![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7942 closed defect (duplicate)
MemoryError saving session
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.18363
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-17.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Thu Nov 3 18:16:52 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-16.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Thu Nov 3 18:04:27 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-9.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Thu Nov 3 16:58:28 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-9.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Thu Nov 3 13:06:47 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-6.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Thu Nov 3 12:21:08 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-1.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Thu Nov 3 10:28:43 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221102-1.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Wed Nov 2 19:29:44 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221028-1.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Fri Oct 28 14:27:17 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-13.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Fri Oct 14 16:19:55 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-9.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Fri Oct 14 15:25:10 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-7.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Fri Oct 14 14:43:25 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-3.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Fri Oct 14 12:43:27 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-2.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Fri Oct 14 10:35:38 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-11.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Thu Oct 13 17:27:46 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-7.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Thu Oct 13 16:05:18 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/PCO371_1_lg-
> coot-12.pdb
Summary of feedback from opening
E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/PCO371_1_lg-coot-12.pdb
---
warning | Cannot find consistent set of bond orders for ring system containing
atom C26 in residue LIG /L:501
Chain information for PCO371_1_lg-coot-12.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/ZLH_xwide.mrc
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
> lighting soft
> set bgColor white
> hide atoms
> show cartoons
> hide #!2 models
> select /R
2115 atoms, 2177 bonds, 3 pseudobonds, 257 residues, 2 models selected
> color (#!1 & sel) light sea green
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel crimson
> ui tool show "Color Zone"
> color zone #2 near #1 distance 4.94
> volume splitbyzone #2
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
> hide #1.1 models
> volume #3.1 style mesh
> volume #3.7 style mesh
> transparency sel 80
> help help:user/tools/colorzone.html
> volume #3.7 level 0.07364
> volume #3.7 level 0.0648
> volume #3.7 style surface
> transparency sel 90
> select clear
> transparency #3.7#!1,3 90
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> color sel byhetero
> volume #3.7 style mesh
> volume #3.7 style surface
> select /A
1950 atoms, 1989 bonds, 1 pseudobond, 235 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep pink
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-1.cxs
> volume #3.7 level 0.02943
> transparency (#!1 & sel) 30
> transparency (#!1 & sel) 10
> select clear
> transparency #3.7#!1,3 30
> transparency #3.7#!1,3 40
> transparency #3.7#!1,3 50
> transparency #3.7#!1,3 60
> surface dust #3 size 20
> undo
> surface dust #3 size 0
> surface dust #3 size 5
> surface dust #3 size 2
> surface dust #3 size 3
> select clear
> volume #3.7 style mesh
> volume #3.7 style surface
> select /B
2616 atoms, 2663 bonds, 341 residues, 1 model selected
> color sel orange
> select /N
980 atoms, 1001 bonds, 129 residues, 1 model selected
> color sel gray
> select /G
436 atoms, 442 bonds, 57 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> select clear
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-1.cxs
> lighting soft
> cartoon style width 1.5 thickness 0.3
> cartoon style width 2 thickness 0.3
> lighting soft
> lighting simple
> lighting soft
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1.8 thickness 0.3
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-2.cxs
> transparency 10 cartoons
> transparency 5 cartoons
> lighting simple
> lighting soft
> lighting full
> volume #3.7 level 0.02354
> volume #3.7 level 0.02649
> lighting soft
> transparency 2 cartoons
> transparency 0 cartoons
> transparency 10 ribbons
> lighting shadows true intensity 0.5
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> lighting full
> lighting flat
[Repeated 2 time(s)]
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting flat
[Repeated 2 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> transparency 20 ribbons
> transparency 0 ribbons
> lighting soft
[Repeated 1 time(s)]
> transparency2 ribbon
Unknown command: transparency2 ribbon
> transparency 2 ribbons
> cartoon suppressBackboneDisplay false
