMSD between 635 pruned atom pairs is 0.888 angstroms; (across all 1147 pairs:
12.517)
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3.1 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> hide #!3.8 models
> hide #!3.1 models
> show #!2 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.8 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> save "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/Overall-Elg1_RFC-
> PCNA_dssp_v14.cxs"
[Repeated 1 time(s)]
——— End of log from Sat Feb 18 16:30:50 2023 ———
opened ChimeraX session
> hide #!2 models
> show #!1 models
> hide #!1.3 models
> show #!1.1 models
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-
> PCNA/0-MM/0-half/J632-Apo/cryosparc_P47_J328_map_locres.mrc"
Opened cryosparc_P47_J328_map_locres.mrc as #5, grid size 420,420,420, pixel
0.828, shown at level 4.55, step 2, values float32
> close #5
Uncaught (in promise) TypeError: Cannot read properties of null (reading
'insertBefore')
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-PCNA/0-MM/Apo_P29_J632_004.mrc"
Opened Apo_P29_J632_004.mrc as #5, grid size 420,420,420, pixel 0.828, shown
at level 0.1, step 2, values float32
> hide #!1 models
> surface dust #0-9 size 10
> open "/Users/fengwei.zheng/OneDrive - Van Andel
> Institute/Documents/Draft/4_Egl1_RFC-
> PCNA/0-MM/0-half/J632-Apo/cryosparc_P47_J328_map_locres.mrc"
Opened cryosparc_P47_J328_map_locres.mrc as #6, grid size 420,420,420, pixel
0.828, shown at level 4.55, step 2, values float32
> hide #!6 models
> show #!1 models
> volume #5-6 step 1 level 0.25
> hide #!1 models
> show #!6 models
> volume #6 color #b2ffffb3
> volume #6 color #b2ffff
> hide #!6 models
> show #!1 models
> fitmap #5 inMap #1.1 bring #6
Expected a keyword
> hide #!1 models
> show #!6 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
> key true
Map values for surface "surface": minimum 0, mean 3.582, maximum 8.703
> key rainbow :2.5 :3.5 :4.5 :5.5 :6.5 showTool true
> ui mousemode right "color key"
> key pos 0.71847,0.0652488
> ui mousemode right translate
> volume #5 level 0.3
> volume #6 level 0.3
> volume #5 level 0.35
> show #!1 models
> select add #5
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.19588,0.9379,-0.28631,81.544,-0.22909,-0.32765,-0.9166,446.33,-0.95349,-0.11395,0.27905,311.26
> view matrix models
> #5,0.46722,0.88022,0.08315,-85.883,0.73165,-0.33212,-0.5953,229.04,-0.49638,0.33897,-0.79919,353.33
> view matrix models
> #5,-0.91246,-0.40891,-0.014391,392.32,-0.17295,0.35357,0.91928,-24.803,-0.37082,0.8413,-0.39334,167.12
> view matrix models
> #5,-0.44742,-0.81801,-0.3615,453.29,-0.36901,-0.19934,0.9078,109.31,-0.81465,0.53956,-0.21266,261.43
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.44742,-0.81801,-0.3615,400.08,-0.36901,-0.19934,0.9078,133.36,-0.81465,0.53956,-0.21266,277.53
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.84663,0.17613,-0.5022,312.96,-0.40253,-0.82922,0.38778,348.43,-0.34813,0.53045,0.77293,20.014
> view matrix models
> #5,-0.61922,-0.56425,-0.54607,416.85,-0.31942,-0.45429,0.83162,185.17,-0.71731,0.68938,0.10107,176.5
> view matrix models
> #5,-0.37265,-0.89215,-0.25533,381.47,-0.40393,-0.091769,0.91018,119.32,-0.83545,0.44232,-0.32617,319.45
> view matrix models
> #5,-0.072232,-0.93202,0.35513,226.24,-0.63915,0.3166,0.70089,123.29,-0.76568,-0.17636,-0.61857,473.38
> view matrix models
> #5,0.023712,-0.64624,0.76277,83.605,-0.82405,0.41935,0.38091,194.44,-0.56603,-0.63759,-0.52259,505.74
> view matrix models
> #5,-0.81564,0.23975,-0.52655,300.88,0.37275,-0.47828,-0.79518,375.64,-0.44248,-0.84485,0.30074,370.57
> view matrix models
> #5,-0.881,0.36967,-0.29528,245.55,-0.011821,-0.64111,-0.76736,463.38,-0.47298,-0.67255,0.56918,294.98
> view matrix models
> #5,-0.67682,0.72785,-0.11023,113.11,-0.36601,-0.46264,-0.80746,497.16,-0.63871,-0.50616,0.57953,290.48
> view matrix models
> #5,-0.38284,0.92206,0.056951,-1.33,-0.68291,-0.24095,-0.68962,487.82,-0.62215,-0.30291,0.72193,224.83
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.38284,0.92206,0.056951,75.238,-0.68291,-0.24095,-0.68962,457.3,-0.62215,-0.30291,0.72193,195.05
> fitmap #5 inMap #1.1 bring #6
Expected a keyword
> fitmap #5 inMap #1.1
Fit map Apo_P29_J632_004.mrc in map Apo_P29_J632_004.mrc using 125313 points
correlation = 0.4658, correlation about mean = 0.09559, overlap = 1.801e+04
steps = 172, shift = 7.57, angle = 13.6 degrees
Position of Apo_P29_J632_004.mrc (#5) relative to Apo_P29_J632_004.mrc (#1.1)
coordinates:
Matrix rotation and translation
0.99998757 0.00327691 -0.00375862 -4.26903411
-0.00327343 0.99999421 0.00093028 -2.14580035
0.00376164 -0.00091797 0.99999251 0.64788562
Axis -0.18222236 -0.74143457 -0.64580941
Axis point -509.16948697 0.00000000 -1039.55451000
Rotation angle (degrees) 0.29057229
Shift along axis 1.95047339
> fitmap #5 inMap #1.1
Fit map Apo_P29_J632_004.mrc in map Apo_P29_J632_004.mrc using 125313 points
correlation = 0.4652, correlation about mean = 0.09547, overlap = 1.803e+04
steps = 28, shift = 0.0166, angle = 0.02 degrees
Position of Apo_P29_J632_004.mrc (#5) relative to Apo_P29_J632_004.mrc (#1.1)
coordinates:
Matrix rotation and translation
0.99998635 0.00360551 -0.00378107 -4.30762066
-0.00360157 0.99999296 0.00104822 -2.10325239
0.00378482 -0.00103459 0.99999230 0.66406669
Axis -0.19548324 -0.71009875 -0.67642152
Axis point -514.70544884 0.00000000 -1039.87371878
Rotation angle (degrees) 0.30523641
Shift along axis 1.88639551
> view matrix models
> #5,-0.53655,0.83803,-0.09912,140.43,-0.5944,-0.45869,-0.66053,467.88,-0.59901,-0.29549,0.74423,179.01
> fitmap #5 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 = 6.736e+04
steps = 56, shift = 1.65, angle = 0.31 degrees
Position of Apo_P29_J632_004.mrc (#5) relative to Apo_P29_J632_004.mrc (#1.1)
coordinates:
Matrix rotation and translation
1.00000000 -0.00003582 0.00005096 -0.00778457
0.00003582 1.00000000 -0.00007979 0.00476406
-0.00005096 0.00007979 1.00000000 -0.00887981
Axis 0.78825025 0.50341701 0.35388255
Axis point 0.00000000 80.77940671 103.11450309
Rotation angle (degrees) 0.00579971
Shift along axis -0.00688029
> select clear
> 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
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