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Opened 3 years ago
Last modified 3 years ago
#8121 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.17134
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "F:\\\Documents\\\Map\\\SSX1\\\SSX1 Model
> building\\\20220621-4月份新算的结构\\\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
> hide #3 models
> ~select #3
Nothing selected
> select #4
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 23
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 24
CHIRALITY : 0.050 0.241 2159
21 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 01
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
End residue of secondary structure not found: SHEET 22 2222 MET U 1 TH 0 0
Chain information for 20210929_final_for chimeraX.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #4 models
> select #5
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 01
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #5 models
> select #6
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> close #1-5
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 01
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #1 models
> hide sel cartoons
> show sel surfaces
> show sel cartoons
> hide sel surfaces
> select clear
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 1
7
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #2 models
> select #6
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 1
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #3 models
> hide sel atoms
> show sel cartoons
> show sel cartoons
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 1
7
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide #4 models
> hide sel atoms
> show sel cartoons
> close #1-4
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
End residue of secondary structure not found: HELIX 36 36 HIS S 162 LEU 168 1
7
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> hide sel atoms
> select #1
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #6
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> select #1
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> select #6
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> select #1
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> select #6
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
20 messages similar to the above omitted
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
18 messages similar to the above omitted
End residue of secondary structure not found: HELIX 32 32 THR H 90 LEU H 102
01 1
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> select #3
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> close #1-2#6
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
18 messages similar to the above omitted
End residue of secondary structure not found: HELIX 32 32 THR H 90 LEU H 102
01 1
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> select #1
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #3
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> ~select #3
Nothing selected
> select #1
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> ~select #1
Nothing selected
> select #1
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> ~select #1
Nothing selected
> select #3
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> ~select #3
Nothing selected
> open "C:/Users/huasong/Desktop/SSX1 Model building/20210929_final_for
> chimeraX_.pdb"
Summary of feedback from opening C:/Users/huasong/Desktop/SSX1 Model
building/20210929_final_for chimeraX_.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 32 32 THR H 90 LEU H 102
01 1
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20210929_final_for chimeraX_.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> hide #2 models
> show #2 models
> close #3
> close #1
> select /I
2822 atoms, 3168 bonds, 137 residues, 1 model selected
> color sel dark gray
> select /J
2795 atoms, 3132 bonds, 137 residues, 1 model selected
> color sel dark gray
> select clear
> select /G
815 atoms, 825 bonds, 106 residues, 1 model selected
> ui tool show "Color Actions"
> color sel wheat
> color sel burly wood
> select clear
> select /F
648 atoms, 655 bonds, 81 residues, 1 model selected
> color sel pink
> color sel light coral
> color sel pale violet red
> color sel pale violet red
> color sel pale violet red
> color sel light pink
> color sel pale violet red
> color sel pink
> color sel violet
> color sel deep pink
> color sel magenta
> color sel dark violet
> color sel tan
> color sel burly wood
> color sel light coral
> color sel medium violet red
> color sel pale violet red
> select clear
> select /F
648 atoms, 655 bonds, 81 residues, 1 model selected
> color sel light coral
> select clear
> select /G
815 atoms, 825 bonds, 106 residues, 1 model selected
> color sel medium aquamarine
> color sel dark sea green
> select clear
> select /H
707 atoms, 718 bonds, 91 residues, 1 model selected
> color sel light salmon
> color sel dark salmon
> color sel tan
> color sel burly wood
> color sel tan
> color sel burly wood
> select clear
> select /E
783 atoms, 794 bonds, 95 residues, 1 model selected
> color sel medium slate blue
> select clear
> select /U
593 atoms, 599 bonds, 74 residues, 1 model selected
> color sel yellow
> select clear
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> color sel red
> color sel crimson
> select /U
593 atoms, 599 bonds, 74 residues, 1 model selected
> color sel khaki
> color sel pale goldenrod
> color sel gold
> select clear
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> color sel maroon
> color sel dark red
> color sel fire brick
> color sel brown
> color sel tomato
> color sel crimson
> color sel crimson
> select clear
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210920.cxs"
> open "C:/Users/huasong/Desktop/SSX1 Model
> building/job059_postprocess_masked.mrc"
Opened job059_postprocess_masked.mrc as #1, grid size 256,256,256, pixel 1.07,
shown at level 0.00431, step 1, values float32
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide #!1 models
> open "C:/Users/huasong/Desktop/SSX1 Model
> building/job054_run_ct17_class001.mrc"
Opened job054_run_ct17_class001.mrc as #3, grid size 256,256,256, pixel 1.07,
shown at level 0.003, step 1, values float32
> ~select #2
Nothing selected
> select #3
2 models selected
> show #!1 models
> ~select #3
Nothing selected
> hide #!3 models
> volume #1 level 0.02036
> volume #1 level 0.01434
> surface dust #1 size 10.7
> select #2
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> color zone #1 near sel & #2 distance 6.44
> close #3
> ui tool show "Color Zone"
> color zone #1 near #2 distance 1.07
> color zone #1 near #2 distance 4.44
> volume #1 level 0.01037
> volume #1 level 0.015
> volume #1 level 0.016
> volume splitbyzone #1
Opened job059_postprocess_masked.mrc 0 as #3.1, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 1 as #3.2, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 2 as #3.3, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 3 as #3.4, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 4 as #3.5, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 5 as #3.6, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 6 as #3.7, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
Opened job059_postprocess_masked.mrc 7 as #3.8, grid size 256,256,256, pixel
1.07, shown at level 0.016, step 1, values float32
> volume #3.6 level 0.01178
> surface dust #3.1 size 10.7
> surface dust #3.2 size 10.7
> surface dust #3.3 size 10.7
> surface dust #3.4 size 10.7
> surface dust #3.5 size 10.7
> surface dust #3.6 size 10.7
> surface dust #3.7 size 10.7
> surface dust #3.8 size 10.7
> ui tool show "Hide Dust"
> surface dust #3.1 size 1.07
> surface dust #3.1 size 1.07
> surface dust #3.1 size 4.15
> surface dust #3.1 size 5
> surface dust #3.1 size 5
> volume #3.7 level 0.01508
> hide #2 models
> volume #3.6 level 0.02093
> volume #3.6 level 0.01143
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210920.cxs"
> volume #1 level 0.02705
> open "C:/Users/huasong/Desktop/SSX1 Model building/job059_postprocess.mrc"
Opened job059_postprocess.mrc as #4, grid size 256,256,256, pixel 1.07, shown
at level 0.011, step 1, values float32
> hide #!1 models
> hide #1.1 models
> close #1
> close #3
> show #2 models
> surface dust #4 size 6.44
> color zone #4 near #2 distance 6.44
> view sel
> volume #4 level 0.01932
> volume #4 level 0.01694
> volume #4 level 0.01337
> surface dust #4 size 10
> surface dust #4 size 10
> surface dust #4 size 15
> surface dust #4 size 15
> surface dust #4 size 10.7
> surface dust #4 size 10.7
> surface dust #4 size 10.7
> surface dust #4 size 10.7
> volume #4 level 0.01813
> surface dust #4 size 10
> surface dust #4 size 5
> volume #4 level 0.02052
> volume #4 level 0.021
> volume splitbyzone #4
Opened job059_postprocess.mrc 0 as #1.1, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 1 as #1.2, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 2 as #1.3, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 3 as #1.4, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 4 as #1.5, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 5 as #1.6, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 6 as #1.7, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
Opened job059_postprocess.mrc 7 as #1.8, grid size 256,256,256, pixel 1.07,
shown at level 0.021, step 1, values float32
> surface dust #4 size 5
> surface dust #4 size 5
> surface dust #4 size 5
> surface dust #1.1 size 10.7
> surface dust #1.2 size 10.7
> surface dust #1.3 size 10.7
> surface dust #1.4 size 10.7
> surface dust #1.5 size 10.7
> surface dust #1.6 size 10.7
> surface dust #1.7 size 10.7
> surface dust #1.8 size 10.7
> volume #1.7 level 0.01514
> volume #1.7 level 0.01532
> volume #1.6 level 0.01044
> surface dust #1.6 size 2.08
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929.cxs"
> color zone #1.6 near #2 distance 6.44
> volume splitbyzone #1.6
Opened job059_postprocess.mrc 5 0 as #3.1, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 1 as #3.2, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 2 as #3.3, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 3 as #3.4, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 4 as #3.5, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 5 as #3.6, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 6 as #3.7, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
Opened job059_postprocess.mrc 5 7 as #3.8, grid size 256,256,256, pixel 1.07,
shown at level 0.0104, step 1, values float32
> surface dust #1.6 size 2.08
> surface dust #1.1 size 10.7
> surface dust #1.2 size 10.7
> surface dust #1.3 size 10.7
> surface dust #1.4 size 10.7
> surface dust #1.5 size 10.7
> surface dust #1.7 size 10.7
> surface dust #1.8 size 10.7
> surface dust #3.1 size 10.7
> surface dust #3.2 size 10.7
> surface dust #3.3 size 10.7
> surface dust #3.4 size 10.7
> surface dust #3.5 size 10.7
> surface dust #3.6 size 10.7
> surface dust #3.7 size 10.7
> surface dust #3.8 size 10.7
> surface undust #1.6
> surface undust #1.6
> surface undust #3.6
> hide #!3.1 models
> show #!3.1 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3.6 models
> show #!3.6 models
> hide #!3.1 models
> show #!3.1 models
> volume #3.6 level 0.01678
> hide #!3 models
> close #3
> show #!1.6 models
> volume #1.6 level 0.01607
> surface dust #1.6 size 6.44
> surface dust #1.6 size 4
> volume #1.6 level 0.01291
> select clear
> volume #1.6 level 0.0217
> volume #1.6 level 0.01643
> volume #1.6 level 0.01678
> volume #1.6 level 0.015
> transparency #1-2 20
> transparency #1-2 10
> select clear
> select clear
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.cxs"
> volume #!1.1-8 style surface
> transparency #1-2 0
> lighting full
> lighting full
> lighting soft
> lighting simple
> lighting soft
> show #!4 models
> hide #!4 models
> hide #2 models
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.cxs"
——— End of log from Wed Sep 29 16:30:31 2021 ———
opened ChimeraX session
