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Opened 3 years ago
Closed 3 years ago
#8049 closed defect (nonchimerax)
MemoryError saving large image
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.17134
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "F:\\\Documents\\\Map\\\SSX1\\\SSX1 Model
> building\\\20220621-4月份新算的结构\\\Sup fig6\\\WT&119 Comparion\\\Acidic
> patch.cxs"
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc as #3, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened postprocess_masked.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.013, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 0 as #1.1, grid size
256,256,256, pixel 1.07, shown at level 0.0028, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 1 as #1.2, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 2 as #1.3, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 3 as #1.4, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 4 as #1.5, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 5 as #1.6, grid size
256,256,256, pixel 1.07, shown at level 0.008, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 6 as #1.7, grid size
256,256,256, pixel 1.07, shown at level 0.008, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 7 as #1.8, grid size
256,256,256, pixel 1.07, shown at level 0.0134, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 8 as #1.9, grid size
256,256,256, pixel 1.07, shown at level 0.015, step 1, values float32
Log from Mon Oct 31 09:52:31 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "F:\\\Documents\\\Map\\\SSX1\\\SSX1 Model
> building\\\20220621-4月份新算的结构\\\Sup fig6\\\ssx1-119 NCP-model_ele.cxs"
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc as #3, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened postprocess_masked.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.013, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 0 as #1.1, grid size
256,256,256, pixel 1.07, shown at level 0.0028, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 1 as #1.2, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 2 as #1.3, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 3 as #1.4, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 4 as #1.5, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 5 as #1.6, grid size
256,256,256, pixel 1.07, shown at level 0.008, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 6 as #1.7, grid size
256,256,256, pixel 1.07, shown at level 0.008, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 7 as #1.8, grid size
256,256,256, pixel 1.07, shown at level 0.0134, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 8 as #1.9, grid size
256,256,256, pixel 1.07, shown at level 0.015, step 1, values float32
Log from Fri Oct 28 15:53:13 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "F:\\\Documents\\\Map\\\SSX1\\\SSX1 Model
> building\\\20220621-4月份新算的结构\\\Sup fig6\\\ssx1-119 NCP-model.cxs"
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc as #3, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened postprocess_masked.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.013, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 0 as #1.1, grid size
256,256,256, pixel 1.07, shown at level 0.0028, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 1 as #1.2, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 2 as #1.3, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 3 as #1.4, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 4 as #1.5, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 5 as #1.6, grid size
256,256,256, pixel 1.07, shown at level 0.008, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 6 as #1.7, grid size
256,256,256, pixel 1.07, shown at level 0.008, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 7 as #1.8, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 8 as #1.9, grid size
256,256,256, pixel 1.07, shown at level 0.015, step 1, values float32
Log from Thu Aug 25 17:23:51 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "F:\\\Documents\\\Map\\\SSX1\\\SSX1 Model
> building\\\20220621-4月份新算的结构\\\Fig4\\\SSX1_119Ub_NCP.cxs"
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc as #3, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened postprocess_masked.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.013, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 0 as #1.1, grid size
256,256,256, pixel 1.07, shown at level 0.0028, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 1 as #1.2, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 2 as #1.3, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 3 as #1.4, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 4 as #1.5, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 5 as #1.6, grid size
256,256,256, pixel 1.07, shown at level 0.008, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 6 as #1.7, grid size
256,256,256, pixel 1.07, shown at level 0.008, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 7 as #1.8, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 8 as #1.9, grid size
256,256,256, pixel 1.07, shown at level 0.015, step 1, values float32
Log from Tue Aug 16 14:50:08 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "F:\\\Documents\\\Map\\\SSX1\\\SSX1 Model
> building\\\20220621-4月份新算的结构\\\overall map\\\overall map.cxs"
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc as #3, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened postprocess_masked.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.013, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 0 as #1.1, grid size
256,256,256, pixel 1.07, shown at level 0.0028, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 1 as #1.2, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 2 as #1.3, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 3 as #1.4, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 4 as #1.5, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 5 as #1.6, grid size
256,256,256, pixel 1.07, shown at level 0.01, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 6 as #1.7, grid size
256,256,256, pixel 1.07, shown at level 0.01, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 7 as #1.8, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 8 as #1.9, grid size
256,256,256, pixel 1.07, shown at level 0.015, step 1, values float32
Log from Mon Aug 8 15:18:05 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "F:\\\Documents\\\Map\\\SSX1\\\SSX1 Model
> building\\\20220621-4月份新算的结构\\\20220621-4月份新算的结构和2月份的model放在一起 .cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.0154, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0109, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.011, step 1, values float32
Opened job054_run_ct17_class001.mrc as #3, grid size 256,256,256, pixel 1.07,
shown at level 0.00763, step 1, values float32
Opened job288_run_ct22_class001_3.31A.mrc as #6, grid size 256,256,256, pixel
1.07, shown at level 0.0099, step 1, values float32
Opened postprocess.mrc as #9, grid size 256,256,256, pixel 1.07, shown at
level 0.0104, step 1, values float32
Opened postprocess_masked.mrc as #7, grid size 256,256,256, pixel 1.07, shown
at level 0.0106, step 1, values float32
Opened postprocess_masked.mrc as #10, grid size 256,256,256, pixel 1.07, shown
at level 0.0124, step 1, values float32
Opened postprocess_masked.mrc as #11, grid size 256,256,256, pixel 1.07, shown
at level 0.0129, step 1, values float32
Log from Tue Jun 21 18:14:32 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\\\Documents\\\Map\\\SSX1\\\SSX1 Model
> building\\\20220216-修改了D182-E184的密度\\\20220405最终map+原子模型.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.0154, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0109, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.011, step 1, values float32
Opened job054_run_ct17_class001.mrc as #3, grid size 256,256,256, pixel 1.07,
shown at level 0.00763, step 1, values float32
Log from Tue Apr 5 10:24:07 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\\\Documents\\\Map\\\SSX1\\\SSX1 Model
> building\\\20220216-修改了D182-E184的密度\\\最终map+原子模型.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.0154, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0109, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.011, step 1, values float32
Opened job054_run_ct17_class001.mrc as #3, grid size 256,256,256, pixel 1.07,
shown at level 0.00763, step 1, values float32
Log from Wed Feb 16 19:42:15 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\\\Documents\\\Map\\\SSX1\\\SSX1 Model
> building\\\20220216-修改了D182-E184的密度\\\原子模型.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.0154, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0109, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.011, step 1, values float32
Opened job054_run_ct17_class001.mrc as #3, grid size 256,256,256, pixel 1.07,
shown at level 0.00763, step 1, values float32
Log from Wed Feb 16 12:33:54 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\\\Documents\\\Map\\\SSX1\\\SSX1 Model building\\\20211005-changer
> color-最终配色-结构作图\\\6-H3和Ub形成碱性沟槽\\\post结构+refine结构.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.0154, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0109, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.011, step 1, values float32
Opened job054_run_ct17_class001.mrc as #3, grid size 256,256,256, pixel 1.07,
shown at level 0.00763, step 1, values float32
Log from Wed Feb 16 09:51:13 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\\\Documents\\\Map\\\SSX1\\\SSX1 Model building\\\20211005-changer
> color-最终配色-结构作图\\\4-后端和Ub的互作\\\last interact-3.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0155, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.0175, step 1, values float32
Log from Fri Oct 8 11:31:20 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-2-CHANGED.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0155, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.0175, step 1, values float32
Log from Thu Oct 7 22:28:25 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0155, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.0175, step 1, values float32
Log from Thu Oct 7 21:55:38 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-W164 R167-H2B H2A.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0155, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.0175, step 1, values float32
Log from Thu Oct 7 16:18:40 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\\\Documents\\\Map\\\SSX1\\\SSX1 Model building\\\20211005-changer
> color\\\20211005-change color overall map.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0155, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.0175, step 1, values float32
Log from Wed Oct 6 21:40:30 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\\\Documents\\\Map\\\SSX1\\\SSX1 Model
> building\\\20210929_TZB\\\overall map and model_20210929_004.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0155, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.0175, step 1, values float32
Log from Wed Sep 29 18:50:26 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\\\Documents\\\Map\\\SSX1\\\SSX1 Model building\\\zuotu\\\Overall
> map_model\\\overall model_20210929.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0155, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.0175, step 1, values float32
Log from Wed Sep 29 18:27:07 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0155, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.0164, step 1, values float32
Log from Wed Sep 29 16:47:19 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.cxs"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.015, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0153, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Log from Wed Sep 29 16:30:31 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 23
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 24
CHIRALITY : 0.050 0.241 2159
34 messages similar to the above omitted
End residue of secondary structure not found: HELIX 34 34 ILE U 23 GLU U 341 0
12
End residue of secondary structure not found: HELIX 35 35 LEU U 56 TYR U 591 0
4
End residue of secondary structure not found: HELIX 36 36 HIS S 162 EU 168 1 6
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
End residue of secondary structure not found: SHEET 22 2222 MET U 1 TH 0 0
Chain information for 20210929_final.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide atoms
> show cartoons
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 23
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 24
CHIRALITY : 0.050 0.241 2159
21 messages similar to the above omitted
End residue of secondary structure not found: HELIX 34 34 ILE U 23 GLU U 341 0
12
End residue of secondary structure not found: HELIX 35 35 LEU U 56 TYR U 591 0
2
End residue of secondary structure not found: HELIX 36 36 HIS S 162 EU 168 1 6
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
End residue of secondary structure not found: SHEET 22 2222 MET U 1 TH 0 0
Chain information for 20210929_final_for chimeraX.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #1 models
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ~select #2
Nothing selected
> open C:/Users/huasong/Desktop/6fq5.pdb
6fq5.pdb title:
Class 1 : canonical nucleosome [more info...]
Chain information for 6fq5.pdb #3
---
Chain | Description
A E | histone H3
B | histone H4
C G | histone H2A
D H | histone H2B
F | histone H4
I | DNA (147-mer)
J | DNA (147-mer)
> hide #2 models
> select #3
12193 atoms, 13008 bonds, 1068 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 23
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 24
CHIRALITY : 0.050 0.241 2159
21 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 EU 168 1 6
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
End residue of secondary structure not found: SHEET 22 2222 MET U 1 TH 0 0
Chain information for 20210929_final_for chimeraX.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #3 models
> ~select #3
Nothing selected
> select #4
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 23
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 24
CHIRALITY : 0.050 0.241 2159
21 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 01
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
End residue of secondary structure not found: SHEET 22 2222 MET U 1 TH 0 0
Chain information for 20210929_final_for chimeraX.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #4 models
> select #5
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 01
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #5 models
> select #6
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> close #1-5
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 01
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #1 models
> hide sel cartoons
> show sel surfaces
> show sel cartoons
> hide sel surfaces
> select clear
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 1
7
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #2 models
> select #6
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 1
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #3 models
> hide sel atoms
> show sel cartoons
> show sel cartoons
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 1
7
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #4 models
> hide sel atoms
> show sel cartoons
> close #1-4
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 1
7
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide sel atoms
> select #1
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #6
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> select #1
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> select #6
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> select #1
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> select #6
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
18 messages similar to the above omitted
End residue of secondary structure not found: HELIX 32 32 THR H 90 LEU H 102
01 1
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> select #3
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> close #1-2#6
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
