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Opened 3 years ago
Closed 3 years ago
#7892 closed defect (duplicate)
Negative decimal places for distance format
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | 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\\\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
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> hide #!1.6 models
> hide #!1.7 models
> hide #!1.8 models
> hide #!1.9 models
> select #1.5
2 models selected
> ~select #1.5
Nothing selected
> select #1.5
2 models selected
> transparency #1.5.1 80
> select clear
> show #2 models
> ~select #2 d
> select subtract #2 d
Expected a keyword
> ~select #2
Nothing selected
> ~select #2 /b
Nothing selected
> ~select #2 /b
Nothing selected
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel cartoons
> select #2 /b
668 atoms, 675 bonds, 83 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> ~select #2
Nothing selected
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> show sel cartoons
> ~select #2
Nothing selected
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> ~select #2
Nothing selected
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel cartoons
> select #2 /d
707 atoms, 718 bonds, 91 residues, 1 model selected
> show sel atoms
> select clear
> select #2 /d
707 atoms, 718 bonds, 91 residues, 1 model selected
> select #2 /d
707 atoms, 718 bonds, 91 residues, 1 model selected
> color sel byhetero
> select clear
> ui tool show "Map Eraser"
> volume erase #1.5 center 148.28,126.66,116.73 radius 13.802
> volume erase #1.5 center 135.04,115.33,113.95 radius 13.802
> volume erase #1.5 center 115.19,111.2,116.86 radius 13.802
> volume erase #1.5 center 136.77,111.03,117.09 radius 13.802
> volume erase #1.5 center 136.99,113.8,127.34 radius 13.802
> volume erase #1.5 center 116.63,119.77,125.63 radius 13.802
> volume erase #1.5 center 131.23,123.98,130.12 radius 13.802
> volume erase #1.5 center 111.51,127.89,115.01 radius 13.802
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 516.59
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 → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Negative decimal places for distance format |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Duplicate #7881