> ui tool show "Hide Dust"
> surface dust #1.1 size 1.07
> surface dust #1.6 size 2
> surface dust #1.6 size 5
> surface dust #1.1 size 10.7
> surface dust #1.2 size 10.7
> surface dust #1.3 size 10.7
> surface dust #1.4 size 10.7
> surface dust #1.5 size 10.7
> surface dust #1.6 size 10.7
> surface dust #1.7 size 10.7
> surface dust #1.8 size 10.7
> surface undust #1.6
> surface dust #1.6 size 2
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.cxs"
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.png" width 3206 height 2000
> supersample 4
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_002.cxs"
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_002.png" width 3206 height 2000
> supersample 4
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_003.cxs"
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_003.png" width 3206 height 2000
> supersample 4
> volume #1.7 level 0.01551
> show #2 models
> hide #2 models
> surface dust #1.6 size 2
> surface dust #1.6 size 2
> surface dust #1.6 size 3
> surface dust #1.6 size 2
> surface dust #1.6 size 2.5
> select clear
> ui tool show "Side View"
> volume #1.8 level 0.01779
> view
> volume #1.8 level 0.01645
> show #2 models
> hide #!1 models
> select /I:0
22 atoms, 24 bonds, 1 residue, 1 model selected
> show #!1 models
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.cxs"
No map chosen to save
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.tiff" width 3206 height 2000
> supersample 4
> select clear
> surface dust #1.6 size 3
> surface dust #1.6 size 2
> surface dust #1.6 size 2.5
> surface dust #1.6 size 2
> surface dust #1.6 size 3
> surface dust #1.6 size 4
> surface dust #1.6 size 2
> surface dust #1.6 size 2.5
> hide #2 models
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall map and model_20210929_001.cxs"
——— End of log from Wed Sep 29 16:47:19 2021 ———
opened ChimeraX session
> hide #!1 models
> show #2 models
> show #!1 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.6 models
> hide #!1.7 models
> hide #2 models
> show #2 models
> hide #!1.5 models
> transparency #2#1.8#!1 50
> select /I:0
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 205 atom styles
> color sel byhetero
> style sel ball
Changed 205 atom styles
> select clear
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> style sel ball
Changed 205 atom styles
> style sel stick
Changed 205 atom styles
> select clear
> volume #1.8 level 0.01752
> select /I
2822 atoms, 3168 bonds, 137 residues, 1 model selected
> select clear
> save "C:/Users/huasong/Desktop/SSX1 Model building/zuotu/Overall
> map_model/overall model_20210929.cxs"
——— End of log from Wed Sep 29 18:27:07 2021 ———
opened ChimeraX session
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!4 models
> ui tool show "Side View"
> save "D:/Documents/Map/SSX1/SSX1 Model building/20210929_TZB/overall map and
> model_20210929_004.cxs"
——— End of log from Wed Sep 29 18:50:26 2021 ———
opened ChimeraX session
> hide #!4 models
> show #!1.7 models
> show #!1.6 models
> show #!1.5 models
> show #!1.4 models
> show #!1.3 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> hide #2 models
> show #!1.1 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.5 models
> show #2 models
> show #!1.5 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> select clear
> select #1.8
2 models selected
> volume sel style surface
> transparency sel 0
> select clear
Drag select of 1.2 job059_postprocess.mrc 1 , 1.3 job059_postprocess.mrc 2 ,
1.4 job059_postprocess.mrc 3 , 1.5 job059_postprocess.mrc 4 , 1.6
job059_postprocess.mrc 5 , 1.7 job059_postprocess.mrc 6 , 1.8
job059_postprocess.mrc 7 , 137 atoms, 1122 residues, 120 bonds
> color sel byhetero
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/G LYS 118 CD
/G LYS 118 CE
/G LYS 118 NZ
/G LYS 118 CG
Deleting 5' phosphates from: /J DC -73, /I DT -63
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 20210929_final_for chimeraX_.pdb_A SES surface #2.1:
minimum, -13.42, mean 1.84, maximum 12.71
Coulombic values for 20210929_final_for chimeraX_.pdb_B SES surface #2.2:
minimum, -8.84, mean 3.94, maximum 24.66
Coulombic values for 20210929_final_for chimeraX_.pdb_C SES surface #2.3:
minimum, -14.45, mean 2.28, maximum 16.17
Coulombic values for 20210929_final_for chimeraX_.pdb_D SES surface #2.4:
minimum, -12.45, mean 1.25, maximum 11.99
Coulombic values for 20210929_final_for chimeraX_.pdb_E SES surface #2.5:
minimum, -11.62, mean 1.63, maximum 12.32
Coulombic values for 20210929_final_for chimeraX_.pdb_F SES surface #2.6:
minimum, -8.12, mean 3.47, maximum 17.60
Coulombic values for 20210929_final_for chimeraX_.pdb_G SES surface #2.7:
minimum, -16.37, mean 2.12, maximum 15.08
Coulombic values for 20210929_final_for chimeraX_.pdb_H SES surface #2.8:
minimum, -12.68, mean 1.25, maximum 11.97
Coulombic values for 20210929_final_for chimeraX_.pdb_I SES surface #2.9:
minimum, -23.98, mean -14.26, maximum -3.09
Coulombic values for 20210929_final_for chimeraX_.pdb_J SES surface #2.10:
minimum, -25.82, mean -14.24, maximum -2.88
Coulombic values for 20210929_final_for chimeraX_.pdb_S SES surface #2.11:
minimum, -11.34, mean -0.79, maximum 9.56
Coulombic values for 20210929_final_for chimeraX_.pdb_U SES surface #2.12:
minimum, -12.75, mean -0.30, maximum 18.17
To also show corresponding color key, enter the above coulombic command and
add key true
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> hide sel surfaces
> select /U
593 atoms, 599 bonds, 74 residues, 1 model selected
> hide sel surfaces
> select clear
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> color (#!2 & sel) magenta
> hide #!1.8 models
> select clear
> select /S:166
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:89@OD1
1 atom, 1 residue, 1 model selected
> select /S:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /E:41@CE1
1 atom, 1 residue, 1 model selected
> select /S:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> view
> hide #!1 models
Drag select of 20210929_final_for chimeraX_.pdb_A SES surface,
20210929_final_for chimeraX_.pdb_B SES surface, 20210929_final_for
chimeraX_.pdb_C SES surface, 20210929_final_for chimeraX_.pdb_D SES surface,
20210929_final_for chimeraX_.pdb_E SES surface, 20210929_final_for
chimeraX_.pdb_F SES surface, 20210929_final_for chimeraX_.pdb_G SES surface,
20210929_final_for chimeraX_.pdb_H SES surface, 20210929_final_for
chimeraX_.pdb_I SES surface, 20210929_final_for chimeraX_.pdb_J SES surface,
137 atoms, 1122 residues, 120 bonds
> hide sel surfaces
> select clear
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> hide sel atoms
> select clear
> show #!1.8 models
> hide #!1.8 models
> show #!1.8 models
> select /A
801 atoms, 813 bonds, 97 residues, 1 model selected
> hide #!1.2 models
> show #!1.2 models
> ui tool show "Color Actions"
> hide #!1.2 models
> color sel dodger blue
> show #!1.2 models
> select clear
> hide #!1.2 models
> show #!1.2 models
> hide #!1 models
> select /E
783 atoms, 794 bonds, 95 residues, 1 model selected
> color sel dodger blue
> color sel cornflower blue
> color sel royal blue
> color sel cornflower blue
> color sel dodger blue
> color sel cornflower blue
> color sel dodger blue
> color sel cornflower blue
> color sel slate blue
> color sel cornflower blue
> color sel deep sky blue
> color sel cornflower blue
> color sel dodger blue
> select clear
> show #!1 models
> hide #!1 models
> select /D
707 atoms, 718 bonds, 91 residues, 1 model selected
> select /C
825 atoms, 835 bonds, 107 residues, 1 model selected
> color sel forest green
> color sel dark sea green
> color sel medium sea green
> color sel forest green
> select clear
> select /G
815 atoms, 825 bonds, 106 residues, 1 model selected
> color sel forest green
> select clear
> show #!1 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.6 models
> show #!1.6 models
> lighting soft
> hide #!1 models
> lighting simple
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> color sel light gray
> color sel dark gray
> color sel light gray
> color sel gray
> color sel dark gray
> color sel light gray
> color sel dark gray
> select clear
> ui tool show "Side View"
> lighting flat
> lighting simple
> lighting full
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> lighting full
> lighting flat
> lighting simple
> lighting flat
> lighting simple
> lighting simple
> lighting simple
> lighting simple
> graphics silhouettes false
> lighting flat
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> show sel atoms
> select clear
> view
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting shadows true
> graphics silhouettes true
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> show #!1 models
> lighting simple
> lighting soft
> lighting flat
> lighting soft
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall model-
> change colors.cxs" includeMaps true
> hide #!1 models
> lighting flat
> show #!1 models
> lighting soft
> camera
Camera parameters:
type: mono
position: -37.092 576.05 218.05
view direction: 0.40142 -0.90224 -0.15758
field of view: 30 degrees
> preset "molecular surfaces" "ghostly white"
Changed 12158 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "chain id coloring (opaque)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> preset "molecular surfaces" "atomic coloring (transparent)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> undo
> undo
> undo
> undo
> undo
> undo
> ui tool show "Side View"
> ui tool show "Side View"
> ui tool show "Side View"
> view
> view
> set bgColor black
> set bgColor gray
> set bgColor white
Drag select of 1.2 job059_postprocess.mrc 1 , 1.3 job059_postprocess.mrc 2 ,
1.4 job059_postprocess.mrc 3 , 1.5 job059_postprocess.mrc 4 , 1.6
job059_postprocess.mrc 5 , 1.7 job059_postprocess.mrc 6 , 1.8
job059_postprocess.mrc 7 , 137 atoms, 1122 residues, 120 bonds
> select clear
> hide #!1 models
> show #!1 models
> ui mousemode right "mark maximum"
> ui mousemode right "mark plane"
> ui mousemode right "mark surface"
> ui mousemode right "mark center"
> ui mousemode right clip
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right "move picked models"
> view matrix models #1.4,1,0,0,-9.6083,0,1,0,-4.4321,0,0,1,17.572
> undo
> ui mousemode right distance
> ui mousemode right distance
> volume #!1.1-8 step 1
> volume #!1.1-8 step 2
> undo
> show #!1 models
> transparency #2.1-12#1.1.1#1.2.1#1.3.1#1.4.1#1.5.1#1.6.1#1.7.1#1.8.1 50
> transparency #2.1-12#1.1.1#1.2.1#1.3.1#1.4.1#1.5.1#1.6.1#1.7.1#1.8.1 0
> hide #!2 models
> show #!2 models
> hide #!1.8 models
> show #!1.8 models
> volume #!1.1-8 step 2
> volume #!1.1-8 step 1
> hide #!1 models
> show #!1 models
> select /C
825 atoms, 835 bonds, 107 residues, 1 model selected
> hide #!1.4 models
> ui tool show "Color Actions"
> color sel medium spring green
> color sel green
> hide #!1.8 models
> hide #!1 models
> select clear
> lighting simple
> graphics silhouettes false
> ui mousemode right translate
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/1.tif" width
> 2924 height 2000 supersample 4 transparentBackground true
> show #!1 models
> view
> view
> lighting flat
> lighting soft
> lighting soft ambientIntensity 1.8
> lighting soft ambientIntensity 2
> lighting soft intensity 0.2
> lighting soft intensity 0.4
> view
> show #!1.8 models
> hide #!1 models
> show #!1 models
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> show #!1.4 models
> hide #!1 models
> select /C
825 atoms, 835 bonds, 107 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium sea green
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> select clear
> hide #!1 models
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> lighting soft intensity 0.6
> lighting soft intensity 0.5
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> show #!1 models
> lighting soft
> lighting simple
> lighting soft
> lighting soft intensity 0.5
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-3-change color.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/20211006overall
> model-change colors-2.cxs" includeMaps true