18 messages similar to the above omitted
End residue of secondary structure not found: HELIX 32 32 THR H 90 LEU H 102
01 1
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> select #1
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #3
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> ~select #3
Nothing selected
> select #1
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> ~select #1
Nothing selected
> select #1
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> ~select #1
Nothing selected
> select #3
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> ~select #3
Nothing selected
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 32 32 THR H 90 LEU H 102
01 1
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> hide #2 models
> show #2 models
> close #3
> close #1
> select /I
2822 atoms, 3168 bonds, 137 residues, 1 model selected
> color sel dark gray
> select /J
2795 atoms, 3132 bonds, 137 residues, 1 model selected
> color sel dark gray
> select clear
> select /G
815 atoms, 825 bonds, 106 residues, 1 model selected
> ui tool show "Color Actions"
> color sel wheat
> color sel burly wood
> select clear
> select /F
648 atoms, 655 bonds, 81 residues, 1 model selected
> color sel pink
> color sel light coral
> color sel pale violet red
> color sel pale violet red
> color sel pale violet red
> color sel light pink
> color sel pale violet red
> color sel pink
> color sel violet
> color sel deep pink
> color sel magenta
> color sel dark violet
> color sel tan
> color sel burly wood
> color sel light coral
> color sel medium violet red
> color sel pale violet red
> select clear
> select /F
648 atoms, 655 bonds, 81 residues, 1 model selected
> color sel light coral
> select clear
> select /G
815 atoms, 825 bonds, 106 residues, 1 model selected
> color sel medium aquamarine
> color sel dark sea green
> select clear
> select /H
707 atoms, 718 bonds, 91 residues, 1 model selected
> color sel light salmon
> color sel dark salmon
> color sel tan
> color sel burly wood
> color sel tan
> color sel burly wood
> select clear
> select /E
783 atoms, 794 bonds, 95 residues, 1 model selected
> color sel medium slate blue
> select clear
> select /U
593 atoms, 599 bonds, 74 residues, 1 model selected
> color sel yellow
> select clear
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> color sel red
> color sel crimson
> select /U
593 atoms, 599 bonds, 74 residues, 1 model selected
> color sel khaki
> color sel pale goldenrod
> color sel gold
> select clear
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> color sel maroon
> color sel dark red
> color sel fire brick
> color sel brown
> color sel tomato
> color sel crimson
> color sel crimson
> select clear
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210920.cxs"
> open "C:/Users/huasong/Desktop/SSX1 Model
> building/job059_postprocess_masked.mrc"
Opened job059_postprocess_masked.mrc as #1, grid size 256,256,256, pixel 1.07,
shown at level 0.00431, step 1, values float32
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide #!1 models
> open "C:/Users/huasong/Desktop/SSX1 Model
> building/job054_run_ct17_class001.mrc"
Opened job054_run_ct17_class001.mrc as #3, grid size 256,256,256, pixel 1.07,
shown at level 0.003, step 1, values float32
> ~select #2
Nothing selected
> select #3
2 models selected
> show #!1 models
> ~select #3
Nothing selected
> hide #!3 models
> volume #1 level 0.02036
> volume #1 level 0.01434
> surface dust #1 size 10.7
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> color zone #1 near sel & #2 distance 6.44
> close #3
> ui tool show "Color Zone"
> color zone #1 near #2 distance 1.07
> color zone #1 near #2 distance 4.44
> volume #1 level 0.01037
> volume #1 level 0.015
> volume #1 level 0.016
> volume splitbyzone #1
Opened job059_postprocess_masked.mrc 0 as #3.1, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 1 as #3.2, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 2 as #3.3, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 3 as #3.4, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 4 as #3.5, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 5 as #3.6, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 6 as #3.7, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 7 as #3.8, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
> volume #3.6 level 0.01178
> surface dust #3.1 size 10.7
> surface dust #3.2 size 10.7
> surface dust #3.3 size 10.7
> surface dust #3.4 size 10.7
> surface dust #3.5 size 10.7
> surface dust #3.6 size 10.7
> surface dust #3.7 size 10.7
> surface dust #3.8 size 10.7
> ui tool show "Hide Dust"
> surface dust #3.1 size 1.07
> surface dust #3.1 size 1.07
> surface dust #3.1 size 4.15
> surface dust #3.1 size 5
> surface dust #3.1 size 5
> volume #3.7 level 0.01508
> hide #2 models
> volume #3.6 level 0.02093
> volume #3.6 level 0.01143
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210920.cxs"
> volume #1 level 0.02705
> open "C:/Users/huasong/Desktop/SSX1 Model building/job059_postprocess.mrc"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.011, step 1, values float32
> hide #!1 models
> hide #1.1 models
> close #1
> close #3
> show #2 models
> surface dust #4 size 6.44
> color zone #4 near #2 distance 6.44
> view sel
> volume #4 level 0.01932
> volume #4 level 0.01694
> volume #4 level 0.01337
> surface dust #4 size 10
> surface dust #4 size 10
> surface dust #4 size 15
> surface dust #4 size 15
> surface dust #4 size 10.7
> surface dust #4 size 10.7
> surface dust #4 size 10.7
> surface dust #4 size 10.7
> volume #4 level 0.01813
> surface dust #4 size 10
> surface dust #4 size 5
> volume #4 level 0.02052
> volume #4 level 0.021
> volume splitbyzone #4
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
> surface dust #4 size 5
> surface dust #4 size 5
> surface dust #4 size 5
> surface dust #1.1 size 10.7
> surface dust #1.2 size 10.7
> surface dust #1.3 size 10.7
> surface dust #1.4 size 10.7
> surface dust #1.5 size 10.7
> surface dust #1.6 size 10.7
> surface dust #1.7 size 10.7
> surface dust #1.8 size 10.7
> volume #1.7 level 0.01514
> volume #1.7 level 0.01532
> volume #1.6 level 0.01044
> surface dust #1.6 size 2.08
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929.cxs"
> color zone #1.6 near #2 distance 6.44
> volume splitbyzone #1.6
Opened job059_postprocess.mrc 5 0 as #3.1, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 1 as #3.2, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 2 as #3.3, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 3 as #3.4, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 4 as #3.5, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 5 as #3.6, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 6 as #3.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 7 as #3.8, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
> surface dust #1.6 size 2.08
> surface dust #1.1 size 10.7
> surface dust #1.2 size 10.7
> surface dust #1.3 size 10.7
> surface dust #1.4 size 10.7
> surface dust #1.5 size 10.7
> surface dust #1.7 size 10.7
> surface dust #1.8 size 10.7
> surface dust #3.1 size 10.7
> surface dust #3.2 size 10.7
> surface dust #3.3 size 10.7
> surface dust #3.4 size 10.7
> surface dust #3.5 size 10.7
> surface dust #3.6 size 10.7
> surface dust #3.7 size 10.7
> surface dust #3.8 size 10.7
> surface undust #1.6
> surface undust #1.6
> surface undust #3.6
> hide #!3.1 models
> show #!3.1 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3.6 models
> show #!3.6 models
> hide #!3.1 models
> show #!3.1 models
> volume #3.6 level 0.01678
> hide #!3 models
> close #3
> show #!1.6 models
> volume #1.6 level 0.01607
> surface dust #1.6 size 6.44
> surface dust #1.6 size 4
> volume #1.6 level 0.01291
> select clear
> volume #1.6 level 0.0217
> volume #1.6 level 0.01643
> volume #1.6 level 0.01678
> volume #1.6 level 0.015
> transparency #1-2 20
> transparency #1-2 10
> select clear
> select clear
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.cxs"
> volume #!1.1-8 style surface
> transparency #1-2 0
> lighting full
> lighting full
> lighting soft
> lighting simple
> lighting soft
> show #!4 models
> hide #!4 models
> hide #2 models
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.cxs"
——— End of log from Wed Sep 29 16:30:31 2021 ———
opened ChimeraX session
> ui tool show "Hide Dust"
> surface dust #1.1 size 1.07
> surface dust #1.6 size 2
> surface dust #1.6 size 5
> surface dust #1.1 size 10.7
> surface dust #1.2 size 10.7
> surface dust #1.3 size 10.7
> surface dust #1.4 size 10.7
> surface dust #1.5 size 10.7
> surface dust #1.6 size 10.7
> surface dust #1.7 size 10.7
> surface dust #1.8 size 10.7
> surface undust #1.6
> surface dust #1.6 size 2
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.cxs"
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.png" width 3206 height 2000
> supersample 4
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_002.cxs"
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_002.png" width 3206 height 2000
> supersample 4
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_003.cxs"
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_003.png" width 3206 height 2000
> supersample 4
> volume #1.7 level 0.01551
> show #2 models
> hide #2 models
> surface dust #1.6 size 2
> surface dust #1.6 size 2
> surface dust #1.6 size 3
> surface dust #1.6 size 2
> surface dust #1.6 size 2.5
> select clear
> ui tool show "Side View"
> volume #1.8 level 0.01779
> view
> volume #1.8 level 0.01645
> show #2 models
> hide #!1 models
> select /I:0
22 atoms, 24 bonds, 1 residue, 1 model selected
> show #!1 models
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.cxs"
No map chosen to save
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.tiff" width 3206 height 2000
> supersample 4
> select clear
> surface dust #1.6 size 3
> surface dust #1.6 size 2
> surface dust #1.6 size 2.5
> surface dust #1.6 size 2
> surface dust #1.6 size 3
> surface dust #1.6 size 4
> surface dust #1.6 size 2
> surface dust #1.6 size 2.5
> hide #2 models
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.cxs"
——— End of log from Wed Sep 29 16:47:19 2021 ———
opened ChimeraX session
> hide #!1 models
> show #2 models
> show #!1 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.6 models
> hide #!1.7 models
> hide #2 models
> show #2 models
> hide #!1.5 models
> transparency #2#1.8#!1 50
> select /I:0
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 205 atom styles
> color sel byhetero
> style sel ball
Changed 205 atom styles
> select clear
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> style sel ball
Changed 205 atom styles
> style sel stick
Changed 205 atom styles
> select clear
> volume #1.8 level 0.01752
> select /I
2822 atoms, 3168 bonds, 137 residues, 1 model selected
> select clear
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall model_20210929.cxs"
——— End of log from Wed Sep 29 18:27:07 2021 ———
opened ChimeraX session
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!4 models
> ui tool show "Side View"
> save "D:/Documents/Map/SSX1/SSX1 Model building/20210929_TZB/overall map and
> model_20210929_004.cxs"
——— End of log from Wed Sep 29 18:50:26 2021 ———
opened ChimeraX session
> hide #!4 models
> show #!1.7 models
> show #!1.6 models
> show #!1.5 models
> show #!1.4 models
> show #!1.3 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> hide #2 models
> show #!1.1 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.5 models
> show #2 models
> show #!1.5 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> select clear
> select #1.8
2 models selected
> volume sel style surface
> transparency sel 0
> select clear
Drag select of 1.2 job059_postprocess.mrc 1 , 1.3 job059_postprocess.mrc 2 ,
1.4 job059_postprocess.mrc 3 , 1.5 job059_postprocess.mrc 4 , 1.6
job059_postprocess.mrc 5 , 1.7 job059_postprocess.mrc 6 , 1.8
job059_postprocess.mrc 7 , 137 atoms, 1122 residues, 120 bonds
> color sel byhetero
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/G LYS 118 CD
/G LYS 118 CE
/G LYS 118 NZ
/G LYS 118 CG
Deleting 5' phosphates from: /J DC -73, /I DT -63
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 20210929_final_for chimeraX_.pdb_A SES surface #2.1:
minimum, -13.42, mean 1.84, maximum 12.71
Coulombic values for 20210929_final_for chimeraX_.pdb_B SES surface #2.2:
minimum, -8.84, mean 3.94, maximum 24.66
Coulombic values for 20210929_final_for chimeraX_.pdb_C SES surface #2.3:
minimum, -14.45, mean 2.28, maximum 16.17
Coulombic values for 20210929_final_for chimeraX_.pdb_D SES surface #2.4:
minimum, -12.45, mean 1.25, maximum 11.99
Coulombic values for 20210929_final_for chimeraX_.pdb_E SES surface #2.5:
minimum, -11.62, mean 1.63, maximum 12.32
Coulombic values for 20210929_final_for chimeraX_.pdb_F SES surface #2.6:
minimum, -8.12, mean 3.47, maximum 17.60
Coulombic values for 20210929_final_for chimeraX_.pdb_G SES surface #2.7:
minimum, -16.37, mean 2.12, maximum 15.08
Coulombic values for 20210929_final_for chimeraX_.pdb_H SES surface #2.8:
minimum, -12.68, mean 1.25, maximum 11.97
Coulombic values for 20210929_final_for chimeraX_.pdb_I SES surface #2.9:
minimum, -23.98, mean -14.26, maximum -3.09
Coulombic values for 20210929_final_for chimeraX_.pdb_J SES surface #2.10:
minimum, -25.82, mean -14.24, maximum -2.88
Coulombic values for 20210929_final_for chimeraX_.pdb_S SES surface #2.11:
minimum, -11.34, mean -0.79, maximum 9.56
Coulombic values for 20210929_final_for chimeraX_.pdb_U SES surface #2.12:
minimum, -12.75, mean -0.30, maximum 18.17
To also show corresponding color key, enter the above coulombic command and
add key true
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> hide sel surfaces
> select /U
593 atoms, 599 bonds, 74 residues, 1 model selected
> hide sel surfaces
> select clear
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> color (#!2 & sel) magenta
> hide #!1.8 models
> select clear
> select /S:166
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:89@OD1
1 atom, 1 residue, 1 model selected
> select /S:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /E:41@CE1
1 atom, 1 residue, 1 model selected
> select /S:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> view
> hide #!1 models
Drag select of 20210929_final_for chimeraX_.pdb_A SES surface,
20210929_final_for chimeraX_.pdb_B SES surface, 20210929_final_for
chimeraX_.pdb_C SES surface, 20210929_final_for chimeraX_.pdb_D SES surface,
20210929_final_for chimeraX_.pdb_E SES surface, 20210929_final_for
chimeraX_.pdb_F SES surface, 20210929_final_for chimeraX_.pdb_G SES surface,
20210929_final_for chimeraX_.pdb_H SES surface, 20210929_final_for
chimeraX_.pdb_I SES surface, 20210929_final_for chimeraX_.pdb_J SES surface,
137 atoms, 1122 residues, 120 bonds
> hide sel surfaces
> select clear
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> hide sel atoms
> select clear
> show #!1.8 models
> hide #!1.8 models
> show #!1.8 models
> select /A
801 atoms, 813 bonds, 97 residues, 1 model selected
> hide #!1.2 models
> show #!1.2 models
> ui tool show "Color Actions"
> hide #!1.2 models
> color sel dodger blue
> show #!1.2 models
> select clear
> hide #!1.2 models
> show #!1.2 models
> hide #!1 models
> select /E
783 atoms, 794 bonds, 95 residues, 1 model selected
> color sel dodger blue
> color sel cornflower blue
> color sel royal blue
> color sel cornflower blue
> color sel dodger blue
> color sel cornflower blue
> color sel dodger blue
> color sel cornflower blue
> color sel slate blue
> color sel cornflower blue
> color sel deep sky blue
> color sel cornflower blue
> color sel dodger blue
> select clear
> show #!1 models
> hide #!1 models
> select /D
707 atoms, 718 bonds, 91 residues, 1 model selected
> select /C
825 atoms, 835 bonds, 107 residues, 1 model selected
> color sel forest green
> color sel dark sea green
> color sel medium sea green
> color sel forest green
> select clear
> select /G
815 atoms, 825 bonds, 106 residues, 1 model selected
> color sel forest green
> select clear
> show #!1 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.6 models
> show #!1.6 models
> lighting soft
> hide #!1 models
> lighting simple
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> color sel light gray
> color sel dark gray
> color sel light gray
> color sel gray
> color sel dark gray
