Opened 3 years ago

Closed 3 years ago

#8121 closed defect (can't reproduce)

Negative decimal places for distance format

Reported by: chimerax-bug-report@… Owned by:
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett) 

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\\\SupFig10\\\SSX1-AEBP2.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 Thu Nov 24 15:07:53 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\\\SSX1和其他reader结构比较\\\SSX1-AEBP2\\\AEBP2.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 Nov 9 14:32:51 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "F:\\\Documents\\\Map\\\SSX1\\\SSX1 Model
> building\\\SSX1和其他reader结构比较\\\SSX1-JARID2\\\JARID2-Ub surface.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 Mon Apr 11 16:01:38 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\\\SSX1和其他reader结构比较\\\SSX1-JARID2.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 Sat Apr 2 14:08:23 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\\\SSX1和其他reader结构比较\\\53BP1-Dot1-BARD1-SSX1-JARID2.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 Mon Mar 7 21:25:31 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  
  

[deleted a lot of the log to fit within ticket size limits]

> distance style radius 0.381

> distance style radius 0.371

> distance style radius 0.371

> distance style radius 0.361

> distance style radius 0.361

> distance style decimalPlaces -2

Invalid "decimalPlaces" argument: Must be greater than or equal to 0  

> distance style decimalPlaces -1

Invalid "decimalPlaces" argument: Must be greater than or equal to 0  

> distance style decimalPlaces 0

> distance style decimalPlaces 1

> distance style decimalPlaces 1

> distance style decimalPlaces 2

> distance style decimalPlaces 2

> distance style decimalPlaces 3

> distance style decimalPlaces 3

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> save "F:/Documents/Map/SSX1/SSX1 Model
> building/20220621-4月份新算的结构/SupFig10/SSX1-AEBP2.cxs" includeMaps true

——— End of log from Thu Nov 24 15:07:53 2022 ———

opened ChimeraX session  

> select

124101 atoms, 131116 bonds, 1991 pseudobonds, 12114 residues, 48 models
selected  

> color (#12#!11 & sel) dark gray

> select clear

> select /s

2097 atoms, 2134 bonds, 261 residues, 5 models selected  

> select clear

> hide #12 models

> select #11/I:48

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #11/I:49

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel ball

Changed 11 atom styles  

> color sel byhetero

> select clear

> select #11/F:72

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel ball

Changed 11 atom styles  

> color sel byhetero

> select clear

> select add #11/F:72@CA

1 atom, 1 residue, 1 model selected  

> select add #11/I:49@CA

2 atoms, 2 residues, 2 models selected  

> ui tool show Distances

Traceback (most recent call last):  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 540, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1265, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\dist_ui\\__init__.py",
line 45, in start_tool  
return DistanceTool(session, tool_name)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\dist_ui\tool.py", line
88, in __init__  
self._fill_table()  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\dist_ui\tool.py", line
150, in _fill_table  
strings = a1.string(), a2.string(relative_to=a1), fmt % pb.length  
ValueError: unsupported format character '-' (0x2d) at index 2  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\ui\gui.py", line 1552,
in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\run.py",
line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2852, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\ui\cmd.py", line 203,
in ui_tool_show  
bi.start_tool(session, name)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 545, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances
in bundle ChimeraX-DistUI:  
unsupported format character '-' (0x2d) at index 2  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances
in bundle ChimeraX-DistUI:  
unsupported format character '-' (0x2d) at index 2  
  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 545, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show Distances

> distance #11/F:72@CA #11/I:49@CA

Traceback (most recent call last):  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\dist_ui\tool.py", line
103, in _create_distance  
run(self.session, "distance %s %s" % tuple(a.string(style="command") for a in
sel_atoms))  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\run.py",
line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2852, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\dist_monitor\cmd.py",
line 118, in distance  
session.logger.info(("Distance between %s and %s: " +
session.pb_dist_monitor.distance_format)  
ValueError: unsupported format character '-' (0x2d) at index 30  
  
ValueError: unsupported format character '-' (0x2d) at index 30  
  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\dist_monitor\cmd.py",
line 118, in distance  
session.logger.info(("Distance between %s and %s: " +
session.pb_dist_monitor.distance_format)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\triggerset.py",
line 130, in invoke  
return self._func(self._name, data)  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\dist_monitor\monitor.py", line 110, in _changes_handler  
self._update_distances(pseudobonds=[pb])  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\dist_monitor\monitor.py", line 139, in _update_distances  
label_settings['text'] = fmt % pb.length  
ValueError: unsupported format character '-' (0x2d) at index 2  
  
Error processing trigger "changes":  
ValueError: unsupported format character '-' (0x2d) at index 2  
  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\dist_monitor\monitor.py", line 139, in _update_distances  
label_settings['text'] = fmt % pb.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.length  
  
See log for complete Python traceback.  
  

> distance style symbol false

Traceback (most recent call last):  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\ui\options\options.py",
line 170, in make_callback  
self._callback(self)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\dist_ui\tool.py", line
78, in <lambda>  
run(ses, "distance style " + cmd_suffix  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\run.py",
line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2852, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\dist_monitor\cmd.py",
line 195, in distance_style  
session.pb_dist_monitor.show_units = symbol  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\dist_monitor\monitor.py", line 91, in _set_show_units  
self._update_distances()  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\dist_monitor\monitor.py", line 139, in _update_distances  
label_settings['text'] = fmt % pb.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\dist_monitor\monitor.py", line 139, in _update_distances  
label_settings['text'] = fmt % pb.length  
  
See log for complete Python traceback.  
  

> distance style symbol true

Traceback (most recent call last):  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\ui\options\options.py",
line 170, in make_callback  
self._callback(self)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\dist_ui\tool.py", line
78, in <lambda>  
run(ses, "distance style " + cmd_suffix  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\run.py",
line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2852, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\dist_monitor\cmd.py",
line 195, in distance_style  
session.pb_dist_monitor.show_units = symbol  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\dist_monitor\monitor.py", line 91, in _set_show_units  
self._update_distances()  
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\dist_monitor\monitor.py", line 139, in _update_distances  
label_settings['text'] = fmt % pb.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\dist_monitor\monitor.py", line 139, in _update_distances  
label_settings['text'] = fmt % pb.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.length  
  
See log for complete Python traceback.  
  

> select clear

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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.length  
  
See log for complete Python traceback.  
  

> hide #!10 models

> show #!10 models

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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.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 1980, in description  
return str(self.pbond) + " " + dist_fmt % self.pbond.length  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 526.47
OpenGL renderer: NVIDIA GeForce GTX 1660/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 专业版 (Build 17134)
Memory: 17,110,605,824
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9400F CPU @ 2.90GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
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    sphinxcontrib-htmlhelp: 2.0.0
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    sphinxcontrib-serializinghtml: 1.1.5
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    webcolors: 1.11.1
    wheel: 0.36.0
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    WMI: 1.5.1

Change History (1)

comment:1 by pett, 3 years ago

Component: Unassigned → Structure Analysis
Description: modified (diff)
Platform: → all
Project: → ChimeraX
Resolution: → can't reproduce
Status: new → closed
Summary: ChimeraX bug report submission → Negative decimal places for distance format

Duplicate #7881

Early versions of "distance style" or its settings tool must have allowed negative decimal places.

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