> hide #!1 models
> preset cartoons/nucleotides cylinders/stubs
Changed 12158 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> lighting soft
> lighting soft intensity 0.3
> lighting soft intensity 0.2
> lighting soft intensity 0.1
> lighting shadows true
> lighting soft intensity 0.2
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel atoms
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> lighting flat
> lighting soft
> lighting simple
> lighting simple
> lighting soft
> lighting soft intensity 0.2
> lighting soft intensity 0.15
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-cylinders.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> select /G
815 atoms, 825 bonds, 106 residues, 1 model selected
> color sel lime green
> color sel medium aquamarine
> color sel medium sea green
> select clear
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-cylinders.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-cylinders-2.tif" width 2924 height 2000 supersample
> 4 transparentBackground true
> graphics silhouettes true width 1.5
> graphics silhouettes true width 1.3
> graphics silhouettes true width 2
> graphics silhouettes true width 1.5
> cartoon style cylinder width 5
Expected an atoms specifier or a keyword
> cartoon style helix modeHelix tube radius 5
> cartoon style helix modeHelix tube radius 3
> cartoon style helix modeHelix tube radius 2.5
> cartoon style helix modeHelix tube radius 15
> cartoon style helix modeHelix tube radius 2.2
> cartoon style helix modeHelix tube radius 2.5
> cartoon style loop modeh tube rad 2.5
Expected an atoms specifier or a keyword
> cartoon style sheet modeh tube rad 2.5
Expected an atoms specifier or a keyword
> cartoon style sheet modeh tube rad 2.5
Expected an atoms specifier or a keyword
> cartoon style sheet modeh tube rad 2.5
Expected an atoms specifier or a keyword
> cartoon style protein width 0.5 thickness 0.5
> cartoon style protein width 2 thickness 2
> cartoon style protein width 1 thickness 1
> cartoon style protein width 0.6 thickness 0.6
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel atoms
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> lighting soft
> cartoon style HELIX width 3 thick 1
Expected an atoms specifier or a keyword
> cartoon style helix width 3 thickness 1
> cartoon style helix width 3 thickness 0.7
> cartoon style helix width 2.5 thickness 0.7
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> cartoon style helix width 2.5 thickness 0.7
> cartoon style helix width 3 thickness 0.7
> cartoon style protein width 3 thickness 0.7
> cartoon style protein width 2 thickness 0.5
> cartoon style protein width 3 thickness 0.5
> cartoon style protein width 3 thickness 1
> lighting soft intensity 0.4
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel atoms
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> cartoon style protein width 1 thickness 0.5
> cartoon style protein width 2 thickness 0.5
> cartoon style protein width 3 thickness 0.5
> cartoon style protein width 2.5 thickness 0.7
> lighting soft intensity 0.5
> lighting soft intensity 0.1
> lighting soft intensity 0.3
> graphics silhouettes false
> graphics silhouettes true
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-rebion.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> lighting soft intensity 0.4
> lighting soft intensity 0.3
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-rebion-2.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel atoms
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> lighting soft intensity 0.3
> lighting soft intensity 0.2
> cartoon style protein width 0.5 thickness 0.5
> cartoon style protein width 1 thickness 0.5
> cartoon style protein width 1 thickness 0.7
> cartoon style protein width 2 thickness 0.7
> cartoon style protein width 1 thickness 0.7
> cartoon style protein width 5 thickness 0.7
> cartoon style protein width 1 thickness 0.7
> cartoon style protein width 2 thickness 0.7
> cartoon style protein width12 thick 0.7
Expected a keyword
> cartoon style protein width 1 thickness 0.7
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel atoms
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> cartoon style protein width 1 thickness 0.7
> cartoon style heliex width 2 thick 0.7
Expected an atoms specifier or a keyword
> cartoon style helix width 2 thickness 0.7
> cartoon style helix width 2.5 thickness 0.7
> cartoon style helix width 2.5 thickness 1
> cartoon style helix width 3 thickness 1
> cartoon style helix width 5 thickness 1
> cartoon style helix modeHelix tube radius 2.5
> cartoon style helix modeHelix tube radius 2
> cartoon style helix modeHelix tube radius 2.3
> cartoon style helix modeHelix tube radius 2.2
> graphics silhouettes true width 1.5
> graphics silhouettes true width 2
> graphics silhouettes true width 1.7
> lighting soft intensity 0.4
> lighting soft intensity 0.3
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-cylinders.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211004TZB/overall
> view-2-change color-atom-cylinders-2.tif" width 2924 height 2000 supersample
> 4 transparentBackground true
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel atoms
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel atoms
> select clear
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-change color overall map.cxs" includeMaps true
——— End of log from Wed Oct 6 21:40:30 2021 ———
opened ChimeraX session
Drag select of 1122 residues
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #2.1 models
> select clear
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #2.7 models
> show #2.7 models
> select clear
Drag select of 1.2 job059_postprocess.mrc 1 , 1.3 job059_postprocess.mrc 2 ,
1.4 job059_postprocess.mrc 3 , 1.5 job059_postprocess.mrc 4 , 1.6
job059_postprocess.mrc 5 , 1.7 job059_postprocess.mrc 6 , 1.8
job059_postprocess.mrc 7 , 1122 residues
Drag select of 1.2 job059_postprocess.mrc 1 , 1.3 job059_postprocess.mrc 2 ,
1.4 job059_postprocess.mrc 3 , 1.5 job059_postprocess.mrc 4 , 1.6
job059_postprocess.mrc 5 , 1.7 job059_postprocess.mrc 6 , 1.8
job059_postprocess.mrc 7 , 1122 residues
> select
12363 atoms, 13136 bonds, 1122 residues, 20 models selected
> coulombic sel
Coulombic values for 20210929_final_for chimeraX_.pdb_A SES surface #2.1:
minimum, -13.42, mean 1.84, maximum 12.71
Coulombic values for 20210929_final_for chimeraX_.pdb_B SES surface #2.2:
minimum, -8.84, mean 3.94, maximum 24.66
Coulombic values for 20210929_final_for chimeraX_.pdb_C SES surface #2.3:
minimum, -14.45, mean 2.28, maximum 16.17
Coulombic values for 20210929_final_for chimeraX_.pdb_D SES surface #2.4:
minimum, -12.45, mean 1.25, maximum 11.99
Coulombic values for 20210929_final_for chimeraX_.pdb_E SES surface #2.5:
minimum, -11.62, mean 1.63, maximum 12.32
Coulombic values for 20210929_final_for chimeraX_.pdb_F SES surface #2.6:
minimum, -8.12, mean 3.47, maximum 17.60
Coulombic values for 20210929_final_for chimeraX_.pdb_G SES surface #2.7:
minimum, -16.37, mean 2.12, maximum 15.08
Coulombic values for 20210929_final_for chimeraX_.pdb_H SES surface #2.8:
minimum, -12.68, mean 1.25, maximum 11.97
Coulombic values for 20210929_final_for chimeraX_.pdb_I SES surface #2.9:
minimum, -23.98, mean -14.26, maximum -3.09
Coulombic values for 20210929_final_for chimeraX_.pdb_J SES surface #2.10:
minimum, -25.82, mean -14.24, maximum -2.88
Coulombic values for 20210929_final_for chimeraX_.pdb_S SES surface #2.11:
minimum, -11.34, mean -0.79, maximum 9.56
Coulombic values for 20210929_final_for chimeraX_.pdb_U SES surface #2.12:
minimum, -12.75, mean -0.30, maximum 18.17
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!1 models
> select /S
205 atoms, 210 bonds, 23 residues, 1 model selected
> hide sel atoms
> hide sel surfaces
> select /U
593 atoms, 599 bonds, 74 residues, 1 model selected
> hide sel surfaces
> select /I
2819 atoms, 3165 bonds, 137 residues, 1 model selected
> hide sel surfaces
> select /J
2792 atoms, 3129 bonds, 137 residues, 1 model selected
> hide sel surfaces
> select clear
> lighting flat
> select /S:167
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /S:164
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /S:169
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel byhetero
> select /S:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select /C:65@CD1
1 atom, 1 residue, 1 model selected
> select clear
> cartoon style protein width 1 thickness 1
> cartoon style helix modeHelix tube radius 2
> cartoon style helix modeHelix tube radius 5
> cartoon style protein width 2 thickness 0.5
> cartoon style protein width 2 thickness 1
> cartoon style protein width 2 thickness 0.6
> graphics silhouettes true width 1.5
> graphics silhouettes true width 3
> graphics silhouettes true width 2
> graphics silhouettes true width 2.5
> graphics silhouettes true width 2.2
> lighting soft intensity 0.4
> lighting flat intensity 0.4
> lighting flat intensity 0.2
> lighting flat intensity 0.1
> ui tool show "Side View"
> view
> graphics silhouettes true width 1.5
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/electric acidic patch .tif" width 2924 height 2000 supersample 4
> transparentBackground true
> select
12363 atoms, 13136 bonds, 1122 residues, 20 models selected
> hide sel surfaces
> select clear
> lighting soft
> undo
> undo
> undo
> select clear
> undo
> undo
> undo
> undo
> undo
> undo
> view
> view
> select /S:169
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> lighting soft intensity 0.4
> lighting soft intensity 0.3
> select /D:47
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /D:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /C:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-W164 R167-H2B H2A.cxs" includeMaps true
——— End of log from Thu Oct 7 16:18:40 2021 ———
opened ChimeraX session
> select /S:164
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:167
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /D:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /D:47
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /I:-27
19 atoms, 20 bonds, 1 residue, 1 model selected
> select /S:169
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /S:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /B:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:93
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> hide sel atoms
> select /C:92
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /C:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> ui tool show "Side View"
> select /C:61
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /C:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /C:64
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> show sel atoms
> color sel byhetero
> select clear
> lighting soft intensity 0.4
> lighting soft direction 0,-1,-1
> lighting soft direction -1,-1,-1
> lighting soft direction -1,0,-1
> lighting soft direction -1,0,0
> lighting soft direction 1,0,0
> lighting soft direction 0,0,0
> lighting soft direction 0,0,0
> lighting soft direction 0,0,1
> lighting soft direction 1,0,1
> lighting soft direction 1,1,1
> lighting soft direction 1,1,1
> lighting soft direction 0,0,1
> lighting soft direction 0,2,3
> lighting soft direction -1,0,0
> lighting soft intensity 0.4
> lighting soft diection 1,0,0
Expected a keyword
> lighting soft direction 1,0,0
> lighting soft direction 0,1,0
> lighting soft direction 0,1,1
> lighting soft direction 0,1,1
> lighting soft direction 0,1,1
> lighting soft direction 0,1,1
> view
> view orient
> view orient
> lighting soft direction 0,1,0
> lighting soft intensity 1
> view
> cofr frontCenter
> ui tool show ViewDockX
No suitable models found for ViewDockX
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0，0,1
Unknown command: Lighting soft direction 0，0,1
> Lighting soft direction 0，0,1
Unknown command: Lighting soft direction 0，0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,1
Unknown command: Lighting soft direction 0,0,1
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> view orient