> color sel light gray
> color sel dark gray
> select clear
> ui tool show "Side View"
> lighting flat
> lighting simple
> lighting full
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> lighting full
> lighting flat
> lighting simple
> lighting flat
> lighting simple
> lighting simple
> lighting simple
> lighting simple
> graphics silhouettes false
> lighting flat
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> show sel atoms
> select clear
> view
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting shadows true
> graphics silhouettes true
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> show #!1 models
> lighting simple
> lighting soft
> lighting flat
> lighting soft
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall model-
> change colors.cxs" includeMaps true
> hide #!1 models
> lighting flat
> show #!1 models
> lighting soft
> camera
Camera parameters:
type: mono
position: -37.092 576.05 218.05
view direction: 0.40142 -0.90224 -0.15758
field of view: 30 degrees
> preset "molecular surfaces" "ghostly white"
Changed 12158 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "chain id coloring (opaque)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> preset "molecular surfaces" "atomic coloring (transparent)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> undo
> undo
> undo
> undo
> undo
> undo
> ui tool show "Side View"
> ui tool show "Side View"
> ui tool show "Side View"
> view
> view
> set bgColor black
> set bgColor gray
> set bgColor white
Drag select of 1.2 job059_postprocess.mrc 1 , 1.3 job059_postprocess.mrc 2 ,
1.4 job059_postprocess.mrc 3 , 1.5 job059_postprocess.mrc 4 , 1.6
job059_postprocess.mrc 5 , 1.7 job059_postprocess.mrc 6 , 1.8
job059_postprocess.mrc 7 , 137 atoms, 1122 residues, 120 bonds
> select clear
> hide #!1 models
> show #!1 models
> ui mousemode right "mark maximum"
> ui mousemode right "mark plane"
> ui mousemode right "mark surface"
> ui mousemode right "mark center"
> ui mousemode right clip
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right "move picked models"
> view matrix models #1.4,1,0,0,-9.6083,0,1,0,-4.4321,0,0,1,17.572
> undo
> ui mousemode right distance
> ui mousemode right distance
> volume #!1.1-8 step 1
> volume #!1.1-8 step 2
> undo
> show #!1 models
> transparency #2.1-12#1.1.1#1.2.1#1.3.1#1.4.1#1.5.1#1.6.1#1.7.1#1.8.1 50
> transparency #2.1-12#1.1.1#1.2.1#1.3.1#1.4.1#1.5.1#1.6.1#1.7.1#1.8.1 0
> hide #!2 models
> show #!2 models
> hide #!1.8 models
> show #!1.8 models
> volume #!1.1-8 step 2
> volume #!1.1-8 step 1
> hide #!1 models
> show #!1 models
> select /C
825 atoms, 835 bonds, 107 residues, 1 model selected
> hide #!1.4 models
> ui tool show "Color Actions"
> color sel medium spring green
> color sel green
> hide #!1.8 models
> hide #!1 models
> select clear
> lighting simple
> graphics silhouettes false
> ui mousemode right translate
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/1.tif" width
> 2924 height 2000 supersample 4 transparentBackground true
> show #!1 models
> view
> view
> lighting flat
> lighting soft
> lighting soft ambientIntensity 1.8
> lighting soft ambientIntensity 2
> lighting soft intensity 0.2
> lighting soft intensity 0.4
> view
> show #!1.8 models
> hide #!1 models
> show #!1 models
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> show #!1.4 models
> hide #!1 models
> select /C
825 atoms, 835 bonds, 107 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium sea green
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> select clear
> hide #!1 models
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> lighting soft intensity 0.6
> lighting soft intensity 0.5
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> show #!1 models
> lighting soft
> lighting simple
> lighting soft
> lighting soft intensity 0.5
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-3-change color.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/20211006overall
> model-change colors-2.cxs" includeMaps true
> hide #!1 models
> preset cartoons/nucleotides cylinders/stubs
Changed 12158 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> lighting soft
> lighting soft intensity 0.3
> lighting soft intensity 0.2
> lighting soft intensity 0.1
> lighting shadows true
> lighting soft intensity 0.2
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel atoms
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> lighting flat
> lighting soft
> lighting simple
> lighting simple
> lighting soft
> lighting soft intensity 0.2
> lighting soft intensity 0.15
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-cylinders.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> select /G
815 atoms, 825 bonds, 106 residues, 1 model selected
> color sel lime green
> color sel medium aquamarine
> color sel medium sea green
> select clear
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-cylinders.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-cylinders-2.tif" width 2924 height 2000 supersample
> 4 transparentBackground true
> graphics silhouettes true width 1.5
> graphics silhouettes true width 1.3
> graphics silhouettes true width 2
> graphics silhouettes true width 1.5
> cartoon style cylinder width 5
Expected an atoms specifier or a keyword
> cartoon style helix modeHelix tube radius 5
> cartoon style helix modeHelix tube radius 3
> cartoon style helix modeHelix tube radius 2.5
> cartoon style helix modeHelix tube radius 15
> cartoon style helix modeHelix tube radius 2.2
> cartoon style helix modeHelix tube radius 2.5
> cartoon style loop modeh tube rad 2.5
Expected an atoms specifier or a keyword
> cartoon style sheet modeh tube rad 2.5
Expected an atoms specifier or a keyword
> cartoon style sheet modeh tube rad 2.5
Expected an atoms specifier or a keyword
> cartoon style sheet modeh tube rad 2.5
Expected an atoms specifier or a keyword
> cartoon style protein width 0.5 thickness 0.5
> cartoon style protein width 2 thickness 2
> cartoon style protein width 1 thickness 1
> cartoon style protein width 0.6 thickness 0.6
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel atoms
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> lighting soft
> cartoon style HELIX width 3 thick 1
Expected an atoms specifier or a keyword
> cartoon style helix width 3 thickness 1
> cartoon style helix width 3 thickness 0.7
> cartoon style helix width 2.5 thickness 0.7
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> cartoon style helix width 2.5 thickness 0.7
> cartoon style helix width 3 thickness 0.7
> cartoon style protein width 3 thickness 0.7
> cartoon style protein width 2 thickness 0.5
> cartoon style protein width 3 thickness 0.5
> cartoon style protein width 3 thickness 1
> lighting soft intensity 0.4
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel atoms
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> cartoon style protein width 1 thickness 0.5
> cartoon style protein width 2 thickness 0.5
> cartoon style protein width 3 thickness 0.5
> cartoon style protein width 2.5 thickness 0.7
> lighting soft intensity 0.5
> lighting soft intensity 0.1
> lighting soft intensity 0.3
> graphics silhouettes false
> graphics silhouettes true
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-rebion.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> lighting soft intensity 0.4
> lighting soft intensity 0.3
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-rebion-2.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel atoms
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> lighting soft intensity 0.3
> lighting soft intensity 0.2
> cartoon style protein width 0.5 thickness 0.5
> cartoon style protein width 1 thickness 0.5
> cartoon style protein width 1 thickness 0.7
> cartoon style protein width 2 thickness 0.7
> cartoon style protein width 1 thickness 0.7
> cartoon style protein width 5 thickness 0.7
> cartoon style protein width 1 thickness 0.7
> cartoon style protein width 2 thickness 0.7
> cartoon style protein width12 thick 0.7
Expected a keyword
> cartoon style protein width 1 thickness 0.7
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel atoms
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> cartoon style protein width 1 thickness 0.7
> cartoon style heliex width 2 thick 0.7
Expected an atoms specifier or a keyword
> cartoon style helix width 2 thickness 0.7
> cartoon style helix width 2.5 thickness 0.7
> cartoon style helix width 2.5 thickness 1
> cartoon style helix width 3 thickness 1
> cartoon style helix width 5 thickness 1
> cartoon style helix modeHelix tube radius 2.5
> cartoon style helix modeHelix tube radius 2
> cartoon style helix modeHelix tube radius 2.3
> cartoon style helix modeHelix tube radius 2.2
> graphics silhouettes true width 1.5
> graphics silhouettes true width 2
> graphics silhouettes true width 1.7
> lighting soft intensity 0.4
> lighting soft intensity 0.3
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-cylinders.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-cylinders-2.tif" width 2924 height 2000 supersample
> 4 transparentBackground true
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel atoms
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-change color overall map.cxs" includeMaps true
——— End of log from Wed Oct 6 21:40:30 2021 ———
opened ChimeraX session
Drag select of 1122 residues
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #2.1 models
> select clear
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #2.7 models
> show #2.7 models
> select clear
Drag select of 1.2 job059_postprocess.mrc 1 , 1.3 job059_postprocess.mrc 2 ,
1.4 job059_postprocess.mrc 3 , 1.5 job059_postprocess.mrc 4 , 1.6
job059_postprocess.mrc 5 , 1.7 job059_postprocess.mrc 6 , 1.8
job059_postprocess.mrc 7 , 1122 residues
Drag select of 1.2 job059_postprocess.mrc 1 , 1.3 job059_postprocess.mrc 2 ,
1.4 job059_postprocess.mrc 3 , 1.5 job059_postprocess.mrc 4 , 1.6
job059_postprocess.mrc 5 , 1.7 job059_postprocess.mrc 6 , 1.8
job059_postprocess.mrc 7 , 1122 residues
> select
12363 atoms, 13136 bonds, 1122 residues, 20 models selected
> coulombic sel
Coulombic values for 20210929_final_for chimeraX_.pdb_A SES surface #2.1:
minimum, -13.42, mean 1.84, maximum 12.71
Coulombic values for 20210929_final_for chimeraX_.pdb_B SES surface #2.2:
minimum, -8.84, mean 3.94, maximum 24.66
Coulombic values for 20210929_final_for chimeraX_.pdb_C SES surface #2.3:
minimum, -14.45, mean 2.28, maximum 16.17
Coulombic values for 20210929_final_for chimeraX_.pdb_D SES surface #2.4:
minimum, -12.45, mean 1.25, maximum 11.99
Coulombic values for 20210929_final_for chimeraX_.pdb_E SES surface #2.5:
minimum, -11.62, mean 1.63, maximum 12.32
Coulombic values for 20210929_final_for chimeraX_.pdb_F SES surface #2.6:
minimum, -8.12, mean 3.47, maximum 17.60
Coulombic values for 20210929_final_for chimeraX_.pdb_G SES surface #2.7:
minimum, -16.37, mean 2.12, maximum 15.08
Coulombic values for 20210929_final_for chimeraX_.pdb_H SES surface #2.8:
minimum, -12.68, mean 1.25, maximum 11.97
Coulombic values for 20210929_final_for chimeraX_.pdb_I SES surface #2.9:
minimum, -23.98, mean -14.26, maximum -3.09
Coulombic values for 20210929_final_for chimeraX_.pdb_J SES surface #2.10:
minimum, -25.82, mean -14.24, maximum -2.88
Coulombic values for 20210929_final_for chimeraX_.pdb_S SES surface #2.11:
minimum, -11.34, mean -0.79, maximum 9.56
Coulombic values for 20210929_final_for chimeraX_.pdb_U SES surface #2.12:
minimum, -12.75, mean -0.30, maximum 18.17
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!1 models
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> hide sel atoms
> hide sel surfaces
> select /U
593 atoms, 599 bonds, 74 residues, 1 model selected
> hide sel surfaces
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel surfaces
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel surfaces
> select clear
> lighting flat
> select /S:167
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /S:164
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /S:169
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel byhetero
> select /S:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select /C:65@CD1
1 atom, 1 residue, 1 model selected
> select clear
> cartoon style protein width 1 thickness 1
> cartoon style helix modeHelix tube radius 2
> cartoon style helix modeHelix tube radius 5
> cartoon style protein width 2 thickness 0.5
> cartoon style protein width 2 thickness 1
> cartoon style protein width 2 thickness 0.6
> graphics silhouettes true width 1.5
> graphics silhouettes true width 3
> graphics silhouettes true width 2
> graphics silhouettes true width 2.5
> graphics silhouettes true width 2.2
> lighting soft intensity 0.4
> lighting flat intensity 0.4
> lighting flat intensity 0.2
> lighting flat intensity 0.1
> ui tool show "Side View"
> view
> graphics silhouettes true width 1.5
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/electric acidic patch .tif" width 2924 height 2000 supersample 4
> transparentBackground true
> select
12363 atoms, 13136 bonds, 1122 residues, 20 models selected
> hide sel surfaces
> select clear
> lighting soft
> undo
> undo
> undo
> select clear
> undo
> undo
> undo
> undo
> undo
> undo
> view
> view
> select /S:169
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> lighting soft intensity 0.4
> lighting soft intensity 0.3
> select /D:47
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /D:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /C:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-W164 R167-H2B H2A.cxs" includeMaps true
——— End of log from Thu Oct 7 16:18:40 2021 ———
opened ChimeraX session
> select /S:164
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:167
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /D:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /D:47
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /I:-27
19 atoms, 20 bonds, 1 residue, 1 model selected
> select /S:169
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /S:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /B:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:93
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> hide sel atoms
> select /C:92
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /C:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> ui tool show "Side View"
> select /C:61
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /C:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /C:64
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> show sel atoms
> color sel byhetero
> select clear
> lighting soft intensity 0.4
> lighting soft direction 0,-1,-1
> lighting soft direction -1,-1,-1
> lighting soft direction -1,0,-1
> lighting soft direction -1,0,0
> lighting soft direction 1,0,0
> lighting soft direction 0,0,0
> lighting soft direction 0,0,0
> lighting soft direction 0,0,1
> lighting soft direction 1,0,1
> lighting soft direction 1,1,1
> lighting soft direction 1,1,1
> lighting soft direction 0,0,1
> lighting soft direction 0,2,3
> lighting soft direction -1,0,0
> lighting soft intensity 0.4
> lighting soft diection 1,0,0
Expected a keyword
> lighting soft direction 1,0,0
> lighting soft direction 0,1,0
> lighting soft direction 0,1,1
> lighting soft direction 0,1,1
> lighting soft direction 0,1,1
> lighting soft direction 0,1,1
> view
> view orient
> view orient
> lighting soft direction 0,1,0
> lighting soft intensity 1
> view
> cofr frontCenter
> ui tool show ViewDockX
No suitable models found for ViewDockX
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0，0,1
Unknown command: Lighting soft direction 0，0,1
> Lighting soft direction 0，0,1
Unknown command: Lighting soft direction 0，0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> view orient
> lighting soft
> help help:user
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting shadows ture
Unknown command: Lighting shadows ture
> Lighting soft shadows ture
Unknown command: Lighting soft shadows ture
> Lighting soft shadows true
Unknown command: Lighting soft shadows true
> Lighting soft shadows true
Unknown command: Lighting soft shadows true
> Lighting shadows true
Unknown command: Lighting shadows true
> Lighting shadows true
Unknown command: Lighting shadows true
> Lighting shadows true
Unknown command: Lighting shadows true
