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Opened 3 years ago
Closed 3 years ago
#8121 closed defect (can't reproduce)
Negative decimal places for distance format
| Reported by: | 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 )
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
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 (1)
comment:1 by , 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 |
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Duplicate #7881
Early versions of "distance style" or its settings tool must have allowed negative decimal places.