> lighting soft
> help help:user
> Lighting soft direction 0,0,0
Unknown command: Lighting soft direction 0,0,0
> Lighting shadows ture
Unknown command: Lighting shadows ture
> Lighting soft shadows ture
Unknown command: Lighting soft shadows ture
> Lighting soft shadows true
Unknown command: Lighting soft shadows true
> Lighting soft shadows true
Unknown command: Lighting soft shadows true
> Lighting shadows true
Unknown command: Lighting shadows true
> Lighting shadows true
Unknown command: Lighting shadows true
> Lighting shadows true
Unknown command: Lighting shadows true
> Lighting shadows true
Unknown command: Lighting shadows true
> Lighting shadows true
Unknown command: Lighting shadows true
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting direction 0,-1,-1
Unknown command: Lighting direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> lighting soft intensity 0.4
> lighting soft shadows ture
Invalid "shadows" argument: Expected true or false (or 1 or 0)
> lighting soft shadows true
> lighting soft shadows false
> lighting soft shadows true
> lighting soft shadows true
> lighting soft shadows true
> lighting soft intensity 0.5
> lighting soft shadows true
> lighting soft intensity 0.4
> lighting soft shadows false
> lighting soft shadows 5
Invalid "shadows" argument: Expected true or false (or 1 or 0)
> lighting soft shadows true
> lighting soft intensity 0.4
> lighting soft shadows true
> graphics silhouettes true width 1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> Lighting soft direction 0,-1,-1
Unknown command: Lighting soft direction 0,-1,-1
> lighting soft intensity 0.5
> lighting soft intensity 0.6
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-L168 R169-H2B H2A-2.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> graphics silhouettes true width 2
> graphics silhouettes true width 1
> view
> lighting soft direction 1,1,1
> lighting soft direction 1,1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-L168 R169-H2B H2A-3.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> lighting soft intensity 0.5
> lighting soft intensity 0.4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-L168 R169-H2B H2A-4.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> lighting soft direction 0,1,1
> lighting soft direction 0,1,-1
> lighting soft direction 0,1,-1
> lighting soft intensity 0.4
> lighting soft direction 0,-1,-1
> lighting soft intensity 0.4
> lighting soft ambientIntensity 1.8
> lighting soft ambientIntensity 1.5
> lighting soft intensity 0.4
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,1
> lighting soft intensity 0.4
> lighting soft intensity 0.6
> graphics silhouettes true width 1
> graphics silhouettes true width 2
> graphics silhouettes true width 1
> graphics silhouettes true width 0.5
> graphics silhouettes true width 0.8
> graphics silhouettes true width 01
> graphics silhouettes true width 1
> graphics silhouettes true width 0.5
> graphics silhouettes true width 1
> graphics silhouettes true width 1.2
> graphics silhouettes true width 1.5
> graphics silhouettes true width 1
> lighting soft ambientIntensity 1.8
> lighting soft ambientIntensity 1
> lighting soft ambientIntensity 1.5
> lighting soft ambientIntensity 110
> lighting soft ambientIntensity 10
> lighting soft ambientIntensity 4
> lighting soft ambientIntensity 2
> lighting soft ambientIntensity 1
> lighting soft ambientIntensity 2
> lighting soft ambientIntensity 1.5
> lighting soft
> lighting flat
> lighting soft
> lighting soft intensity 0.4
> lighting soft intensity 0.6
> lighting soft intensity 0.8
> lighting soft direction 1,0,0
> lighting soft direction 1,0,-1
> lighting soft direction -1,-1,-1
> view
> select clear
> view orient
> lighting soft intensity 0.4
> lighting soft diection 0,-1,-1
Expected a keyword
> lighting soft diection 0,-1,-1
Expected a keyword
> lighting soft diection -1,-1,-1
Expected a keyword
> lighting soft diection -1,-1,-1
Expected a keyword
> lighting soft diection -1,-1,-1
Expected a keyword
> lighting soft diection -1,-1,-1
Expected a keyword
> lighting soft direction 0,-1,-1
> lighting soft intensity 0.8
> lighting soft intensity 02
> lighting soft intensity 0.4
> lighting soft intensity 0.6
> view
> lighting soft direction 0,1,1
> lighting soft intensity 0.4
> lighting soft direction 0,-1,-1
> lighting soft intensity 0.4
> lighting soft direction 1,0,0
> lighting soft direction 1,1,1
> lighting soft direction 1,1,1
> lighting soft direction 1,1,1
> lighting soft intensity 0.4
> lighting soft direction 0,-1,1
> lighting soft intensity 0.4
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft direction 1,-1,-1
> lighting soft intensity 0.5
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-L168 R169-H2B H2A-5.tif" width 2924 height 2000 supersample 4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-L168R169-H2B H2A.cxs" includeMaps true
> show #!1 models
> hide #!1 models
> select /S:169
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:61
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:64
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:92
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> view
> show #!1 models
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true width 1
> graphics silhouettes true width 0.5
> graphics silhouettes true width 2
> graphics silhouettes true width 1
> lighting flat
> lighting flat
> lighting soft intensity 0.2
> lighting flat intensity 0.2
> lighting flat intensity 0.4
> lighting flat intensity 0.1
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-falt overall view.cxs" includeMaps true
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer
> color/20211005-falt overall view.tif" width 2924 height 2000 supersample 4
> transparentBackground true
> lighting soft
> hide #!1 models
> select /S:175
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /S:177
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /S:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> show sel atoms
> select /S:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /E:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select /C:81
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select /C:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select /C:89
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /C:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select /C:69
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 5 atom styles
> style sel stick
Changed 5 atom styles
> color sel byhetero
> select /C:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel byhetero
> select clear
> lighting flat intensity 0.4
> lighting flat intensity 0.2
> lighting flat intensity 0.1
> lighting soft intensity 0.1
> lighting soft intensity 0.4
> lighting soft intensity 0.5
> lighting soft intensity 0.6
> lighting soft intensity 0.4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/mid
> interact.tif" width 2924 height 2000 supersample 4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/mid
> interact-2.tif" width 2924 height 2000 supersample 4
> graphics silhouettes true width 1.5
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/mid
> interact-3.tif" width 2924 height 2000 supersample 4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/mid
> interact.cxs" includeMaps true
> select /S:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:177
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:175
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:89
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:81
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> view
> graphics silhouettes true width 1
> select /S:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> view sel
> show sel atoms
> undo
> select /S:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /S:182
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select /U:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /U:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /U:70
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /U:44
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /U:49
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> lighting soft intensity 0.4
> lighting soft intensity 0.2
> lighting soft direction 1,-1,-1
> select /U:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> lighting soft intensity 0.4
> lighting soft direction 0,-1,-1
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact.cxs" includeMaps true
——— End of log from Thu Oct 7 21:55:38 2021 ———
opened ChimeraX session
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-8.tif" width 2924 height 2000 supersample 4
> select /E:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-9.tif" width 2924 height 2000 supersample 4
> select /U:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-10.tif" width 2924 height 2000 supersample 4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-2-CHANGED.cxs" includeMaps true
——— End of log from Thu Oct 7 22:28:25 2021 ———
opened ChimeraX session
> select /E:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-11.tif" width 2924 height 2000 supersample 4
> save "D:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color/last
> interact-3.cxs" includeMaps true
——— End of log from Fri Oct 8 11:31:20 2021 ———
opened ChimeraX session
> view
> hide #!2 models
> show #!1 models
> hide #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!1.6 models
> lighting soft ambientIntensity 1.3
> lighting soft ambientIntensity 1.5
No map chosen to save
No map chosen to save
> ui tool show "Side View"
> hide #!1.8 models
> show #!1.8 models
> select #2.8
707 atoms, 91 residues, 1 model selected
> ~select #2.8
1 model selected
> show #!2 models
> hide #2.2 models
> hide #2.1 models
> hide #2.3 models
> hide #2.4 models
> hide #2.9 models
> hide #2.10 models
> hide #2.8 models
> hide #2.11 models
> hide #2.12 models
> hide #2.7 models
> hide #2.6 models
> hide #2.5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #2.2 models
> show #2.1 models
> select #2.1
801 atoms, 97 residues, 1 model selected
> select #2.3
825 atoms, 107 residues, 1 model selected
> ~select #2.3
1 model selected
> select #2.3
825 atoms, 107 residues, 1 model selected
> show #2.3 models
> show #2.4 models
> show #2.5 models
> show #2.9 models
> show #2.8 models
> show #2.7 models
> show #2.6 models
> show #2.10 models
> show #2.11 models
> show #2.12 models
> select clear
> hide #!2 models
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-UB-SSX1 map.tif" width 1343 height 874 supersample 4
> transparentBackground true
> show #!2 models
> lighting soft ambientIntensity 1.8
> select #1.2
4 models selected
> transparency #1.2.1 50
> transparency #1.2.1 40
> select #1.7
3 models selected
> transparency #1.7.1 40
> select #1.8
3 models selected
> transparency #1.8.1 40
> select clear
> select /U:49
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /E:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select /E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> volume #1.2 level 0.01539
> volume #1.7 level 0.01366
> volume #1.7 level 0.01088
> volume #1.8 level 0.01237
> show #!1.6 models
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-Ub形成碱性沟槽.cxs" includeMaps true
> hide #!1.6 models
> lighting soft ambientIntensity 1.5
> lighting soft ambientIntensity 1.6
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-UB-SSX1 完整map.tif" width 1343 height 874 supersample 4
> transparentBackground true
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-UB-SSX1 完整map.tif" width 2000 height 1302 supersample
> 3
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-UB-SSX1 完整map.tif" width 3000 height 1952 supersample
> 3
> lighting flat
> lighting full
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> hide #!1.8 models
> show #!1.8 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> color byhetero
> show surfaces
> hide #2.4 models
> show #2.4 models
> hide #2.4 models
> hide #2.3 models
> hide #2.12 models
> show #2.12 models
> hide #2.11 models