> Lighting shadows true
Unknown command: Lighting shadows true
> Lighting shadows true
Unknown command: Lighting shadows true
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> lighting soft intensity 0.4
> lighting soft shadows ture
Invalid "shadows" argument: Expected true or false (or 1 or 0)
> lighting soft shadows true
> lighting soft shadows false
> lighting soft shadows true
> lighting soft shadows true
> lighting soft shadows true
> lighting soft intensity 0.5
> lighting soft shadows true
> lighting soft intensity 0.4
> lighting soft shadows false
> lighting soft shadows 5
Invalid "shadows" argument: Expected true or false (or 1 or 0)
> lighting soft shadows true
> lighting soft intensity 0.4
> lighting soft shadows true
> graphics silhouettes true width 1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> lighting soft intensity 0.5
> lighting soft intensity 0.6
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-L168 R169-H2B H2A-2.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> graphics silhouettes true width 2
> graphics silhouettes true width 1
> view
> lighting soft direction 1,1,1
> lighting soft direction 1,1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-L168 R169-H2B H2A-3.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> lighting soft intensity 0.5
> lighting soft intensity 0.4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-L168 R169-H2B H2A-4.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> lighting soft direction 0,1,1
> lighting soft direction 0,1,-1
> lighting soft direction 0,1,-1
> lighting soft intensity 0.4
> lighting soft direction 0,-1,-1
> lighting soft intensity 0.4
> lighting soft ambientIntensity 1.8
> lighting soft ambientIntensity 1.5
> lighting soft intensity 0.4
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,1
> lighting soft intensity 0.4
> lighting soft intensity 0.6
> graphics silhouettes true width 1
> graphics silhouettes true width 2
> graphics silhouettes true width 1
> graphics silhouettes true width 0.5
> graphics silhouettes true width 0.8
> graphics silhouettes true width 01
> graphics silhouettes true width 1
> graphics silhouettes true width 0.5
> graphics silhouettes true width 1
> graphics silhouettes true width 1.2
> graphics silhouettes true width 1.5
> graphics silhouettes true width 1
> lighting soft ambientIntensity 1.8
> lighting soft ambientIntensity 1
> lighting soft ambientIntensity 1.5
> lighting soft ambientIntensity 110
> lighting soft ambientIntensity 10
> lighting soft ambientIntensity 4
> lighting soft ambientIntensity 2
> lighting soft ambientIntensity 1
> lighting soft ambientIntensity 2
> lighting soft ambientIntensity 1.5
> lighting soft
> lighting flat
> lighting soft
> lighting soft intensity 0.4
> lighting soft intensity 0.6
> lighting soft intensity 0.8
> lighting soft direction 1,0,0
> lighting soft direction 1,0,-1
> lighting soft direction -1,-1,-1
> view
> select clear
> view orient
> lighting soft intensity 0.4
> lighting soft diection 0,-1,-1
Expected a keyword
> lighting soft diection 0,-1,-1
Expected a keyword
> lighting soft diection -1,-1,-1
Expected a keyword
> lighting soft diection -1,-1,-1
Expected a keyword
> lighting soft diection -1,-1,-1
Expected a keyword
> lighting soft diection -1,-1,-1
Expected a keyword
> lighting soft direction 0,-1,-1
> lighting soft intensity 0.8
> lighting soft intensity 02
> lighting soft intensity 0.4
> lighting soft intensity 0.6
> view
> lighting soft direction 0,1,1
> lighting soft intensity 0.4
> lighting soft direction 0,-1,-1
> lighting soft intensity 0.4
> lighting soft direction 1,0,0
> lighting soft direction 1,1,1
> lighting soft direction 1,1,1
> lighting soft direction 1,1,1
> lighting soft intensity 0.4
> lighting soft direction 0,-1,1
> lighting soft intensity 0.4
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft intensity 0.5
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-L168 R169-H2B H2A-5.tif" width 2924 height 2000 supersample 4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-L168R169-H2B H2A.cxs" includeMaps true
> show #!1 models
> hide #!1 models
> select /S:169
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:61
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:64
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:92
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> view
> show #!1 models
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true width 1
> graphics silhouettes true width 0.5
> graphics silhouettes true width 2
> graphics silhouettes true width 1
> lighting flat
> lighting flat
> lighting soft intensity 0.2
> lighting flat intensity 0.2
> lighting flat intensity 0.4
> lighting flat intensity 0.1
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-falt overall view.cxs" includeMaps true
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-falt overall view.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> lighting soft
> hide #!1 models
> select /S:175
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /S:177
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /S:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> show sel atoms
> select /S:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /E:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select /C:81
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select /C:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select /C:89
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /C:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select /C:69
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 5 atom styles
> style sel stick
Changed 5 atom styles
> color sel byhetero
> select /C:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel byhetero
> select clear
> lighting flat intensity 0.4
> lighting flat intensity 0.2
> lighting flat intensity 0.1
> lighting soft intensity 0.1
> lighting soft intensity 0.4
> lighting soft intensity 0.5
> lighting soft intensity 0.6
> lighting soft intensity 0.4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/mid
> interact.tif" width 2924 height 2000 supersample 4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/mid
> interact-2.tif" width 2924 height 2000 supersample 4
> graphics silhouettes true width 1.5
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/mid
> interact-3.tif" width 2924 height 2000 supersample 4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/mid
> interact.cxs" includeMaps true
> select /S:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:177
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:175
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:89
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:81
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> view
> graphics silhouettes true width 1
> select /S:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> view sel
> show sel atoms
> undo
> select /S:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /S:182
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select /U:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /U:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /U:70
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /U:44
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /U:49
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> lighting soft intensity 0.4
> lighting soft intensity 0.2
> lighting soft direction 1,-1,-1
> select /U:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> lighting soft intensity 0.4
> lighting soft direction 0,-1,-1
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact.cxs" includeMaps true
——— End of log from Thu Oct 7 21:55:38 2021 ———
opened ChimeraX session
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-8.tif" width 2924 height 2000 supersample 4
> select /E:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-9.tif" width 2924 height 2000 supersample 4
> select /U:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-10.tif" width 2924 height 2000 supersample 4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-2-CHANGED.cxs" includeMaps true
——— End of log from Thu Oct 7 22:28:25 2021 ———
opened ChimeraX session
> select /E:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-11.tif" width 2924 height 2000 supersample 4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-3.cxs" includeMaps true
——— End of log from Fri Oct 8 11:31:20 2021 ———
opened ChimeraX session
> view
> hide #!2 models
> show #!1 models
> hide #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!1.6 models
> lighting soft ambientIntensity 1.3
> lighting soft ambientIntensity 1.5
No map chosen to save
No map chosen to save
> ui tool show "Side View"
> hide #!1.8 models
> show #!1.8 models
> select #2.8
707 atoms, 91 residues, 1 model selected
> ~select #2.8
1 model selected
> show #!2 models
> hide #2.2 models
> hide #2.1 models
> hide #2.3 models
> hide #2.4 models
> hide #2.9 models
> hide #2.10 models
> hide #2.8 models
> hide #2.11 models
> hide #2.12 models
> hide #2.7 models
> hide #2.6 models
> hide #2.5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #2.2 models
> show #2.1 models
> select #2.1
801 atoms, 97 residues, 1 model selected
> select #2.3
825 atoms, 107 residues, 1 model selected
> ~select #2.3
1 model selected
> select #2.3
825 atoms, 107 residues, 1 model selected
> show #2.3 models
> show #2.4 models
> show #2.5 models
> show #2.9 models
> show #2.8 models
> show #2.7 models
> show #2.6 models
> show #2.10 models
> show #2.11 models
> show #2.12 models
> select clear
> hide #!2 models
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-UB-SSX1 map.tif" width 1343 height 874 supersample 4
> transparentBackground true
> show #!2 models
> lighting soft ambientIntensity 1.8
> select #1.2
4 models selected
> transparency #1.2.1 50
> transparency #1.2.1 40
> select #1.7
3 models selected
> transparency #1.7.1 40
> select #1.8
3 models selected
> transparency #1.8.1 40
> select clear
> select /U:49
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /E:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select /E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> volume #1.2 level 0.01539
> volume #1.7 level 0.01366
> volume #1.7 level 0.01088
> volume #1.8 level 0.01237
> show #!1.6 models
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-Ub形成碱性沟槽.cxs" includeMaps true
> hide #!1.6 models
> lighting soft ambientIntensity 1.5
> lighting soft ambientIntensity 1.6
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-UB-SSX1 完整map.tif" width 1343 height 874 supersample 4
> transparentBackground true
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-UB-SSX1 完整map.tif" width 2000 height 1302 supersample
> 3
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-UB-SSX1 完整map.tif" width 3000 height 1952 supersample
> 3
> lighting flat
> lighting full
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> hide #!1.8 models
> show #!1.8 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> color byhetero
> show surfaces
> hide #2.4 models
> show #2.4 models
> hide #2.4 models
> hide #2.3 models
> hide #2.12 models
> show #2.12 models
> hide #2.11 models
> show #2.11 models
> hide #2.11 models
> show #2.11 models
> hide #!2.10 models
> show #!2.10 models
> hide #!2.10 models
> hide #!2.9 models
> hide #2.5 models
> show #2.5 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide #2.11 models
> show #2.11 models
> hide #2.12 models
> show #2.12 models
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> hide #2.7 models
> hide #2.6 models
> lighting soft
> lighting flat
> hide #2.5 models
> show #2.5 models
> hide #2.12 models
> show #2.12 models
> hide #2.11 models
> show #2.11 models
> hide #2.11 models
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-Ub形成碱性沟槽-电性图.cxs" includeMaps true
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting flat
> hide #!1.8 models
> show #!1.8 models
> hide #!1.8 models
> show #!1.8 models
> hide #!1.7 models
> hide #!1.2 models
> volume #1.8 style mesh
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> graphics silhouettes false
> lighting full
> lighting soft
> hide #!1.8 models
> lighting soft
> graphics silhouettes true
> lighting soft ambientIntensity 1.6
> lighting soft ambientIntensity 2
> graphics silhouettes false
> lighting soft ambientIntensity 1
> lighting soft ambientIntensity 1.5
> lighting simple
> lighting flat
> lighting full
> lighting soft
> lighting full
> lighting soft ambientIntensity 2
> lighting soft intensity 0.4
> lighting soft intensity 0.6
> lighting soft intensity 0.8
> lighting soft
> lighting soft intensity 1
> lighting soft intensity 0.6
> hide #!2.12 models
> show #!2.12 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.12 models
> show #!2.12 models
> hide #!2.5 models
> show #!2.5 models
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-Ub形成碱性沟槽-电性图.cxs" includeMaps true
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-UB碱性沟槽电性图.tif" width 3000 height 1952 supersample 4
> transparentBackground true
> lighting flat
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-UB碱性沟槽电性图-2-flat模式.tif" width 3000 height 1952
> supersample 4 transparentBackground true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide atoms
> show cartoons
> hide cartoons
> hide surfaces
> show cartoons
> show #!1.8 models
> hide #!1.8 models
> select /E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /E:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select /E:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /E:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select /S:182
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select /S:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select /U:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select /U:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /E:51
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /E:50
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select /E:51
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> undo
> undo
> undo
> select /E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select clear
Drag select of 10 atoms, 17 residues, 8 bonds
> show sel cartoons
> select clear
> select clear
> select /E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /E:51
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 19 atoms, 25 residues, 17 bonds
> show sel cartoons
> show sel cartoons
> select clear
> select /E:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> show #2.4 models
> hide #2.4 models
> hide #!2 models
> show #!2 models
> select /S:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /S:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /S:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /E:51
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /E
783 atoms, 794 bonds, 95 residues, 1 model selected
> show sel cartoons
> select clear
> lighting soft
> lighting soft intensity 1
> lighting shadows true
> lighting shadows false
> select clear
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/原子模型.tif" width 3000 height 1952 supersample 4
> show #!1.8 models
> volume #1.8 level 0.009933
> volume #1.8 level 0.01102
> hide #!2.5 models
> show #!2.5 models
> hide #!1.8 models
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/原子模型-2.tif" width 3000 height 1952 supersample 4
> transparentBackground true
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/原子模型.cxs" includeMaps true
> lighting soft intensity 0.8
> lighting soft intensity 0.6
> lighting soft intensity 0.5
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/原子模型-2.tif" width 3000 height 1952 supersample 4
> transparentBackground true
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/原子模型.tif" width 3000 height 1952 supersample 4
> transparentBackground true
> show #!1.8 models
> open E:/Documents/Map/SSX1/job054_run_ct17_class001.mrc
Opened job054_run_ct17_class001.mrc as #3, grid size 256,256,256, pixel 1.07,
shown at level 0.003, step 1, values float32
> volume #3 level 0.007632
> hide #!1.8 models
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/post结构+refine结构.cxs" includeMaps true
——— End of log from Wed Feb 16 09:51:13 2022 ———
opened ChimeraX session
> hide #!3 models
> view
> open "E:/Documents/Map/SSX1/SSX1 Model building/Wincoot PDB