> ui tool show "Side View"
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-3.cxs
> lighting soft
> lighting full
> lighting simple
> lighting flat
> graphics silhouettes false
> save 20221013-PTH1R-1.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 5 ribbons
> transparency 10 ribbons
> transparency 20 ribbons
> transparency 30 ribbons
> save 20221013-PTH1R-1.tif width 2000 height 2000 supersample 3
> transparentBackground true
> lighting simple
> lighting full
> save 20221013-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 10 ribbons
> save 20221013-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 20 ribbons
> transparency 30 ribbons
> save 20221013-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 20 ribbons
> save 20221013-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 10 ribbons
> save 20221013-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> save 20221013-PTH1R-3.tif width 2000 height 2000 supersample 3
> transparentBackground true
> save 20221013-PTH1R-4.tif width 2000 height 2000 supersample 3
> transparentBackground true
> lighting shadows false
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting full
> lighting shadows false
> save 20221013-PTH1R-5.tif width 2000 height 2000 supersample 3
> transparentBackground true
> size sel stickRadius 0.3
Changed 0 bond radii
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> size sel stickRadius 0.3
Changed 48 bond radii
> size sel stickRadius 0.2
Changed 48 bond radii
> volume #3.7 level 0.02649
> size sel stickRadius 0.25
Changed 48 bond radii
> size sel stickRadius 0.2
Changed 48 bond radii
> select clear
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-4.cxs
> select /R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 11 atom styles
> select clear
> color #!1,3 byhetero
> select /R:416
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> show sel atoms
> select add /R:415
15 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 15 atom styles
> select clear
> select /R:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
Drag select of 1 residues
> select clear
> select /R:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /R:413
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select /R:412
7 atoms, 6 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 7 atom styles
> select clear
> select /R:411
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select clear
> select /R:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select clear
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-5.cxs
> size sel stickRadius 0.25
Changed 0 bond radii
> size sel stickRadius 0.25
Changed 0 bond radii
> select /R:302
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select /R:302
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 9 atom styles
> select clear
> select /R:458
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select /R:459
12 atoms, 12 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 12 atom styles
> select clear
> transparency 20 cartoons
> transparency 30 cartoons
> select /R:223
10 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 10 atom styles
> select clear
> select /R:219
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 11 atom styles
> select /R:463
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select clear
> select /R:465
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 9 atom styles
> select clear
> select /A:359
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 9 atom styles
> select /A:360
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select /A:358
12 atoms, 12 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 12 atom styles
> select clear
> transparency 50 cartoons
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-6.cxs
> select /R:392
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
223 atoms, 225 bonds, 28 residues, 1 model selected
> cartoon hide sel
> select add /R:318
232 atoms, 233 bonds, 29 residues, 1 model selected
> select up
468 atoms, 480 bonds, 58 residues, 1 model selected
> hide sel cartoons
> select add /R:311
479 atoms, 491 bonds, 59 residues, 1 model selected
> select down
479 atoms, 491 bonds, 59 residues, 1 model selected
> select down
479 atoms, 491 bonds, 59 residues, 1 model selected
> select subtract /R:311
468 atoms, 480 bonds, 58 residues, 1 model selected
> select add /R:311
479 atoms, 491 bonds, 59 residues, 1 model selected
> select down
479 atoms, 491 bonds, 59 residues, 1 model selected
> select down
479 atoms, 491 bonds, 59 residues, 1 model selected
> select add /R:312
487 atoms, 498 bonds, 60 residues, 1 model selected
> select add /R:313
492 atoms, 502 bonds, 61 residues, 1 model selected
> select add /R:314
503 atoms, 513 bonds, 62 residues, 1 model selected
> select add /R:315
514 atoms, 524 bonds, 63 residues, 1 model selected
> select add /R:316
520 atoms, 529 bonds, 64 residues, 1 model selected
> hide sel cartoons
> select add /R:393
528 atoms, 536 bonds, 65 residues, 1 model selected
> hide sel cartoons
> select add /R:211
540 atoms, 548 bonds, 66 residues, 1 model selected
> select up
790 atoms, 814 bonds, 95 residues, 1 model selected
> select up
2115 atoms, 2177 bonds, 257 residues, 1 model selected
> select down
790 atoms, 814 bonds, 95 residues, 1 model selected
> hide sel cartoons
> undo
> select clear
> select /R:211