> show #2.11 models
> hide #2.11 models
> show #2.11 models
> hide #!2.10 models
> show #!2.10 models
> hide #!2.10 models
> hide #!2.9 models
> hide #2.5 models
> show #2.5 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide #2.11 models
> show #2.11 models
> hide #2.12 models
> show #2.12 models
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> hide #2.7 models
> hide #2.6 models
> lighting soft
> lighting flat
> hide #2.5 models
> show #2.5 models
> hide #2.12 models
> show #2.12 models
> hide #2.11 models
> show #2.11 models
> hide #2.11 models
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-Ub形成碱性沟槽-电性图.cxs" includeMaps true
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting flat
> hide #!1.8 models
> show #!1.8 models
> hide #!1.8 models
> show #!1.8 models
> hide #!1.7 models
> hide #!1.2 models
> volume #1.8 style mesh
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> graphics silhouettes false
> lighting full
> lighting soft
> hide #!1.8 models
> lighting soft
> graphics silhouettes true
> lighting soft ambientIntensity 1.6
> lighting soft ambientIntensity 2
> graphics silhouettes false
> lighting soft ambientIntensity 1
> lighting soft ambientIntensity 1.5
> lighting simple
> lighting flat
> lighting full
> lighting soft
> lighting full
> lighting soft ambientIntensity 2
> lighting soft intensity 0.4
> lighting soft intensity 0.6
> lighting soft intensity 0.8
> lighting soft
> lighting soft intensity 1
> lighting soft intensity 0.6
> hide #!2.12 models
> show #!2.12 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.12 models
> show #!2.12 models
> hide #!2.5 models
> show #!2.5 models
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-Ub形成碱性沟槽-电性图.cxs" includeMaps true
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-UB碱性沟槽电性图.tif" width 3000 height 1952 supersample 4
> transparentBackground true
> lighting flat
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/H3-UB碱性沟槽电性图-2-flat模式.tif" width 3000 height 1952
> supersample 4 transparentBackground true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide atoms
> show cartoons
> hide cartoons
> hide surfaces
> show cartoons
> show #!1.8 models
> hide #!1.8 models
> select /E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /E:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select /E:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /E:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select /S:182
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select /S:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select /U:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select /U:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /E:51
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /E:50
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select /E:51
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> undo
> undo
> undo
> select /E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select clear
Drag select of 10 atoms, 17 residues, 8 bonds
> show sel cartoons
> select clear
> select clear
> select /E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /E:51
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 19 atoms, 25 residues, 17 bonds
> show sel cartoons
> show sel cartoons
> select clear
> select /E:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!2.5 models
> show #!2.5 models
> hide #!2.5 models
> show #!2.5 models
> show #2.4 models
> hide #2.4 models
> hide #!2 models
> show #!2 models
> select /S:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /S:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /S:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /S:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /E:51
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /E
783 atoms, 794 bonds, 95 residues, 1 model selected
> show sel cartoons
> select clear
> lighting soft
> lighting soft intensity 1
> lighting shadows true
> lighting shadows false
> select clear
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/原子模型.tif" width 3000 height 1952 supersample 4
> show #!1.8 models
> volume #1.8 level 0.009933
> volume #1.8 level 0.01102
> hide #!2.5 models
> show #!2.5 models
> hide #!1.8 models
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/原子模型-2.tif" width 3000 height 1952 supersample 4
> transparentBackground true
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/原子模型.cxs" includeMaps true
> lighting soft intensity 0.8
> lighting soft intensity 0.6
> lighting soft intensity 0.5
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/原子模型-2.tif" width 3000 height 1952 supersample 4
> transparentBackground true
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/原子模型.tif" width 3000 height 1952 supersample 4
> transparentBackground true
> show #!1.8 models
> open E:/Documents/Map/SSX1/job054_run_ct17_class001.mrc
Opened job054_run_ct17_class001.mrc as #3, grid size 256,256,256, pixel 1.07,
shown at level 0.003, step 1, values float32
> volume #3 level 0.007632
> hide #!1.8 models
> save "E:/Documents/Map/SSX1/SSX1 Model building/20211005-changer color-最终配色-
> 结构作图/6-H3和Ub形成碱性沟槽/post结构+refine结构.cxs" includeMaps true
——— End of log from Wed Feb 16 09:51:13 2022 ———
opened ChimeraX session
> hide #!3 models
> view
> open "E:/Documents/Map/SSX1/SSX1 Model building/Wincoot PDB
> Save/20220216_TZB_reversed_D182P183E184.pdb"
Summary of feedback from opening E:/Documents/Map/SSX1/SSX1 Model
building/Wincoot PDB Save/20220216_TZB_reversed_D182P183E184.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.009 0.093 13141
Ignored bad PDB record found on line 22
ANGLE : 0.885 11.471 18915
Ignored bad PDB record found on line 23
CHIRALITY : 0.050 0.241 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.006 0.054 1443
17 messages similar to the above omitted
End residue of secondary structure not found: HELIX 32 32 THR H 90 LEU H 102
01 1
Start residue of secondary structure not found: SHEET 9 9 9 GLY D 50 ILE D 51
0
Start residue of secondary structure not found: SHEET 10 1010 THR D 85 ILE D
86 0
Start residue of secondary structure not found: SHEET 19 1919 GLY H 50 ILE H
51 0
Start residue of secondary structure not found: SHEET 20 2020 THR H 85 ILE H
86 0
Chain information for 20220216_TZB_reversed_D182P183E184.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> select #5
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> hide #!2 models
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #5 models
> show #5 models
> show #2.1 models
> hide #2.1 models
> hide #2.5 models
> hide #!2 models
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> hide #5 models
> show #2.1 models
> show #2.2 models
> show #2.3 models
> show #2.4 models
> show #2.5 models
> show #2.6 models
> show #2.7 models
> show #2.8 models
> show #!2.10 models
> show #2.11 models
> show #!2.9 models
> hide #!2 models
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> hide #2.7 models
> hide #2.8 models
> hide #!2.9 models
> hide #!2.10 models
> hide #2.11 models
> hide #2.12 models
> show #5 models
> show #!2 models
> hide #!2 models
> select #5/I
2822 atoms, 3168 bonds, 137 residues, 1 model selected
> color sel dark gray
> select #5/J
2795 atoms, 3132 bonds, 137 residues, 1 model selected
> color sel dark gray
> show #!2 models
> hide #!2 models
> select #5/U
593 atoms, 599 bonds, 74 residues, 1 model selected
> ui tool show "Color Actions"
> color sel yellow
> select #5/S
205 atoms, 210 bonds, 23 residues, 1 model selected
> color sel magenta
> select #5/A
801 atoms, 813 bonds, 97 residues, 1 model selected
> color sel dodger blue
> select #5/E
783 atoms, 794 bonds, 95 residues, 1 model selected
> color sel dodger blue
> select #5/D
707 atoms, 718 bonds, 91 residues, 1 model selected
> color sel light salmon
> color sel salmon
> lighting flat
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color sel wheat
> hide #!2 models
> color sel burly wood
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #5/B
668 atoms, 675 bonds, 83 residues, 1 model selected
> show #!2 models
> hide #!2 models
> color sel light coral
> select #5/C
825 atoms, 835 bonds, 107 residues, 1 model selected
> color sel medium aquamarine
> color sel medium sea green
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #5/D
707 atoms, 718 bonds, 91 residues, 1 model selected
> select #5/F
648 atoms, 655 bonds, 81 residues, 1 model selected
> show #!2 models
> hide #!2 models
> color sel salmon
> select #5/G
815 atoms, 825 bonds, 106 residues, 1 model selected
> show #!2 models
> hide #!2 models
> color sel medium sea green
> color sel forest green
> color sel lime green
> color sel lime
> color sel yellow green
> color sel sea green
> color sel medium aquamarine
> color sel medium sea green
> select #5/H
707 atoms, 718 bonds, 91 residues, 1 model selected
> show #!2 models
> hide #!2 models
> color sel wheat
> color sel burly wood
> select clear
> hide #5 models
> show #5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1.8 models
> hide #!1.8 models
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/20220216-修改了D182-E184的密度/最终map+原子模型.cxs" includeMaps true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> view
> view
> show #!1.8 models
> hide #!1.8 models
> select #5/S:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #5/S:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel byhetero
> select #5/I:4
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> color sel byhetero
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select #5/S:181@CA
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> hide sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> hide sel atoms
> hide sel cartoons
> hide sel cartoons
> hide sel cartoons
> hide sel cartoons
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select clear
> select #5/S:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> select clear
> select #5/S:182
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #5/E:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #5/E:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> select #5/U:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #5/U:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> show #!1.8 models
> show #!1.7 models
> show #!1.2 models
> volume #1.7 style mesh
> volume #1.2
> volume #1.2 style mesh
> volume #1.2 style surface
> volume #1.7 style surface
> select clear
> hide #!1.2 models
> hide #!1.7 models
> show #!1.7 models
> hide #!1.7 models
> hide #!1.8 models
> ui tool show "Side View"
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/20220216-修改了D182-E184的密度/原子模型.cxs" includeMaps true
——— End of log from Wed Feb 16 12:33:54 2022 ———
opened ChimeraX session
> cartoon style protein thickness 0.6
> select #5/U
593 atoms, 599 bonds, 74 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/20220216-修改了D182-E184的密度/最终map+原子模型.cxs" includeMaps true
> select clear
> cartoon style protein thickness 0.5
> select #5/U:72@NH1
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> color sel byhetero
> select #5/U:42@CB
1 atom, 1 residue, 1 model selected
> color sel byhetero
> style sel stick
Changed 1 atom style
> show sel atoms
> select clear
> select #5/U:42@CB
1 atom, 1 residue, 1 model selected
> color sel byhetero
> color sel byhetero
> style sel stick
Changed 1 atom style
> style sel stick
Changed 1 atom style
> style sel stick
Changed 1 atom style
> select #5/U:42
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #5/U:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/20220216-修改了D182-E184的密度/最终map+原子模型.cxs" includeMaps true
——— End of log from Wed Feb 16 19:42:15 2022 ———
opened ChimeraX session
> view orient
> select #5/U:44
8 atoms, 7 bonds, 1 residue, 1 model selected
> open 5KGF
Summary of feedback from opening 5KGF fetched from pdb
---
notes | Fetching compressed mmCIF 5kgf from
http://files.rcsb.org/download/5kgf.cif
Fetching CCD M2L from http://ligand-expo.rcsb.org/reports/M/M2L/M2L.cif
5kgf title:
Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome,
at 4.5 A resolution [more info...]