> Save/20220216_TZB_reversed_D182P183E184.pdb"
Summary of feedback from opening E:/Documents/Map/SSX1/SSX1 Model
building/Wincoot PDB Save/20220216_TZB_reversed_D182P183E184.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
17 messages similar to the above omitted
End residue of secondary structure not found: HELIX 32 32 THR H 90 LEU H 102
01 1
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20220216_TZB_reversed_D182P183E184.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> select #5
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> hide #!2 models
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #5 models
> show #5 models
> show #2.1 models
> hide #2.1 models
> hide #2.5 models
> hide #!2 models
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> hide #5 models
> show #2.1 models
> show #2.2 models
> show #2.3 models
> show #2.4 models
> show #2.5 models
> show #2.6 models
> show #2.7 models
> show #2.8 models
> show #!2.10 models
> show #2.11 models
> show #!2.9 models
> hide #!2 models
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> hide #2.7 models
> hide #2.8 models
> hide #!2.9 models
> hide #!2.10 models
> hide #2.11 models
> hide #2.12 models
> show #5 models
> show #!2 models
> hide #!2 models
> select #5/I
2822 atoms, 3168 bonds, 137 residues, 1 model selected
> color sel dark gray
> select #5/J
2795 atoms, 3132 bonds, 137 residues, 1 model selected
> color sel dark gray
> show #!2 models
> hide #!2 models
> select #5/U
593 atoms, 599 bonds, 74 residues, 1 model selected
> ui tool show "Color Actions"
> color sel yellow
> select #5/S
205 atoms, 210 bonds, 23 residues, 1 model selected
> color sel magenta
> select #5/A
801 atoms, 813 bonds, 97 residues, 1 model selected
> color sel dodger blue
> select #5/E
783 atoms, 794 bonds, 95 residues, 1 model selected
> color sel dodger blue
> select #5/D
707 atoms, 718 bonds, 91 residues, 1 model selected
> color sel light salmon
> color sel salmon
> lighting flat
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color sel wheat
> hide #!2 models
> color sel burly wood
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #5/B
668 atoms, 675 bonds, 83 residues, 1 model selected
> show #!2 models
> hide #!2 models
> color sel light coral
> select #5/C
825 atoms, 835 bonds, 107 residues, 1 model selected
> color sel medium aquamarine
> color sel medium sea green
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #5/D
707 atoms, 718 bonds, 91 residues, 1 model selected
> select #5/F
648 atoms, 655 bonds, 81 residues, 1 model selected
> show #!2 models
> hide #!2 models
> color sel salmon
> select #5/G
815 atoms, 825 bonds, 106 residues, 1 model selected
> show #!2 models
> hide #!2 models
> color sel medium sea green
> color sel forest green
> color sel lime green
> color sel lime
> color sel yellow green
> color sel sea green
> color sel medium aquamarine
> color sel medium sea green
> select #5/H
707 atoms, 718 bonds, 91 residues, 1 model selected
> show #!2 models
> hide #!2 models
> color sel wheat
> color sel burly wood
> select clear
> hide #5 models
> show #5 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 #!2 models
> show #!1.8 models
> hide #!1.8 models
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/20220216-修改了D182-E184的密度/最终map+原子模型.cxs" includeMaps true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> view
> view
> show #!1.8 models
> hide #!1.8 models
> select #5/S:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #5/S:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel byhetero
> select #5/I:4
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> color sel byhetero
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select #5/S:181@CA
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> hide sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> hide sel atoms
> hide sel cartoons
> hide sel cartoons
> hide sel cartoons
> hide sel cartoons
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select clear
> select #5/S:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> select clear
> select #5/S:182
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #5/E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #5/E:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> select #5/U:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #5/U:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> show #!1.8 models
> show #!1.7 models
> show #!1.2 models
> volume #1.7 style mesh
> volume #1.2
> volume #1.2 style mesh
> volume #1.2 style surface
> volume #1.7 style surface
> select clear
> hide #!1.2 models
> hide #!1.7 models
> show #!1.7 models
> hide #!1.7 models
> hide #!1.8 models
> ui tool show "Side View"
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/20220216-修改了D182-E184的密度/原子模型.cxs" includeMaps true
——— End of log from Wed Feb 16 12:33:54 2022 ———
opened ChimeraX session
> cartoon style protein thickness 0.6
> select #5/U
593 atoms, 599 bonds, 74 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/20220216-修改了D182-E184的密度/最终map+原子模型.cxs" includeMaps true
> select clear
> cartoon style protein thickness 0.5
> select #5/U:72@NH1
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> color sel byhetero
> select #5/U:42@CB
1 atom, 1 residue, 1 model selected
> color sel byhetero
> style sel stick
Changed 1 atom style
> show sel atoms
> select clear
> select #5/U:42@CB
1 atom, 1 residue, 1 model selected
> color sel byhetero
> color sel byhetero
> style sel stick
Changed 1 atom style
> style sel stick
Changed 1 atom style
> style sel stick
Changed 1 atom style
> select #5/U:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #5/U:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/20220216-修改了D182-E184的密度/最终map+原子模型.cxs" includeMaps true
——— End of log from Wed Feb 16 19:42:15 2022 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!1.2 models
> show #!1.1 models
> hide #!1.1 models
> hide #!1.2 models
> select #5/S
205 atoms, 210 bonds, 23 residues, 1 model selected
> hide sel atoms
> select #5/E
783 atoms, 794 bonds, 95 residues, 1 model selected
> hide sel atoms
> select #5/U
593 atoms, 599 bonds, 74 residues, 1 model selected
> hide sel atoms
> select clear
> view orient
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> hide #!1.3 models
> select #1.2
4 models selected
> transparency #1.2.1 0
> select clear
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> show #!1.6 models
> show #!1.7 models
> show #!1.8 models
> select #1.8
2 models selected
> transparency #1.8.1 0
> volume #1.8 style surface
> select clear
> select #1.7
4 models selected
> transparency #1.7.1 0
> select clear
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/20220216-修改了D182-E184的密度/20220405最终map+原子模型.cxs" includeMaps true
——— End of log from Tue Apr 5 10:24:07 2022 ———
opened ChimeraX session
> hide #5 models
> show #5 models
> hide #!1 models
> show #!1 models
> open "E:/Documents/Map/SSX1/SSX1 Model building/Cryo-Map/20220415-SSX1-119UB
> NCP -Recaculate/unwrapp state/job288_run_ct22_class001_3.31A.mrc"
Opened job288_run_ct22_class001_3.31A.mrc as #6, grid size 256,256,256, pixel
1.07, shown at level 0.00634, step 1, values float32
> volume #6 level 0.01106
> hide #!1 models
> volume #6 level 0.009406
> volume #6 level 0.01259
> volume #6 level 0.01058
> hide #!6 models
> select #5/E:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> show #!6 models
> hide #!6 models
> select #5/S:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> show #!6 models
> hide #!6 models
> select #5/S:180
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select clear
> show #!6 models
> hide #!6 models
> select #5/U:68
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> color sel byhetero
> show #!6 models
> hide #!6 models
> select #5/S:177
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> color sel byhetero
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> volume #6 level 0.009406
> hide #!6 models
> select #5/U:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> volume #6 level 0.01365
> volume #6 level 0.01294
> show #!1 models
> ui tool show "Fit in Map"
Fit map job288_run_ct22_class001_3.31A.mrc in map job059_postprocess.mrc 0
using 86068 points
correlation = 0.01914, correlation about mean = -0.02671, overlap = 0.0119
steps = 124, shift = 2.65, angle = 4.88 degrees
Position of job288_run_ct22_class001_3.31A.mrc (#6) relative to
job059_postprocess.mrc 0 (#1.1) coordinates:
Matrix rotation and translation
0.99947566 -0.02146222 -0.02424401 5.69892133
0.02330233 0.99665285 0.07835881 -13.98758504
0.02248110 -0.07888267 0.99663039 5.65732477
Axis -0.92475817 -0.27479661 0.26326632
Axis point 0.00000000 63.77579064 181.01014715
Rotation angle (degrees) 4.87703820
Shift along axis 0.06300004
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
Fit map job288_run_ct22_class001_3.31A.mrc in map job059_postprocess.mrc 1
using 86068 points
correlation = 0.277, correlation about mean = 0.1524, overlap = 6.191
steps = 84, shift = 1.24, angle = 1.85 degrees
Position of job288_run_ct22_class001_3.31A.mrc (#6) relative to
job059_postprocess.mrc 1 (#1.2) coordinates:
Matrix rotation and translation
0.99972172 0.02265150 -0.00658691 -1.42015474
-0.02279085 0.99950008 -0.02191264 7.00970079
0.00608727 0.02205666 0.99973819 -4.37901002
Axis 0.68180184 -0.19652979 -0.70464338
Axis point 311.99776711 88.79533165 0.00000000
Rotation angle (degrees) 1.84781869
Shift along axis 0.73976131
> hide #!1 models
> volume #6 level 0.01094
> volume #6 level 0.009406
> hide #!6 models
> select #5/E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select #5/E:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> show #!6 models
> hide #!6 models
> select #5/E:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> show #!6 models
> hide #!6 models
> select #5/E:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> show #!6 models
> volume #6 level 0.007285
> hide #!6 models
> select #5/S:182
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select clear
> show #!6 models
> volume #6 level 0.01271
> hide #!6 models
> select #5/S:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> color sel byhetero
> show sel atoms
> style sel stick
Changed 9 atom styles
> show #!6 models
> hide #!6 models
> select #5/U:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #!6 models
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #6
2 models selected
> select clear
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!1 models
> hide #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> ui tool show "Color Zone"
> hide #!6 models
> show #!6 models
> color zone #6 near #5 distance 6.44
> color zone #6 near #5 distance 3.52
> hide #!1.8 models
> show #!1.8 models
> hide #!1 models
> color zone #6 near #5 distance 3.04
> color zone #6 near #5 distance 3.02
> color zone #6 near #5 distance 3
> color zone #6 near #5 distance 3.8
> volume splitbyzone #6
Opened job288_run_ct22_class001_3.31A.mrc 0 as #7.1, grid size 256,256,256,
pixel 1.07, shown at level 0.0127, step 1, values float32
Opened job288_run_ct22_class001_3.31A.mrc 1 as #7.2, grid size 256,256,256,
pixel 1.07, shown at level 0.0127, step 1, values float32
Opened job288_run_ct22_class001_3.31A.mrc 2 as #7.3, grid size 256,256,256,
pixel 1.07, shown at level 0.0127, step 1, values float32
Opened job288_run_ct22_class001_3.31A.mrc 3 as #7.4, grid size 256,256,256,
pixel 1.07, shown at level 0.0127, step 1, values float32
Opened job288_run_ct22_class001_3.31A.mrc 4 as #7.5, grid size 256,256,256,
pixel 1.07, shown at level 0.0127, step 1, values float32
Opened job288_run_ct22_class001_3.31A.mrc 5 as #7.6, grid size 256,256,256,
pixel 1.07, shown at level 0.0127, step 1, values float32
Opened job288_run_ct22_class001_3.31A.mrc 6 as #7.7, grid size 256,256,256,
pixel 1.07, shown at level 0.0127, step 1, values float32
Opened job288_run_ct22_class001_3.31A.mrc 7 as #7.8, grid size 256,256,256,
pixel 1.07, shown at level 0.0127, step 1, values float32
Opened job288_run_ct22_class001_3.31A.mrc 8 as #7.9, grid size 256,256,256,
pixel 1.07, shown at level 0.0127, step 1, values float32
Opened job288_run_ct22_class001_3.31A.mrc 9 as #7.10, grid size 256,256,256,
pixel 1.07, shown at level 0.0127, step 1, values float32
Opened job288_run_ct22_class001_3.31A.mrc 10 as #7.11, grid size 256,256,256,
pixel 1.07, shown at level 0.0127, step 1, values float32
Opened job288_run_ct22_class001_3.31A.mrc 11 as #7.12, grid size 256,256,256,
pixel 1.07, shown at level 0.0127, step 1, values float32
> volume #1.8 level 0.01102
> volume #7.12 level 0.006871
> volume #7.11 level 0.008135
> volume #7.6 level 0.01179
> volume #7.2 level 0.00608
> help help:user/tools/colorzone.html
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!6 models
> color single #6
> close #7.12
> volume #7.9 level 0.01254
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!6 models
> show #!7 models
> hide #!7 models
> volume #6 level 0.01011
> hide #5 models
> show #5 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!1.6 models
> hide #!1.7 models
> hide #!1.8 models
> hide #!6 models
> show #!6 models
> select #6
2 models selected
> volume #6 style mesh
> select clear
> volume #6 style surface
> select #6
2 models selected
> ~select #6
Nothing selected
> select #6
2 models selected
> ~select #6
Nothing selected
> select #6
2 models selected
> transparency #6.1 30
> select clear
> select #5/S:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select clear
> volume #6 level 0.008652
> volume #6 level 0.007093
> ui tool show "Side View"
> ui tool show "Side View"
> view orient
> volume #6 level 0.01042
> select #5/S:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select clear
> select #5/U:9
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select clear
> select #5/U:10
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 4 atom styles
> select clear
> select #5/C:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> color sel byhetero
> select clear
> select #5/U:10
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/U:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #5/C:110
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #6
2 models selected
> volume #6 level 0.008236
> volume #6 level 0.01011
> select #5/U:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> select #5/C:118
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #5/C:119
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel byhetero
> select clear
> select #5/U:74
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> select clear
> select clear
> save "E:/Documents/Map/SSX1/SSX1 Model building/Cryo-Map/20220415-SSX1-119UB
> NCP -Recaculate/unwrapp state/20220621-Fit
> map/job288_run_ct22_class001.cmap" models #6
> select clear
> select add #5/E:52@NH2
1 atom, 1 residue, 1 model selected
> select add #5/S:182@OD1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #5/E:52@NH2 #5/S:182@OD1
Distance between 20220216_TZB_reversed_D182P183E184.pdb #5/E ARG 52 NH2 and /S
ASP 182 OD1: 3.725Å
> select clear
> volume #6 level 0.00886
> volume #6 level 0.01167
> volume #6 level 0.01073
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> show #!1.6 models
> show #!1.8 models
> show #!1.7 models
> hide #!1 models
> select clear
> volume #6 level 0.008964
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> select #5/U:69
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> color sel byhetero
> select clear
> select #5/U:70
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select clear
> select add #5/U:70@CG1
1 atom, 1 residue, 1 model selected
> select add #5/S:182@OD2
2 atoms, 2 residues, 1 model selected
> distance #5/U:70@CG1 #5/S:182@OD2
Distance between 20220216_TZB_reversed_D182P183E184.pdb #5/U VAL 70 CG1 and /S
ASP 182 OD2: 3.659Å
> select clear
> select clear
> show #!3 models
> volume #6 level 0.008236
> hide #!1.6 models
> show #!1.6 models
> hide #!6 models
> hide #!1 models
> hide #5 models
> hide #!8 models
> show #!8 models
> show #!4 models
> hide #!3 models
> hide #!1.7 models
> hide #!1.8 models
> show #!1.7 models
> show #!1.8 models
> hide #!1.4 models
> show #!1.4 models
> hide #!4 models
> hide #!1 models
> show #!7 models
> hide #!1.4 models
> show #!1.4 models
> show #!6 models
> hide #!1 models
> hide #!7 models
> show #5 models
