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#7892 closed defect (duplicate)

Negative decimal places for distance format

Reported by:	chimerax-bug-report@…	Owned by:	pett
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 pett, 3 years ago

Component:	Unassigned → Structure Analysis
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Negative decimal places for distance format

comment:2 by pett, 3 years ago

Resolution:	→ duplicate
Status:	accepted → closed

Duplicate #7881

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