Chain information for 5kgf #6
---
Chain | Description
A E | Histone H3.2
B F | Histone H4
C G | Histone H2A type 1
D H | Histone H2B type 1-C/E/F/G/I
I | DNA (145-mer)
J | DNA (145-mer)
K L | Tumor suppressor p53-binding protein 1
M O | Ubiquitin
> select #6
13782 atoms, 14595 bonds, 327 pseudobonds, 1276 residues, 2 models selected
> ~select #6
Nothing selected
> select #6
13782 atoms, 14595 bonds, 327 pseudobonds, 1276 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> select clear
> select #6
13782 atoms, 14595 bonds, 327 pseudobonds, 1276 residues, 2 models selected
> select clear
> ui tool show Matchmaker
> matchmaker #6/O to #5/U pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20220216_TZB_reversed_D182P183E184.pdb, chain U (#5) with 5kgf,
chain O (#6), sequence alignment score = 312.3
RMSD between 60 pruned atom pairs is 1.135 angstroms; (across all 74 pairs:
1.703)
> hide #!1 models
> hide #!6 models
> show #!6 models
> hide #5 models
> select #6/O
601 atoms, 607 bonds, 76 residues, 1 model selected
> color sel yellow
> select clear
> select #6/K
166 atoms, 165 bonds, 21 residues, 1 model selected
> color sel red
> select clear
> show #!1.8 models
> hide #!1.8 models
> show #5 models
> hide #!6 models
> show #!6 models
> hide #5 models
> select #6/O:74
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> select #6/O:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/SSX1和其他reader结构比较/53BP1-SSX1.cxs" includeMaps true
> hide #!6 models
> show #5 models
> select #5/U:69
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
Drag select of 1 residues
> show sel atoms
> style sel stick
Changed 8 atom styles
> select clear
> view orient
> show #!6 models
> hide #5 models
> select #6/O:68
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> color sel byhetero
> select #6/O:44
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> select #6/O:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select clear
> select #6/O:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #6/O:74
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #6/H:105
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #6/H:106
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> color sel byhetero
> select clear
> select #6/H:119
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select clear
> open 7E8I
Summary of feedback from opening 7E8I fetched from pdb
---
note | Fetching compressed mmCIF 7e8i from
http://files.rcsb.org/download/7e8i.cif
7e8i title:
Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin
[more info...]
Chain information for 7e8i #7
---
Chain | Description
A E | Histone H3
B F | Histone H4
C G | Histone H2A
D H | Histone H2B 1.1
I | DNA (145-mer)
J | DNA (145-mer)
K | BRCA1-associated RING domain protein 1
L | Polyubiquitin-B
> select #7
15271 atoms, 16145 bonds, 354 pseudobonds, 1466 residues, 3 models selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> select clear
> ui tool show Matchmaker
> matchmaker #7/L to #5/U pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20220216_TZB_reversed_D182P183E184.pdb, chain U (#5) with 7e8i,
chain L (#7), sequence alignment score = 333.3
RMSD between 65 pruned atom pairs is 0.993 angstroms; (across all 74 pairs:
1.683)
> hide #!6 models
> show #!1.8 models
> hide #!1.8 models
> show #5 models
> select #7/K
2653 atoms, 2717 bonds, 1 pseudobond, 334 residues, 2 models selected
> select clear
> select #7/L:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> select clear
> hide #!7 models
> select #5/U:36
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #5/J:-8
19 atoms, 20 bonds, 1 residue, 1 model selected
> show #!7 models
> select #7/L:64
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> color sel red
> select #7/L:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #7/L:62
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> color sel red
> select clear
> hide #!7 models
> hide #5 models
> show #5 models
> select #5/U
593 atoms, 599 bonds, 74 residues, 1 model selected
> show sel surfaces
> color (#!5 & sel) yellow
> select clear
> select #5/U:44@CD1
1 atom, 1 residue, 1 model selected
> color (#!5 & sel) blue
> select clear
> select #5/U:70@CG2
1 atom, 1 residue, 1 model selected
> color (#!5 & sel) blue
> select clear
> select #5/U:70@CB
1 atom, 1 residue, 1 model selected
> color (#!5 & sel) blue
> select clear
> show #!6 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> open 6O96
Summary of feedback from opening 6O96 fetched from pdb
---
warnings | Unknown polymer entity '9' near line 17696
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
notes | Fetching compressed mmCIF 6o96 from
http://files.rcsb.org/download/6o96.cif
Fetching CCD SAH from http://ligand-expo.rcsb.org/reports/S/SAH/SAH.cif
6o96 title:
Dot1L bound to the H2BK120 Ubiquitinated nucleosome [more info...]
Chain information for 6o96 #8
---
Chain | Description
A E | Histone H3.2
B F | Histone H4
C G | Histone H2A
D H | Histone H2B 1.1
I | DNA (146-mer)
J | DNA (146-mer)
K | Histone-lysine N-methyltransferase, H3 lysine-79 specific
L | Polyubiquitin-B
> select #8
15194 atoms, 16075 bonds, 379 pseudobonds, 1454 residues, 3 models selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,60.773,0,1,0,51.544,0,0,1,30.722
> select clear
> matchmaker #8/L to #5/U pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20220216_TZB_reversed_D182P183E184.pdb, chain U (#5) with 6o96,
chain L (#8), sequence alignment score = 318.3
RMSD between 59 pruned atom pairs is 1.093 angstroms; (across all 74 pairs:
1.685)
> hide #!5 models
> show #!5 models
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/SSX1和其他reader结构比较/53BP1-Dot1-BARD1-SSX1.cxs" includeMaps true
> hide #!8 models
> open 6WKR
Summary of feedback from opening 6WKR fetched from pdb
---
warnings | Unknown polymer entity '14' near line 35601
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
notes | Fetching compressed mmCIF 6wkr from
http://files.rcsb.org/download/6wkr.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD M3L from http://ligand-expo.rcsb.org/reports/M/M3L/M3L.cif
6wkr title:
PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome [more info...]