> view orient
> open "E:/Documents/Map/SSX1/SSX1 Model building/Cryo-Map/20220415-SSX1-119UB
> NCP -Recaculate/unwrapp
> state/job328_postprocessing_Bfactor-20/postprocess.mrc"
Opened postprocess.mrc as #9, grid size 256,256,256, pixel 1.07, shown at
level 0.00654, step 1, values float32
> volume #9 level 0.01044
> ui tool show "Fit in Map"
Fit map postprocess.mrc in map job288_run_ct22_class001_3.31A.mrc using 108356
points
correlation = 0.9951, correlation about mean = 0.9642, overlap = 48.72
steps = 56, shift = 1.23, angle = 1.88 degrees
Position of postprocess.mrc (#9) relative to
job288_run_ct22_class001_3.31A.mrc (#6) coordinates:
Matrix rotation and translation
0.99999972 0.00045657 -0.00059307 0.02471766
-0.00045667 0.99999988 -0.00016592 0.08173736
0.00059300 0.00016619 0.99999981 -0.10248216
Axis 0.21658994 -0.77353067 -0.59559978
Axis point 169.65360694 0.00000000 40.44094026
Rotation angle (degrees) 0.04392652
Shift along axis 0.00316559
> hide #!6 models
> show #!6 models
> hide #!6 models
> ui tool show "Hide Dust"
> surface dust #9 size 6.44
> surface dust #9 size 6.44
> hide #!9 models
> show #!9 models
> hide #5 models
> show #5 models
> hide #!9 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #5 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> close #7
> show #!6 models
> hide #!8 models
> show #!8 models
> hide #!3 models
> show #!9 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> volume #6 level 0.009899
> hide #!6 models
> show #!6 models
> hide #!9 models
> show #!9 models
> open "E:/Documents/Map/SSX1/SSX1 Model building/Cryo-Map/20220415-SSX1-119UB
> NCP -Recaculate/unwrapp
> state/job328_postprocessing_Bfactor-20/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #7, grid size 256,256,256, pixel 1.07, shown
at level 0.00592, step 1, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1091+0+23 (frame:
1936x1130-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1057+0+23 (frame: 1936x1096-8-8) margins: 8, 31, 8, 8
minimum size: 477x1091 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=493,1130
maxtrack=0,0)
> volume #7 level 0.009211
Fit map postprocess_masked.mrc in map job288_run_ct22_class001_3.31A.mrc using
120963 points
correlation = 0.9947, correlation about mean = 0.967, overlap = 49.89
steps = 56, shift = 1.23, angle = 1.89 degrees
Position of postprocess_masked.mrc (#7) relative to
job288_run_ct22_class001_3.31A.mrc (#6) coordinates:
Matrix rotation and translation
0.99999933 0.00051552 -0.00103504 0.08454590
-0.00051572 0.99999985 -0.00018578 0.09724651
0.00103495 0.00018631 0.99999945 -0.16378479
Axis 0.15885275 -0.88371072 -0.44025125
Axis point 158.46844304 0.00000000 81.64264941
Rotation angle (degrees) 0.06710438
Shift along axis -0.00040098
> hide #!9 models
> hide #!8 models
> surface dust #7 size 6.44
> volume #7 level 0.01165
> volume #7 level 0.01055
> hide #!6 models
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/20220621-4月份新算的结构/20220621-4月份新算的结构和2月份的model放在一起 .cxs" includeMaps
> true
> open "E:/Documents/Map/SSX1/SSX1 Model building/Cryo-Map/20220415-SSX1-119UB
> NCP -Recaculate/unwrapp
> state/job329_postprocessing_Bfactor-30/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #10, grid size 256,256,256, pixel 1.07, shown
at level 0.00593, step 1, values float32
Fit map postprocess_masked.mrc in map job288_run_ct22_class001_3.31A.mrc using
167670 points
correlation = 0.9876, correlation about mean = 0.9491, overlap = 53.74
steps = 56, shift = 1.22, angle = 1.88 degrees
Position of postprocess_masked.mrc (#10) relative to
job288_run_ct22_class001_3.31A.mrc (#6) coordinates:
Matrix rotation and translation
0.99999932 0.00049224 -0.00105418 0.09689371
-0.00049233 0.99999987 -0.00009410 0.08197722
0.00105414 0.00009462 0.99999944 -0.15592128
Axis 0.08083747 -0.90310456 -0.42174336
Axis point 148.13964416 0.00000000 91.85240688
Rotation angle (degrees) 0.06687920
Shift along axis -0.00044259
> volume #10 level 0.00973
> surface dust #10 size 6.44
> hide #!7 models
> volume #10 level 0.01176
> volume #10 level 0.01312
> volume #10 level 0.01244
> select #10
2 models selected
> transparency #10.1 30
> select clear
> show #5 models
> select #5/S:167
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #5/S:164
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel byhetero
> select clear
> select #5/S:169
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> select #5/S:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> select #5/D:109
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> color sel byhetero
> select clear
> select #5/S:170
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> select #5/S:171
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 11 atom styles
> color sel byhetero
> style sel stick
Changed 11 atom styles
> select clear
> select #5/A:125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/S:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/S:177
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> select #5/S:162
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> color sel byhetero
> select clear
> select #5/C:89
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/S:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> select #5/C:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> select #5/C:75
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> open "E:/Documents/Map/SSX1/SSX1 Model building/Cryo-Map/20220415-SSX1-119UB
> NCP -Recaculate/unwrapp
> state/job330_post_Bfacror_-40/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #11, grid size 256,256,256, pixel 1.07, shown
at level 0.00606, step 1, values float32
> surface dust #11 size 6.44
Fit map postprocess_masked.mrc in map job288_run_ct22_class001_3.31A.mrc using
167696 points
correlation = 0.9769, correlation about mean = 0.9076, overlap = 55.2
steps = 56, shift = 1.22, angle = 1.88 degrees
Position of postprocess_masked.mrc (#11) relative to
job288_run_ct22_class001_3.31A.mrc (#6) coordinates:
Matrix rotation and translation
0.99999968 0.00046387 -0.00065543 0.04213366
-0.00046394 0.99999989 -0.00010642 0.07734539
0.00065538 0.00010672 0.99999978 -0.10179045
Axis 0.13156331 -0.80912862 -0.57271457
Axis point 154.23838645 0.00000000 63.95606154
Rotation angle (degrees) 0.04641009
Shift along axis 0.00125774
> volume #11 level 0.01273
> hide #!10 models
> select #11
2 models selected
> transparency #11.1 30
> select clear
> volume #11 level 0.01444
> volume #11 level 0.0163
> volume #11 level 0.01707
> volume #11 level 0.01568
> volume #11 level 0.01289
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!10 models
> show #!11 models
> hide #!10 models
> select #11
2 models selected
> transparency #11.1 0
> select clear
> hide #!11 models
> show #!10 models
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/20220621-4月份新算的结构/20220621-4月份新算的结构和2月份的model放在一起 .cxs" includeMaps
> true
——— End of log from Tue Jun 21 18:14:32 2022 ———
opened ChimeraX session
> hide #!10 models
> show #!10 models
> show #!11 models
> hide #!11 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> close #10
> close #11
> close #9
> close #8
> hide #!7 models
> close #7
> show #!6 models
> hide #!6 models
> show #!6 models
> close #6
> hide #5 models
> show #5 models
> show #!4 models
> close #4
> show #!3 models
> close #3
> show #!2 models
> hide #!2 models
> show #!2 models
> close #2
> show #!1 models
> open "F:/Documents/Map/SSX1/SSX1 Model building/Wincoot PDB
> Save/202206/202200807_SSX1_119Ub_Second_phenix_real_space_refined-
> coot-0.pdb"
Summary of feedback from opening F:/Documents/Map/SSX1/SSX1 Model
building/Wincoot PDB
Save/202206/202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.010 0.091 13142
Ignored bad PDB record found on line 22
ANGLE : 0.877 18.214 18918
Ignored bad PDB record found on line 23
CHIRALITY : 0.051 0.207 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.005 0.046 1444
16 messages similar to the above omitted
Chain information for 202200807_SSX1_119Ub_Second_phenix_real_space_refined-
coot-0.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> select #5
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> hide #2 models
> show #2 models
> hide #2 models
> hide #5 models
> hide #!1 models
> show #2 models
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> show #5 models
> select #5
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> ~select #2
Nothing selected
> select #5
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> show sel cartoons
> select clear
> ui tool show Matchmaker
> matchmaker #2 to #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 20220216_TZB_reversed_D182P183E184.pdb, chain G (#5) with
202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb, chain G
(#2), sequence alignment score = 524.6
RMSD between 106 pruned atom pairs is 0.229 angstroms; (across all 106 pairs:
0.229)
> open "F:/Documents/Map/SSX1/SSX1 Model building/Cryo-Map/20220415-SSX1-119UB
> NCP -Recaculate/unwrapp state/job329_postprocessing_Bfactor-30/fit
> map/20220622_postprocess_Bfactor-30_fit in map.mrc"
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc as #3, grid size
256,256,256, pixel 1.07, shown at level 0.00593, step 1, values float32
> volume #3 level 0.01516
> 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 #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #!3 models
> select #2/S
205 atoms, 210 bonds, 23 residues, 1 model selected
> color sel magenta
> hide #2 models
> show #2 models
> hide #5 models
> hide #2 models
> show #2 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> select #2/U
593 atoms, 599 bonds, 74 residues, 1 model selected
> color sel yellow
> select clear
> select #2/I
2822 atoms, 3168 bonds, 137 residues, 1 model selected
> color sel dark gray
> select #2/J
2795 atoms, 3132 bonds, 137 residues, 1 model selected
> color sel light gray
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #5 models
> open "F:/Documents/Map/SSX1/SSX1 Model building/Cryo-Map/20220415-SSX1-119UB
> NCP -Recaculate/unwrapp
> state/job_postprocessing_Bfactor_-1/postprocess_masked.mrc"
Opened postprocess_masked.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.00606, step 1, values float32
> volume #4 level 0.01082
> hide #!4 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> select #2/C
825 atoms, 835 bonds, 107 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sea green
> color sel medium aquamarine
> color sel turquoise
> color sel forest green
> color sel lime green
> color sel medium sea green
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #2 models
> show #5 models
> show #2 models
> hide #5 models
> show #5 models
> hide #5 models
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> ~select #2
Nothing selected
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> select #2/G
815 atoms, 825 bonds, 106 residues, 1 model selected
> color sel medium sea green
> color sel sea green
> color sel medium sea green
> select clear
> show #5 models
> hide #5 models
> select #2/A
801 atoms, 813 bonds, 97 residues, 1 model selected
> color sel dodger blue
> select #2/E
783 atoms, 794 bonds, 95 residues, 1 model selected
> color sel dodger blue
> select clear
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> select #2/H
707 atoms, 718 bonds, 91 residues, 1 model selected
> color sel goldenrod
> color sel goldenrod
> color sel peach puff
> color sel peach puff
> color sel moccasin
> color sel wheat
> color sel lavender blush
> color sel papaya whip
> color sel beige
> color sel antique white
> color sel burly wood
> select clear
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> select #2/F
648 atoms, 655 bonds, 81 residues, 1 model selected
> color sel salmon
> show #5 models
> hide #5 models
> show #5 models
> select clear
> select #2/B
668 atoms, 675 bonds, 83 residues, 1 model selected
> color sel salmon
> color sel salmon
> color sel salmon
> select clear
> select #2/D
707 atoms, 718 bonds, 91 residues, 1 model selected
> color sel burly wood
> color sel burly wood
> color sel burly wood
> select clear
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> select #2/I
2822 atoms, 3168 bonds, 137 residues, 1 model selected
> color sel dim gray
> select #2/J
2795 atoms, 3132 bonds, 137 residues, 1 model selected
> color sel dark gray
> select clear
> select #2/I
2822 atoms, 3168 bonds, 137 residues, 1 model selected
> color sel gray
> select clear
> show #!4 models
> hide #!4 models
> show #5 models
> hide #5 models
> show #5 models
> show #!4 models
> hide #5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!1 models
> close #1
> volume #3 level 0.02
> volume #4 level 0.02
> show #!4 models
> volume #3 level 0.015
> volume #4 level 0.015
> hide #!4 models
> ui tool show "Fit in Map"
Fit molecule 202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb
(#2) to map 20220622_postprocess_Bfactor-30_fit in map.mrc (#3) using 12369
atoms
average map value = 0.02447, steps = 56
shifted from previous position = 1.17
rotated from previous position = 1.79 degrees
atoms outside contour = 2473, contour level = 0.015
Position of 202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb
(#2) relative to 20220622_postprocess_Bfactor-30_fit in map.mrc (#3)
coordinates:
Matrix rotation and translation
0.99999997 0.00018689 -0.00018395 0.01075359
-0.00018688 0.99999998 0.00004905 0.02174365
0.00018396 -0.00004901 0.99999998 -0.02040786
Axis -0.18379376 -0.68954989 -0.70052894
Axis point 106.49166631 -54.89111858 0.00000000
Rotation angle (degrees) 0.01528517
Shift along axis -0.00267348
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 71132 points
correlation = 0.9951, correlation about mean = 0.9526, overlap = 45.16
steps = 44, shift = 0.00526, angle = 0.0135 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999997 -0.00001848 0.00023330 -0.03438387
0.00001849 1.00000000 -0.00002860 0.00127585
-0.00023330 0.00002861 0.99999997 0.02959032
Axis 0.12132444 0.98951236 0.07839427
Axis point 127.01411129 0.00000000 147.08820938
Rotation angle (degrees) 0.01350883
Shift along axis -0.00058943
> show #!4 models
Fit molecule 202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb
(#2) to map 20220622_postprocess_Bfactor-30_fit in map.mrc (#3) using 12369
atoms
average map value = 0.02447, steps = 36
shifted from previous position = 0.0203
rotated from previous position = 0.0188 degrees
atoms outside contour = 2480, contour level = 0.015
Position of 202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb
(#2) relative to 20220622_postprocess_Bfactor-30_fit in map.mrc (#3)
coordinates:
Matrix rotation and translation
1.00000000 0.00001039 0.00006277 -0.01852727
-0.00001038 1.00000000 -0.00007427 0.01154319
-0.00006277 0.00007426 1.00000000 0.00270980
Axis 0.75942919 0.64186737 -0.10617714
Axis point 0.00000000 -26.54011591 215.48945935
Rotation angle (degrees) 0.00560298
Shift along axis -0.00694867
Fit molecule 20220216_TZB_reversed_D182P183E184.pdb (#5) to map
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) using 12369 atoms
average map value = 0.02412, steps = 56
shifted from previous position = 1.2
rotated from previous position = 1.9 degrees
atoms outside contour = 2727, contour level = 0.015
Position of 20220216_TZB_reversed_D182P183E184.pdb (#5) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99971433 -0.02292566 0.00675856 1.51008699
0.02276451 0.99947564 0.02302665 -7.01292531
-0.00728292 -0.02286622 0.99971201 4.75784460
Axis -0.69257673 0.21190233 0.68951785
Axis point -0.00000000 181.52145361 315.58052910
Rotation angle (degrees) 1.89866962
Shift along axis 0.74871242
> hide #2 models
> show #2 models
> hide #!3 models
> hide #!4 models
> show #5 models
> hide #2 models
> show #!3 models
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 71132 points
correlation = 0.9951, correlation about mean = 0.9526, overlap = 45.17
steps = 28, shift = 0.00703, angle = 0.0148 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
1.00000000 0.00000213 -0.00002332 0.00245212
-0.00000213 1.00000000 -0.00001392 0.00535575
0.00002332 0.00001392 1.00000000 0.00089058
Axis 0.51102853 -0.85598518 -0.07835314
Axis point -26.76291849 0.00000000 179.70763401
Rotation angle (degrees) 0.00156072
Shift along axis -0.00340112
> hide #5 models
> hide #!3 models
> show #2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> volume #3 level 0.01