Chain information for 6wkr #9
---
Chain | Description
A | Polycomb protein SUZ12
B E | Protein Jumonji
C | Histone-lysine N-methyltransferase EZH2
F T | Ubiquitin
H | DNA (314-mer)
I O | Histone H3.2
J Q | Histone H4
K R | Histone H2A type 1
L | Polycomb protein EED
M S | Histone H2B 1.1
N | Histone-binding protein RBBP4
P | Zinc finger protein AEBP2
Non-standard residues in 6wkr #9
---
MG — magnesium ion
ZN — zinc ion
> select #9
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> select clear
> select clear
> select #9/C
4304 atoms, 4415 bonds, 2 pseudobonds, 607 residues, 2 models selected
> delete atoms (#!9 & sel)
> delete bonds (#!9 & sel)
> select #8/K
2622 atoms, 2689 bonds, 1 pseudobond, 322 residues, 2 models selected
> select #9/L
2874 atoms, 2949 bonds, 362 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #9/A
3341 atoms, 3419 bonds, 7 pseudobonds, 440 residues, 2 models selected
> delete atoms (#!9 & sel)
> delete bonds (#!9 & sel)
> select #9/N
3080 atoms, 3165 bonds, 1 pseudobond, 395 residues, 2 models selected
> delete atoms (#!9 & sel)
> delete bonds (#!9 & sel)
> select #8/K
2622 atoms, 2689 bonds, 1 pseudobond, 322 residues, 2 models selected
> select clear
Drag select of 167 residues, 1 pseudobonds
> delete atoms (#!9 & sel)
> delete bonds (#!9 & sel)
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/SSX1和其他reader结构比较/53BP1-Dot1-BARD1-SSX1-JARID2.cxs" includeMaps
> true
> select #5/U
593 atoms, 599 bonds, 74 residues, 1 model selected
> hide sel surfaces
> select clear
> select #5/U:44
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> select #5/U:44@CG2
1 atom, 1 residue, 1 model selected
> select add #5/S:180@CG2
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #5/U:44@CG2 #5/S:180@CG2
Distance between 20220216_TZB_reversed_D182P183E184.pdb #5/U ILE 44 CG2 and /S
ILE 180 CG2: 4.130Å
> select clear
> select #5/S:180
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> select clear
> select #5/U:68
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> color sel byhetero
> select clear
> select #5/U:68@CE1
1 atom, 1 residue, 1 model selected
> select add #5/S:180@CD1
2 atoms, 2 residues, 2 models selected
> distance #5/U:68@CE1 #5/S:180@CD1
Distance between 20220216_TZB_reversed_D182P183E184.pdb #5/U HIS 68 CE1 and /S
ILE 180 CD1: 4.196Å
> select clear
> select clear
> select #5/U
593 atoms, 599 bonds, 74 residues, 1 model selected
> show sel surfaces
> select #5/U
593 atoms, 599 bonds, 74 residues, 1 model selected
> hide sel surfaces
> select clear
> select #5/U:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #5/U:8@CD1
1 atom, 1 residue, 1 model selected
> select #5/U:8@CD2
1 atom, 1 residue, 1 model selected
> view matrix models #5,1,0,0,13.989,0,1,0,2.1868,0,0,1,-0.37494
> select #5/U:8@CA
1 atom, 1 residue, 1 model selected
> select #5/U:8@CB
1 atom, 1 residue, 1 model selected
> select #5/U:9
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/U:8@CB
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #5/U:8@CD1
1 atom, 1 residue, 1 model selected
> select #5/U:8@CG
1 atom, 1 residue, 1 model selected
> view matrix models #5,1,0,0,23.487,0,1,0,-5.434,0,0,1,-2.5084
> select #5/U:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/U:8@CA
1 atom, 1 residue, 1 model selected
> select #5/U:8@CB
1 atom, 1 residue, 1 model selected
> select #5/I:-54
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #5/U:9
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/U:9
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/U:8@CB
1 atom, 1 residue, 1 model selected
> select #5/U:8@CG
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #5/U:8@CB
1 atom, 1 residue, 1 model selected
> select #5/U:8@CB
1 atom, 1 residue, 1 model selected
> select #5/U:7
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/U:8@CB
1 atom, 1 residue, 1 model selected
> view matrix models #5,1,0,0,19.724,0,1,0,-29.177,0,0,1,6.0333
> select #5/U:8@CA
1 atom, 1 residue, 1 model selected
> select #5/U:9
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/U:8@CA
1 atom, 1 residue, 1 model selected
> select add #5/U:8@CB
2 atoms, 1 residue, 2 models selected
> select add #5/U:8@CG
3 atoms, 1 residue, 2 models selected
> select add #5/U:8@CD2
4 atoms, 1 residue, 2 models selected
> select add #5/U:8@CD1
5 atoms, 1 residue, 2 models selected
> hide sel surfaces
> hide sel surfaces
> hide sel surfaces
> hide sel surfaces
> style sel stick
Changed 5 atom styles
> style sel stick
Changed 5 atom styles
> style sel stick
Changed 5 atom styles
> select clear
> matchmaker #9/I to #5/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20220216_TZB_reversed_D182P183E184.pdb, chain A (#5) with 6wkr,
chain I (#9), sequence alignment score = 458.5
RMSD between 97 pruned atom pairs is 0.677 angstroms; (across all 97 pairs:
0.677)
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/SSX1和其他reader结构比较/53BP1-Dot1-BARD1-SSX1-JARID2.cxs" includeMaps
> true
——— End of log from Mon Mar 7 21:25:31 2022 ———
opened ChimeraX session
> select #9/F
603 atoms, 609 bonds, 76 residues, 1 model selected
> select #1
23 models selected
> ~select #1
Nothing selected
> select #1
23 models selected
> ~select #1
Nothing selected
> select #2
12363 atoms, 13136 bonds, 1122 residues, 3 models selected
> ~select #2
12 models selected
> select #3
2 models selected
> ~select #3
Nothing selected
> select #4
2 models selected
> ~select #4
Nothing selected
> select #5
12369 atoms, 13142 bonds, 2 pseudobonds, 1122 residues, 2 models selected
> ~select #5
1 model selected
> hide #!5 models
> show #!5 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> hide #10.1 models
No visible atoms or bonds selected
> select clear
> select clear
> ui tool show Matchmaker
> ui tool show Distances
> select clear
> hide #!9 models
> show #!9 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #9/F
603 atoms, 609 bonds, 76 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/P
427 atoms, 433 bonds, 1 pseudobond, 69 residues, 2 models selected
> delete atoms (#!9 & sel)
> delete bonds (#!9 & sel)
> select clear
> show #!2 models
> hide #!2 models
> show #!3 models
> ui tool show Matchmaker
> hide #!3 models
> show #!3 models
> hide #!5 models
> hide #!3 models
> show #!5 models
Drag select of 75 atoms, 2340 residues, 64 bonds, 1 pseudobonds
> color (#!5,9 & sel) light gray
> select clear
> select #5/U
593 atoms, 599 bonds, 74 residues, 1 model selected
> color (#!5 & sel) yellow
> select clear
> select #5/S
205 atoms, 210 bonds, 23 residues, 1 model selected
> color sel magenta
> select clear
> select #9/T
604 atoms, 610 bonds, 76 residues, 1 model selected
> color sel orange
> select clear
> select #9/E
203 atoms, 203 bonds, 35 residues, 1 model selected
> color sel cyan
> select clear
> select #5/S
205 atoms, 210 bonds, 23 residues, 1 model selected
> hide sel atoms
> select #5/U
593 atoms, 599 bonds, 74 residues, 1 model selected
> hide sel atoms
> select clear
> lighting soft
> lighting soft intensity 0.4
> cartoon style protein width 0.5 thickness 0.5
> cartoon style protein width 0.5 thickness 1
> cartoon style protein width 1 thickness 0.5
> cartoon style protein width 1.5 thickness 0.5
> undo
> undo
> undo
> undo
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> lighting soft
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> lighting soft intensity 0.4
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/SSX1和其他reader结构比较/SSX1-JARID2.cxs" includeMaps true
——— End of log from Sat Apr 2 14:08:23 2022 ———
opened ChimeraX session
> hide #!1 models
> hide #!5 models
> select #9/T
604 atoms, 610 bonds, 76 residues, 1 model selected
> show sel surfaces
> undo
> undo
> hide #!9 surfaces
> select #9/T
604 atoms, 610 bonds, 76 residues, 1 model selected
> show sel surfaces
> hide #9.1 models
> show #9.1 models
> hide #!9 models
> show #!9 models
> select clear
> select #9/T
604 atoms, 610 bonds, 76 residues, 1 model selected
> hide sel surfaces
> select clear
> select #9/T:44
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!9 & sel) medium blue
> select #9/T:68
10 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!9 & sel) medium blue
> select clear
> select #9/T:70
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!9 & sel) medium blue
> select #9/T:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!9 & sel) medium blue
> select clear
> select #9/T
604 atoms, 610 bonds, 76 residues, 1 model selected
> show sel surfaces
> select clear
> ui tool show "Side View"
> save "E:/Documents/Map/SSX1/SSX1 Model
> building/SSX1和其他reader结构比较/SSX1-JARID2/JARID2-Ub surface.cxs" includeMaps
> true
——— End of log from Mon Apr 11 16:01:38 2022 ———
opened ChimeraX session
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!10 models
> hide #!9 models
> hide #!10 models
> show #!9 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> select #9
13457 atoms, 14327 bonds, 459 pseudobonds, 1218 residues, 3 models selected
> show sel cartoons
> show sel cartoons
> show sel cartoons
> show sel cartoons
> open 6wkr
Summary of feedback from opening 6wkr fetched from pdb
---
warnings | Unknown polymer entity '14' near line 35601
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
6wkr title:
PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome [more info...]
Chain information for 6wkr #11
---
Chain | Description
A | Polycomb protein SUZ12
B E | Protein Jumonji
C | Histone-lysine N-methyltransferase EZH2
F T | Ubiquitin
H | DNA (314-mer)
I O | Histone H3.2
J Q | Histone H4
K R | Histone H2A type 1
L | Polycomb protein EED
M S | Histone H2B 1.1
N | Histone-binding protein RBBP4
P | Zinc finger protein AEBP2
Non-standard residues in 6wkr #11
---
MG — magnesium ion
ZN — zinc ion
> hide atoms
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> ~select #11
Nothing selected
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> show sel cartoons
> select clear
> select #11 /c,n,l
10258 atoms, 10529 bonds, 3 pseudobonds, 1364 residues, 2 models selected
> hide sel cartoons
> select #11 /c,n,l,a
13599 atoms, 13948 bonds, 10 pseudobonds, 1804 residues, 2 models selected
> hide sel cartoons
> select #11 /c,n,l,a,p,b
15236 atoms, 15618 bonds, 12 pseudobonds, 2040 residues, 2 models selected
> select #11 /c,n,l,a,b
13889 atoms, 14242 bonds, 11 pseudobonds, 1846 residues, 2 models selected
> hide sel cartoons
> select up
29296 atoms, 30554 bonds, 13 pseudobonds, 3334 residues, 2 models selected
> select #11 /p:170-295
929 atoms, 951 bonds, 126 residues, 1 model selected
> hide sel cartoons
> select clear
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!9 models
> select #11 /t,e
807 atoms, 813 bonds, 111 residues, 1 model selected
> hide sel cartoons
> select clear
> show #!9 models
> hide #!9 models
> show #!9 models
> select clear
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> ui mousemode right "translate selected models"
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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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.
> view matrix models #11,1,0,0,-66.485,0,1,0,-108.97,0,0,1,-42.153
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 114, in _changes_handler
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
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.
> ~select #11
Nothing selected
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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.
> view matrix models #11,1,0,0,-61.828,0,1,0,-110.2,0,0,1,-28.54
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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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.
> view matrix models #11,1,0,0,-124.14,0,1,0,-124.46,0,0,1,-173.17
> hide #!9 models
> ~select #11
Nothing selected
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> ~select #11
Nothing selected
> select clear
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> show sel surfaces
> hide sel surfaces
> select clear
> view
Drag select of 1250 residues, 1 pseudobonds
> show sel surfaces
> select clear
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> ui tool show "Color Actions"
> color sel light gray
> color (#!11 & sel) #d3d3d3ff
> select clear
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> transparency (#!11 & sel) 50
> select clear
> hide #!11 models
> show #!11 models
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> transparency (#!11 & sel) 30
> select clear
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> select clear
> select #11 /f
603 atoms, 609 bonds, 76 residues, 1 model selected
> color (#!11 & sel) #ffceb9ff
> select clear
> select #11 /p
1347 atoms, 1376 bonds, 1 pseudobond, 194 residues, 2 models selected
> color (#!11 & sel) #ead2e6ff
> hide sel surfaces
> select clear
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!9 models
> show #!11 models
> hide #!9 models
> select #11 /f:8,70,68,44
33 atoms, 30 bonds, 4 residues, 1 model selected
> select #11 /f:71,73,36
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> ~select #11
18 models selected
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> lighting soft
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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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.
> view matrix models #11,1,0,0,-127.77,0,1,0,-116.02,0,0,1,-185.3
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 114, in _changes_handler
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
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.