> volume #4 level 0.01
> show #5 models
> hide #!4 models
> hide #5 models
> show #!3 models
> ui tool show "Hide Dust"
> surface dust #3 size 6.44
> surface dust #4 size 6.44
> show #!4 models
> hide #!3 models
> surface dust #3 size 6.44
> surface dust #4 size 6.44
> show #!3 models
> hide #2 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
> show #5 models
> hide #5 models
> show #2 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #2 models
> show #2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> ui tool show "Color Zone"
> color zone #3 near #2 distance 5.14
> hide #!3 models
> hide #!4 models
> show #!3 models
> color zone #3 near #2 distance 7.43
> color zone #3 near #2 distance 14.48
> color zone #3 near #2 distance 10
> color zone #3 near #2 distance 10
> preset cylinders
Changed 24378 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cylinders
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> color zone #3 near #2 distance 8
> color zone #3 near #2 distance 8
> preset cylinders
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> hide #!3 models
> hide #2 models
> show #2 models
> show #!3 models
> hide #2 models
> hide #!3 models
> show #2 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #2 models
> hide #!4 models
> show #2 models
> show #5 models
> show #!3 models
> show #!4 models
> volume #3 level 0.015
> hide #!4 models
> volume #4 level 0.015
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> surface undust #4
> show #!4 models
> hide #5 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> surface undust #3
> surface undust #3
> surface undust #3
> surface undust #3
> surface undust #3
> surface undust #3
> surface dust #3 size 1.07
> surface dust #3 size 2.04
> surface dust #3 size 2.14
> show #!4 models
> hide #!3 models
> volume #3 level 0.013
> volume #4 level 0.013
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 85465 points
correlation = 0.9948, correlation about mean = 0.9596, overlap = 47.97
steps = 48, shift = 0.015, angle = 0.0136 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999998 -0.00000689 0.00020635 -0.01441475
0.00000688 1.00000000 0.00004800 -0.00444102
-0.00020635 -0.00004799 0.99999998 0.03406001
Axis -0.22642413 0.97348761 0.03246507
Axis point 165.04526752 0.00000000 69.82246599
Rotation angle (degrees) 0.01214491
Shift along axis 0.00004633
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 85465 points
correlation = 0.9948, correlation about mean = 0.9593, overlap = 47.99
steps = 40, shift = 0.00911, angle = 0.0199 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 0.00002271 -0.00014015 0.02191388
-0.00002270 1.00000000 0.00004116 0.00131716
0.00014015 -0.00004116 0.99999999 -0.00858807
Axis -0.27842926 -0.94809705 -0.15358757
Axis point 67.89808522 0.00000000 144.37401703
Rotation angle (degrees) 0.00846959
Shift along axis -0.00603124
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 85465 points
correlation = 0.9947, correlation about mean = 0.959, overlap = 48
steps = 40, shift = 0.015, angle = 0.0167 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00003116 0.00014712 -0.02283555
0.00003116 1.00000000 0.00004180 -0.01181443
-0.00014712 -0.00004179 0.99999999 0.02510119
Axis -0.26777715 0.94257229 0.19963186
Axis point 170.61577723 0.00000000 155.24763452
Rotation angle (degrees) 0.00894303
Shift along axis -0.00001012
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 85465 points
correlation = 0.9948, correlation about mean = 0.9593, overlap = 47.99
steps = 44, shift = 0.00628, angle = 0.017 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00002249 -0.00014865 0.01654418
0.00002250 1.00000000 0.00005508 -0.01165408
0.00014865 -0.00005508 0.99999999 -0.01963810
Axis -0.34402370 -0.92838946 0.14050161
Axis point 134.36280827 0.00000000 116.77087918
Rotation angle (degrees) 0.00917371
Shift along axis 0.00236875
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 85465 points
correlation = 0.9949, correlation about mean = 0.9601, overlap = 47.94
steps = 28, shift = 0.0132, angle = 0.0275 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999994 -0.00010100 0.00032513 -0.04816878
0.00010098 0.99999999 0.00004774 -0.02669224
-0.00032513 -0.00004771 0.99999995 0.04995738
Axis -0.13881963 0.94574652 0.29375608
Axis point 157.13457295 0.00000000 149.83864811
Rotation angle (degrees) 0.01969727
Shift along axis -0.00388204
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 85465 points
correlation = 0.9947, correlation about mean = 0.9592, overlap = 47.99
steps = 44, shift = 0.0107, angle = 0.0263 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00002042 -0.00012677 0.01180003
0.00002042 1.00000000 0.00004965 -0.01083042
0.00012676 -0.00004965 0.99999999 -0.01424570
Axis -0.36065124 -0.92083003 0.14833319
Axis point 116.60412114 0.00000000 103.33179040
Rotation angle (degrees) 0.00788757
Shift along axis 0.00360417
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 85465 points
correlation = 0.9948, correlation about mean = 0.9594, overlap = 47.98
steps = 40, shift = 0.00191, angle = 0.000412 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00002655 -0.00013039 0.01136318
0.00002655 1.00000000 0.00004867 -0.01189939
0.00013039 -0.00004867 0.99999999 -0.01549506
Axis -0.34350299 -0.92026433 0.18740132
Axis point 124.80275021 0.00000000 98.05710820
Rotation angle (degrees) 0.00811788
Shift along axis 0.00414350
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 85465 points
correlation = 0.9948, correlation about mean = 0.9594, overlap = 47.98
steps = 40, shift = 0.000439, angle = 0.000304 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00002598 -0.00012518 0.01019965
0.00002598 1.00000000 0.00004791 -0.01175693
0.00012517 -0.00004791 0.99999999 -0.01465656
Axis -0.35090347 -0.91687014 0.19030477
Axis point 123.80233148 0.00000000 93.84059984
Rotation angle (degrees) 0.00782227
Shift along axis 0.00441127
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 85465 points
correlation = 0.9948, correlation about mean = 0.9594, overlap = 47.98
steps = 40, shift = 0.000758, angle = 0.00154 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00004188 -0.00014676 0.01524387
0.00004189 1.00000000 0.00004937 -0.01431324
0.00014676 -0.00004938 0.99999999 -0.01812752
Axis -0.30780083 -0.91491747 0.26112194
Axis point 130.05905840 0.00000000 111.55619715
Rotation angle (degrees) 0.00919060
Shift along axis 0.00366987
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 85465 points
correlation = 0.9948, correlation about mean = 0.9593, overlap = 47.99
steps = 40, shift = 0.00157, angle = 0.00322 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
1.00000000 -0.00002446 -0.00009344 0.00622882
0.00002446 1.00000000 0.00004754 -0.01141103
0.00009344 -0.00004754 0.99999999 -0.00972806
Axis -0.44159148 -0.86796452 0.22723239
Axis point 116.14289591 0.00000000 90.02053360
Rotation angle (degrees) 0.00616784
Shift along axis 0.00494324
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 85465 points
correlation = 0.9948, correlation about mean = 0.9595, overlap = 47.98
steps = 40, shift = 0.00408, angle = 0.014 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00004612 0.00015082 -0.02315880
0.00004611 1.00000000 0.00004804 -0.01576004
-0.00015082 -0.00004803 0.99999999 0.01997289
Axis -0.29137133 0.91480308 0.27971069
Axis point 136.27695207 0.00000000 157.58835743
Rotation angle (degrees) 0.00944617
Shift along axis -0.00208289
Fit map postprocess_masked.mrc in map 20220622_postprocess_Bfactor-30_fit in
map.mrc using 85465 points
correlation = 0.9948, correlation about mean = 0.9592, overlap = 47.99
steps = 40, shift = 0.00313, angle = 0.0171 degrees
Position of postprocess_masked.mrc (#4) relative to
20220622_postprocess_Bfactor-30_fit in map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00007397 -0.00014589 0.02351326
0.00007398 1.00000000 0.00006521 -0.02019747
0.00014588 -0.00006522 0.99999999 -0.01663431
Axis -0.37034663 -0.82846196 0.42011208
Axis point 117.02507008 0.00000000 163.79527138
Rotation angle (degrees) 0.01008925
Shift along axis 0.00103650
> show #5 models
> hide #5 models
> show #!3 models
> hide #!4 models
> show #!4 models
> color zone #4 near #2 distance 6.44
> hide #!4 models
> hide #!3 models
> show #!3 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 #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> preset ribbons
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #!3 models
> hide #!4 models
> select #2/J
2795 atoms, 3132 bonds, 137 residues, 1 model selected
> hide sel atoms
> select #2/J
2795 atoms, 3132 bonds, 137 residues, 1 model selected
> hide sel atoms
> hide sel atoms
> select #2/I
2822 atoms, 3168 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> show #!3 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
> 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 #!4 models
> show #!4 models
> hide #!4 models
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes true
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> volume #3 level 0.01513
> volume #3 level 0.015
> volume #3 level 0.014
> volume splitbyzone #3
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 0 as #1.1, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 1 as #1.2, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 2 as #1.3, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 3 as #1.4, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 4 as #1.5, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 5 as #1.6, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 6 as #1.7, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 7 as #1.8, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
Opened 20220622_postprocess_Bfactor-30_fit in map.mrc 8 as #1.9, grid size
256,256,256, pixel 1.07, shown at level 0.014, step 1, values float32
> volume #1.1 level 0.002801
> volume #1.6 level 0.01077
> volume #1.6 level 0.01
> volume #1.7 level 0.01
> volume #1.9 level 0.015
> hide #!1 models
> show #!1 models
> show #!1.1 models
> hide #!1.1 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #!1.7 models
> show #!1.7 models
> hide #!1.7 models
> show #!1.7 models
> hide #!1.6 models
> hide #!1.5 models
> show #!1.5 models
> show #!1.6 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.4 models
> show #!1.4 models
> surface dust #1.1 size 6.44
> surface dust #1.2 size 6.44
> surface dust #1.3 size 6.44
> surface dust #1.4 size 6.44
> surface undust #1.4
> surface dust #1.4 size 6.44
> surface dust #1.5 size 6.44
> surface dust #1.7 size 6.44
> surface dust #1.6 size 6.44
> surface dust #1.8 size 6.44
> surface dust #1.9 size 6.44
> surface dust #3 size 2.14
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/overall
> map/overall map.cxs" includeMaps true
——— End of log from Mon Aug 8 15:18:05 2022 ———
opened ChimeraX session
> volume #1.7 level 0.0105
> volume #1.6 level 0.015
> volume #1.6 level 0.05
> volume #1.6 level 0.01
> volume #1.6 level 0.008
> volume #1.7 level 0.008
> save "F:/Documents/Map/SSX1/SSX1 Model
> building/20220621-4月份新算的结构/Fig4/SSX1_119Ub_NCP.cxs" includeMaps true
——— End of log from Tue Aug 16 14:50:08 2022 ———
opened ChimeraX session
> lighting soft intensity 0.4
> lighting soft intensity 0.5
> hide #!1 models
> show #!1 models
> show #2 models
> hide #!1.9 models
> hide #!1.8 models
> hide #!1.7 models
> hide #!1.4 models
> hide #!1.5 models
> show #!1.4 models
> show #!1.5 models
> hide #!1.6 models
> show #!1.6 models
> show #!1.8 models
> show #!1.7 models
> select #1.8
2 models selected
> transparency #1.8.1 50
> select clear
> show #!1.9 models
> hide #!1.9 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> show #!3 models
> hide #!3 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.9 models
> hide #!1.9 models
> close #5
> select /I
2822 atoms, 3168 bonds, 137 residues, 1 model selected
> hide #!1 models
> show #!1 models
> ui tool show "Color Actions"
> color sel light sky blue
> select /J
2795 atoms, 3132 bonds, 137 residues, 1 model selected
> color sel cornflower blue
> hide #!1 models
> select clear
> select /A
801 atoms, 813 bonds, 97 residues, 1 model selected
> color sel light gray
> color sel dark gray
> select /B
668 atoms, 675 bonds, 83 residues, 1 model selected
> color sel dark gray
> select /C
825 atoms, 835 bonds, 107 residues, 1 model selected
> color sel dark gray
> select /D
707 atoms, 718 bonds, 91 residues, 1 model selected
> color sel dark gray
> select /E
783 atoms, 794 bonds, 95 residues, 1 model selected
> color sel dark gray
> select /F
648 atoms, 655 bonds, 81 residues, 1 model selected
> color sel dark gray
> select /H
707 atoms, 718 bonds, 91 residues, 1 model selected
> color sel dark gray
> select /F
648 atoms, 655 bonds, 81 residues, 1 model selected
> select /B
668 atoms, 675 bonds, 83 residues, 1 model selected
> select /D
707 atoms, 718 bonds, 91 residues, 1 model selected
> select /F
648 atoms, 655 bonds, 81 residues, 1 model selected
> select /G
815 atoms, 825 bonds, 106 residues, 1 model selected
> color sel dark gray
> select clear
> show #!1 models
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/ssx1-119 NCP-model.cxs" includeMaps true
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #1.8
2 models selected
> ~select #1.8
Nothing selected
> select #1.8
2 models selected
> ~select #1.8
Nothing selected
> show #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!1.6 models
> hide #!1.7 models
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> select /A
801 atoms, 813 bonds, 97 residues, 1 model selected
> color sel light gray
> select clear
> select /B
668 atoms, 675 bonds, 83 residues, 1 model selected
> color sel light gray
> select clear
> select /C
825 atoms, 835 bonds, 107 residues, 1 model selected
> color sel light gray
> select /D
707 atoms, 718 bonds, 91 residues, 1 model selected
> color sel light gray
> select /E
783 atoms, 794 bonds, 95 residues, 1 model selected
> color sel light gray
> select /F
648 atoms, 655 bonds, 81 residues, 1 model selected
> color sel light gray
> select /G
815 atoms, 825 bonds, 106 residues, 1 model selected
> color sel light gray
> select /G
815 atoms, 825 bonds, 106 residues, 1 model selected
> select /H
707 atoms, 718 bonds, 91 residues, 1 model selected
> color sel light gray
> select clear
> select /H
707 atoms, 718 bonds, 91 residues, 1 model selected
> color sel light gray
> select clear
> hide #2 models
> show #2 models
> hide #!1.1 models
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/ssx1-119 NCP-model.cxs" includeMaps true
——— End of log from Thu Aug 25 17:23:51 2022 ———
opened ChimeraX session
> select #2 /s
205 atoms, 210 bonds, 23 residues, 1 model selected
> show sel atoms
> select clear
> select #2 /s
205 atoms, 210 bonds, 23 residues, 1 model selected
> hide sel atoms
> select #2 /s：177,182,184
Expected a keyword
> select #2 /s：177,182,184
Expected a keyword
> select #2 /s：177，182,184
Expected a keyword
> select #2 /s：177
Expected a keyword
> select #2 /s：177
Expected a keyword
> select #2 /s：177
Expected a keyword
> select #2 /s:177
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2 /s:177,182,184
29 atoms, 27 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select /S:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> volume #1.8 level 0.01335
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> select /S:175
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/SSX1-119 NCP-局部图.png" width 4610 height 3000 supersample 4
> select #1.8
2 models selected
> transparency 80 target s
> transparency 50 target s
> select clear
> select /S:169
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> select /S:164
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #2 /s:164,167,168,169
44 atoms, 44 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/SSX1-119 NCP-局部图.png" width 4610 height 3000 supersample 4
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/ssx1-119 NCP-model-close view.cxs" includeMaps true
> open "F:/Documents/Map/SSX1/SSX1 Model building/SSX1-WT NCP.pdb"
Summary of feedback from opening F:/Documents/Map/SSX1/SSX1 Model
building/SSX1-WT NCP.pdb
---
warnings | Ignored bad PDB record found on line 156
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 157
MOLPROBITY STATISTICS.
Ignored bad PDB record found on line 158
END
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> open "F:/Documents/Map/SSX1/SSX1 Model building/SSX1-WT NCP.pdb"
Summary of feedback from opening F:/Documents/Map/SSX1/SSX1 Model
building/SSX1-WT NCP.pdb
---
warnings | Ignored bad PDB record found on line 156
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 157
MOLPROBITY STATISTICS.
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> select #2 /a,b,c,d,e,f,g,h
5954 atoms, 6033 bonds, 751 residues, 1 model selected
> select #2 /a,b,c,d,e,f,g,h,u
6547 atoms, 6632 bonds, 825 residues, 1 model selected
> show sel surfaces
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/G LYS 118 CD
/G LYS 118 NZ
/G LYS 118 CG
/G LYS 118 CE
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 202200807_SSX1_119Ub_Second_phenix_real_space_refined-
coot-0.pdb_A SES surface #2.1: minimum, -12.74, mean 1.91, maximum 13.10
Coulombic values for 202200807_SSX1_119Ub_Second_phenix_real_space_refined-
coot-0.pdb_B SES surface #2.2: minimum, -8.99, mean 3.96, maximum 16.91
Coulombic values for 202200807_SSX1_119Ub_Second_phenix_real_space_refined-
coot-0.pdb_C SES surface #2.3: minimum, -15.66, mean 2.30, maximum 16.92
Coulombic values for 202200807_SSX1_119Ub_Second_phenix_real_space_refined-
coot-0.pdb_D SES surface #2.4: minimum, -13.50, mean 1.29, maximum 11.45
Coulombic values for 202200807_SSX1_119Ub_Second_phenix_real_space_refined-
coot-0.pdb_E SES surface #2.5: minimum, -12.83, mean 1.65, maximum 12.28
Coulombic values for 202200807_SSX1_119Ub_Second_phenix_real_space_refined-
coot-0.pdb_F SES surface #2.6: minimum, -8.29, mean 3.51, maximum 20.48
Coulombic values for 202200807_SSX1_119Ub_Second_phenix_real_space_refined-
coot-0.pdb_G SES surface #2.7: minimum, -17.08, mean 2.18, maximum 19.33
Coulombic values for 202200807_SSX1_119Ub_Second_phenix_real_space_refined-
coot-0.pdb_H SES surface #2.8: minimum, -13.27, mean 1.28, maximum 11.47
Coulombic values for 202200807_SSX1_119Ub_Second_phenix_real_space_refined-
coot-0.pdb_U SES surface #2.9: minimum, -12.15, mean -0.17, maximum 14.76
To also show corresponding color key, enter the above coulombic command and
add key true
> lighting flat
> select clear
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/ssx1-119 NCP-model_ele.cxs" includeMaps true
——— End of log from Fri Oct 28 15:53:13 2022 ———
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel surfaces
> select clear
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> lighting soft
> select clear
> open "F:/Documents/Map/SSX1/SSX1-WT NCP/wrapped/20221028-phenix revised
> SSX1_wt NCP model/20221028_SSX1_WT NCP_7xd1/20221028_SSX1-WT NCP_final
> model.pdb"
Summary of feedback from opening F:/Documents/Map/SSX1/SSX1-WT
NCP/wrapped/20221028-phenix revised SSX1_wt NCP model/20221028_SSX1_WT
NCP_7xd1/20221028_SSX1-WT NCP_final model.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.010 0.077 12925
Ignored bad PDB record found on line 23
ANGLE : 0.784 8.143 18715
Ignored bad PDB record found on line 24
CHIRALITY : 0.047 0.191 2131
29 messages similar to the above omitted
Chain information for 20221028_SSX1-WT NCP_final model.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
> select #5
12110 atoms, 12925 bonds, 1059 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> ui tool show Matchmaker
> matchmaker #5/D to #2/D pairing 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 202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb,
chain D (#2) with 20221028_SSX1-WT NCP_final model.pdb, chain D (#5), sequence
alignment score = 463.3
RMSD between 90 pruned atom pairs is 0.218 angstroms; (across all 91 pairs:
0.625)
> hide #!1.8 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select all
24479 atoms, 26067 bonds, 2181 residues, 25 models selected
> hide sel atoms
> select clear
> show #!1.8 models
> hide #!1.8 models
> lighting full
> lighting simple
> lighting soft
> 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 #!2 models
> show #!2 models
> select all
24479 atoms, 26067 bonds, 2181 residues, 25 models selected
> hide sel cartoons
> select #1:i,j
Nothing selected
> select #1 /i,j
Nothing selected
> select #2 /i,j
5617 atoms, 6300 bonds, 274 residues, 1 model selected
> show sel cartoons
> select #5 /i,j
6027 atoms, 6760 bonds, 294 residues, 1 model selected
> show sel cartoons
> select clear
> hide #!2 models
> show #!2 models
> hide #5 models
> show #5 models
> show #!1.7 models
> show #!1.6 models
> hide #!1.7 models
> hide #!1.6 models
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/WT&119 Comparion/DNA comparison.cxs" includeMaps true
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/WT&119 Comparion/DNA comparison.png" width 4610 height 3000 supersample
> 4 transparentBackground true
> select all
24479 atoms, 26067 bonds, 2181 residues, 25 models selected
> show sel cartoons
> select clear
> select #5/S:175
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2 /s:164,167,168,169,175
51 atoms, 50 bonds, 5 residues, 1 model selected
> show sel atoms
> select #5 /s:164,167,168,169,175
51 atoms, 50 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 51 atom styles
> select clear
> select #5 /s:164,167,168,169,175
51 atoms, 50 bonds, 5 residues, 1 model selected
> color sel byhetero
> select #2 /s:164,167,168,169,175
51 atoms, 50 bonds, 5 residues, 1 model selected
> color sel byhetero
> select clear
> undo
> undo
> select clear
> ui tool show "Side View"
> view
> select #2 /s:164,167,168,169,175
51 atoms, 50 bonds, 5 residues, 1 model selected
> view sel
> select clear
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/WT&119 Comparion/acidic patch.png" width 4610 height 3000 supersample 4
> transparentBackground true
> select #2 /s:164,167,168,169,175
51 atoms, 50 bonds, 5 residues, 1 model selected
> select clear
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/WT&119 Comparion/Acidic patch.cxs" includeMaps true
——— End of log from Mon Oct 31 09:52:31 2022 ———
opened ChimeraX session
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/WT&119 Comparion/acidic patch-2.png" width 6187 height 4000 supersample
> 4
> select /s:164,167,168,169,177
100 atoms, 100 bonds, 9 residues, 2 models selected
> color sel byhetero
> select clear
> select /s:164,167,168,169,177，175
Expected an objects specifier or a keyword
> select /s:164,167,168,169,177,175
114 atoms, 112 bonds, 11 residues, 2 models selected
> color sel byhetero
> color sel byhetero
> color sel byhetero
> select clear
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/WT&119 Comparion/acidic patch-2.png" width 6187 height 4000 supersample
> 4
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/WT&119 Comparion/H3-Ub-changer color.cxs" includeMaps true
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/WT&119 Comparion/Acidic patch-change color.cxs" includeMaps true
> ui tool show "Side View"
> view
> view
> select clear
> select /i,j
11644 atoms, 13060 bonds, 568 residues, 2 models selected
> select all
24479 atoms, 26067 bonds, 2181 residues, 25 models selected
> hide sel cartoons
> hide sel atoms
> select /i,j
11644 atoms, 13060 bonds, 568 residues, 2 models selected
> show sel cartoons
> select clear
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/WT&119 Comparion/DNA comparison-change color.cxs" includeMaps true
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/WT&119 Comparion/DNA comparison-change color.png" width 6146 height
> 4000 supersample 4
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\run.py",
line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2852, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2852, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\image_formats\\__init__.py", line 45, in save
save_image(session, path, format_name, **kw)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\image_formats\save.py",
line 119, in save_image
i = view.image(width, height, supersample=supersample,
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\graphics\view.py", line
471, in image
pi = Image.fromarray(rgba[::-1, :, :ncomp])
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\PIL\Image.py", line 2766, in
fromarray
obj = obj.tobytes()
MemoryError
MemoryError
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\PIL\Image.py", line 2766, in
fromarray
obj = obj.tobytes()
See log for complete Python traceback.
> save "F:/Documents/Map/SSX1/SSX1 Model building/20220621-4月份新算的结构/Sup
> fig6/WT&119 Comparion/DNA comparison-2.png" width 6146 height 4000
> supersample 4
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\run.py",
line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2852, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2852, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\image_formats\\__init__.py", line 45, in save
save_image(session, path, format_name, **kw)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\image_formats\save.py",
line 119, in save_image
i = view.image(width, height, supersample=supersample,
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\graphics\view.py", line
456, in image
self.draw(c, drawings, swap_buffers = False)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\graphics\view.py", line
165, in draw
self._draw_scene(camera, drawings)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\graphics\view.py", line
212, in _draw_scene
silhouette.start_silhouette_drawing(r)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\graphics\opengl.py",
line 1745, in start_silhouette_drawing
fb = self._silhouette_framebuffer(r)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\graphics\opengl.py",
line 1781, in _silhouette_framebuffer
dt.initialize_depth(size, depth_compare_mode=False)
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\graphics\opengl.py",
line 2904, in initialize_depth
self.initialize_texture(size, format, iformat, tdtype, ncomp,
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\graphics\opengl.py",
line 2930, in initialize_texture
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src/wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src/wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'\xc4\xda\xb4\xe6\xb2\xbb\xd7\xe3',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_DEPTH_COMPONENT24,
6146,
4000,
0,
GL_DEPTH_COMPONENT,
GL_FLOAT,
c_void_p(None),
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_DEPTH_COMPONENT24,
6146,
4000,
0,
GL_DEPTH_COMPONENT,
GL_FLOAT,
c_void_p(None),
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_DEPTH_COMPONENT24,
6146,
4000,
0,
GL_DEPTH_COMPONENT,
GL_FLOAT,
c_void_p(None),
)
)
OpenGL.error.GLError: GLError(
err = 1285,
description = b'\xc4\xda\xb4\xe6\xb2\xbb\xd7\xe3',
baseOperation = glTexImage2D,
pyArgs = (
GL_TEXTURE_2D,
0,
GL_DEPTH_COMPONENT24,
6146,
4000,
0,
GL_DEPTH_COMPONENT,
GL_FLOAT,
c_void_p(None),
),
cArgs = (
GL_TEXTURE_2D,
0,
GL_DEPTH_COMPONENT24,
6146,
4000,
0,
GL_DEPTH_COMPONENT,
GL_FLOAT,
c_void_p(None),
),
cArguments = (
GL_TEXTURE_2D,
0,
GL_DEPTH_COMPONENT24,
6146,
4000,
0,
GL_DEPTH_COMPONENT,
GL_FLOAT,
c_void_p(None),
)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 526.47
OpenGL renderer: NVIDIA GeForce GTX 1660/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 专业版 (Build 17134)
Memory: 17,110,605,824
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9400F CPU @ 2.90GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving large image |
comment:2 by , 3 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
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Ran out of memory trying to save an 6000 x 4000 image. PIL tried to convert the image to bytes to write it to a file and memory allocation failed. Surprising since the machine as 16 GB.