> select #11 /f:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11 /f:61,60,62
25 atoms, 24 bonds, 3 residues, 1 model selected
> color (#!11 & sel) medium blue
> select clear
> lighting soft intensity 0.4
> select clear
> select #11
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 3 models selected
> hide sel surfaces
> select up
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 21 models selected
> select up
29296 atoms, 30554 bonds, 471 pseudobonds, 3334 residues, 21 models selected
> select #11 /f
603 atoms, 609 bonds, 76 residues, 1 model selected
> show sel surfaces
> select clear
> select #11 /f
603 atoms, 609 bonds, 76 residues, 1 model selected
> color (#!11 & sel) byelement
> color (#!11 & sel) #00c6cfff
> color (#!11 & sel) byelement
> color (#!11 & sel) #7fd1aeff
> select #11 /p
1347 atoms, 1376 bonds, 1 pseudobond, 194 residues, 2 models selected
> color (#!11 & sel) #00c6cfff
> select #11 /f:62,60
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #11 /f:62,60,61
25 atoms, 24 bonds, 3 residues, 1 model selected
> color (#!11 & sel) medium blue
> select clear
> save "F:/Documents/Map/SSX1/SSX1 Model
> building/SSX1和其他reader结构比较/SSX1-AEBP2/AEBP2.cxs" includeMaps true
> save "F:/Documents/Map/SSX1/SSX1 Model
> building/SSX1和其他reader结构比较/SSX1-AEBP2/AEBP2.png" width 4640 height 3000
> supersample 4
> select #11 /p
1347 atoms, 1376 bonds, 1 pseudobond, 194 residues, 2 models selected
> color (#!11 & sel) #8685efff
> select clear
> save "F:/Documents/Map/SSX1/SSX1 Model
> building/SSX1和其他reader结构比较/SSX1-AEBP2/AEBP2.png" width 4640 height 3000
> supersample 4
> save "F:/Documents/Map/SSX1/SSX1 Model
> building/SSX1和其他reader结构比较/SSX1-AEBP2/AEBP2.cxs" includeMaps true
——— End of log from Wed Nov 9 14:32:51 2022 ———
opened ChimeraX session
> hide #!11 models
> show #!11 models
> open "F:/Documents/Map/SSX1/SSX1 Model building/Wincoot PDB
> Save/202206/202200807_SSX1_119Ub_Second_phenix_real_space_refined-
> coot-0.pdb"
Summary of feedback from opening F:/Documents/Map/SSX1/SSX1 Model
building/Wincoot PDB
Save/202206/202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb
---
warnings | Ignored bad PDB record found on line 20
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 21
BOND : 0.010 0.091 13142
Ignored bad PDB record found on line 22
ANGLE : 0.877 18.214 18918
Ignored bad PDB record found on line 23
CHIRALITY : 0.051 0.207 2159
Ignored bad PDB record found on line 24
PLANARITY : 0.005 0.046 1444
16 messages similar to the above omitted
Chain information for 202200807_SSX1_119Ub_Second_phenix_real_space_refined-
coot-0.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
D H | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
S | No description available
U | No description available
> select #12
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> select #12
12369 atoms, 13142 bonds, 1122 residues, 1 model selected
> select clear
> ui tool show Matchmaker
> hide #!11 models
> show #!11 models
> matchmaker #9/S to #12/D pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb,
chain D (#12) with 6wkr, chain S (#9), sequence alignment score = 444.8
RMSD between 90 pruned atom pairs is 0.548 angstroms; (across all 91 pairs:
0.593)
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 114, in _changes_handler
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
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.
> matchmaker #9/S to #12/D pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb,
chain D (#12) with 6wkr, chain S (#9), sequence alignment score = 444.8
RMSD between 90 pruned atom pairs is 0.548 angstroms; (across all 91 pairs:
0.593)
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 114, in _changes_handler
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
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.
> matchmaker #9/S to #12/D pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb,
chain D (#12) with 6wkr, chain S (#9), sequence alignment score = 444.8
RMSD between 90 pruned atom pairs is 0.548 angstroms; (across all 91 pairs:
0.593)
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 114, in _changes_handler
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
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.
> matchmaker #9/S to #12/D pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb,
chain D (#12) with 6wkr, chain S (#9), sequence alignment score = 444.8
RMSD between 90 pruned atom pairs is 0.548 angstroms; (across all 91 pairs:
0.593)
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 114, in _changes_handler
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
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.
> hide #12 models
> show #12 models
> show #!9 models
> hide #!11 models
> ui mousemode right "translate selected models"
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!9 models
> matchmaker #11/S to #12/D pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 202200807_SSX1_119Ub_Second_phenix_real_space_refined-coot-0.pdb,
chain D (#12) with 6wkr, chain S (#11), sequence alignment score = 444.8
RMSD between 90 pruned atom pairs is 0.548 angstroms; (across all 91 pairs:
0.593)
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 114, in _changes_handler
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
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.
Drag select of 133 residues
> select clear
> hide #!11 models
> show #!11 models
> select #11 /f
603 atoms, 609 bonds, 76 residues, 1 model selected
> hide sel surfaces
> select clear
> select #11/F:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/F:28
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> select clear
> select #12/U:28
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> select clear
> select #12/U:28
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/U:28@CB
1 atom, 1 residue, 1 model selected
> select clear
> select add #12/U:28@CB
1 atom, 1 residue, 1 model selected
> select add #11/F:2
10 atoms, 8 bonds, 2 residues, 2 models selected
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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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\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 114, in _changes_handler
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
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.
> view matrix models
> #11,0.64832,-0.383,0.65802,-42.611,-0.53375,0.3877,0.75154,2.2962,-0.54295,-0.83845,0.046929,495.23,#12,1,0,0,1.1574,0,1,0,-2.9623,0,0,1,0.50472
> select clear
> select add #11/F:28@CB
1 atom, 1 residue, 1 model selected
> select add #12/U:28@CB
2 atoms, 2 residues, 3 models selected
> select clear
> select add #12/U:28@CB
1 atom, 1 residue, 1 model selected
> select add #11/F:28@CB
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 #12/U:28@CB #11/F:28@CB
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.
> distance #12/U:28@CB #11/F:28@CB
Distance already exists; modify distance properties with 'distance style'
> distance #12/U:28@CB #11/F:28@CB
Distance already exists; modify distance properties with 'distance style'
> distance #12/U:28@CB #11/F:28@CB
Distance already exists; modify distance properties with 'distance style'
> distance #12/U:28@CB #11/F:28@CB
Distance already exists; modify distance properties with 'distance style'
> distance #12/U:28@CB #11/F:28@CB
Distance already exists; modify distance properties with 'distance style'
> select clear
> select add #12/U:28@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #12/U:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 9 atom styles
> color sel byhetero
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> select #11/F:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> color sel byhetero
> select clear
> select add #11/F:27@NZ
1 atom, 1 residue, 1 model selected
> select add #12/U:27@NZ
2 atoms, 2 residues, 3 models selected
> distance #11/F:27@NZ #12/U:27@NZ
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.
> distance #11/F:27@NZ #12/U:27@NZ
Distance already exists; modify distance properties with 'distance style'
> distance #11/F:27@NZ #12/U:27@NZ
Distance already exists; modify distance properties with 'distance style'
> distance #11/F:27@NZ #12/U:27@NZ
Distance already exists; modify distance properties with 'distance style'
> distance #11/F:27@NZ #12/U:27@NZ
Distance already exists; modify distance properties with 'distance style'
> distance #11/F:27@NZ #12/U:27@NZ
Distance already exists; modify distance properties with 'distance style'
> distance #11/F:27@NZ #12/U:27@NZ
Distance already exists; modify distance properties with 'distance style'
> distance #11/F:27@NZ #12/U:27@NZ
Distance already exists; modify distance properties with 'distance style'
> distance #11/F:27@NZ #12/U:27@NZ
Distance already exists; modify distance properties with 'distance style'
> distance #11/F:27@NZ #12/U:27@NZ
Distance already exists; modify distance properties with 'distance style'
> select clear
> select #11/F:28
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/F:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> select subtract #11/F:27@CB
8 atoms, 8 bonds, 1 residue, 2 models selected
> select clear
> select add #11/F:27@CB
1 atom, 1 residue, 1 model selected
> select add #12/U:27@CB
2 atoms, 2 residues, 2 models selected
> distance #11/F:27@CB #12/U:27@CB
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.
> distance #11/F:27@CB #12/U:27@CB
Distance already exists; modify distance properties with 'distance style'
> distance #11/F:27@CB #12/U:27@CB
Distance already exists; modify distance properties with 'distance style'
> distance #11/F:27@CB #12/U:27@CB
Distance already exists; modify distance properties with 'distance style'
> distance #11/F:27@CB #12/U:27@CB
Distance already exists; modify distance properties with 'distance style'
> distance #11/F:27@CB #12/U:27@CB
Distance already exists; modify distance properties with 'distance style'
> select clear
> 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
> close #10
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py",
line 139, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking
self._mouse_pause()
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause
m.pause(self._mouse_pause_position)
File "D:\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 743, in pause
pu.show_text(p.description(), (x+10,y))
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
ValueError: unsupported format character '-' (0x2d) at index 2
ValueError: unsupported format character '-' (0x2d) at index 2
File "D:\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py",
line 1926, in description
return str(self.bond) + " " + dist_fmt % self.bond.length
See log for complete Python traceback.
Exactly two atoms must be selected!
> select clear
> select add #12/U:27@NZ
1 atom, 1 residue, 1 model selected
> select add #11/F:27@NZ
2 atoms, 2 residues, 2 models selected
> distance #12/U:27@NZ #11/F:27@NZ
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.
> select clear
> 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.
> 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.
> distance style dashes 10
> distance style dashes 10
> distance style dashes 9
> distance style dashes 9
> distance style dashes 8
> distance style dashes 8
> distance style dashes 7
> distance style dashes 7
> distance style dashes 6
> distance style dashes 6
> distance style dashes 5
> distance style dashes 5
> distance style dashes 6
> distance style dashes 6
> distance style dashes 7
> distance style dashes 7
> distance style dashes 8
> distance style dashes 8
> distance style dashes 9
> distance style dashes 9
> distance style radius 0.491
> distance style radius 0.491
> distance style radius 0.481
> distance style radius 0.481
> distance style radius 0.471
> distance style radius 0.471
> distance style radius 0.461
> distance style radius 0.461
> distance style radius 0.451
> distance style radius 0.451
> distance style radius 0.441
> distance style radius 0.441
> distance style radius 0.431
> distance style radius 0.431
> distance style radius 0.421
> distance style radius 0.421
> distance style radius 0.411
> distance style radius 0.411
> distance style radius 0.401
> distance style radius 0.401
> distance style radius 0.391
> distance style radius 0.391
> distance style radius 0.381
> 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
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