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
33 atoms, 33 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select /R:207
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
20 atoms, 19 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select /R:204
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
118 atoms, 119 bonds, 16 residues, 1 model selected
> hide sel cartoons
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-7.cxs
——— End of log from Thu Oct 13 16:05:18 2022 ———
opened ChimeraX session
> cartoon style width 1.5 thickness 0.3
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
5 hydrogen bonds found
> select clear
> color #1.2 magenta models transparency 0
> select add /R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
5 hydrogen bonds found
> select clear
> save 20221013-PTH1R-7.tif width 2000 height 2000 supersample 3
> transparentBackground
Missing "transparentBackground" keyword's argument
> save 20221013-PTH1R-7.tif width 2000 height 2000 supersample 3
> transparentBackground
Missing "transparentBackground" keyword's argument
> save 20221013-PTH1R-7.tif width 2000 height 2000 supersample 3
> transparentBackground
Missing "transparentBackground" keyword's argument
> save 20221013-PTH1R-7.tif width 2000 height 2000 supersample 3
> transparentBackground true
> color #1.2 #550000 models transparency 0
> color #1.2 black models transparency 0
> color #1.2 #aaaaff models transparency 0
> color #1.2 #aaffff models transparency 0
> color #1.2 #ffaaff models transparency 0
> color #1.2 magenta models transparency 0
> color #1.2 #5500ff models transparency 0
> color #1.2 magenta models transparency 0
> color #1.2 #ff007f models transparency 0
> color #1.2 #550000 models transparency 0
> color #1.2 #aa0000 models transparency 0
> color #1.2 black models transparency 0
> ui mousemode right distance
> ui mousemode right "tape measure"
> ui mousemode right distance
> select /L:501@O20
1 atom, 1 residue, 1 model selected
> select /R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select /R:417@N
1 atom, 1 residue, 1 model selected
> select /L:501@O20
1 atom, 1 residue, 1 model selected
> select add /R:417
12 atoms, 11 bonds, 2 residues, 1 model selected
> select subtract /R:417
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> ui mousemode right "tape measure"
> ui mousemode right distance
> ui mousemode right select
> ui mousemode right distance
[Repeated 1 time(s)]
> ui mousemode right "tape measure"
> select clear
> marker segment #4 position 111.2,101.4,114.3 toPosition 115.1,97.63,99.11
> color yellow radius 0.1 label 16.09 labelHeight 1.609 labelColor yellow
> undo
[Repeated 1 time(s)]
> marker delete #4
> select clear
> select /R:212
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add /R:213
22 atoms, 21 bonds, 2 residues, 1 model selected
> select add /R:214
33 atoms, 31 bonds, 3 residues, 1 model selected
> hide sel cartoons
> save 20221013-PTH1R-7.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 3 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-8.cxs
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-9.cxs
> hide sel atoms
[Repeated 1 time(s)]
> hide sel target a
[Repeated 1 time(s)]
> show #!3.7 models
> hide #!3.7 models
> hide sel target a
> select /R
2115 atoms, 2177 bonds, 3 pseudobonds, 257 residues, 2 models selected
> hide sel atoms
> select /A
1950 atoms, 1989 bonds, 1 pseudobond, 235 residues, 2 models selected
> hide sel atoms
> select clear
> show #!3.7 models
> save 20221013-PTH1R-8.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 10 cartoons
> save 20221013-PTH1R-9.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 1 time(s)]
> show cartoons
> save 20221013-PTH1R-9.tif width 2000 height 2000 supersample 3
> transparentBackground true
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-10.cxs
> save 20221013-PTH1R-9.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 2 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-11.cxs
——— End of log from Thu Oct 13 17:27:46 2022 ———
opened ChimeraX session
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-1.cxs
> open "E:/huawei/HaozhuoDownloads/PTH1R/mollecule/duotai/PTH34-PTH1R-G112
> Model2_2-coot-21xuyuanjia erliujian2.pdb"
Chain information for PTH34-PTH1R-G112 Model2_2-coot-21xuyuanjia
erliujian2.pdb #4
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> matchmaker 4# to 1#
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> hide #!1 models
> hide #!4 atoms
> show #!4 cartoons
> matchmaker #4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain B (#1) with PTH34-PTH1R-G112
Model2_2-coot-21xuyuanjia erliujian2.pdb, chain B (#4), sequence alignment
score = 1755.9
RMSD between 340 pruned atom pairs is 0.504 angstroms; (across all 341 pairs:
0.518)
> show #!1 models
> hide #!2 models
> open "E:/huawei/HaozhuoDownloads/PTH1R/mollecule/duotai/PTHrP-PTH1R-Gs
> complex2-Lip-10-coot-18xuyuanjiaerliujian2.pdb"
Summary of feedback from opening
E:/huawei/HaozhuoDownloads/PTH1R/mollecule/duotai/PTHrP-PTH1R-Gs
complex2-Lip-10-coot-18xuyuanjiaerliujian2.pdb
---
warnings | End residue of secondary structure not found: HELIX 3 3 GLN A 213
PHE A 215 1 3
Start residue of secondary structure not found: HELIX 4 4 LEU A 233 TRP A 244
1 12
Start residue of secondary structure not found: HELIX 5 5 GLN A 261 ALA A 270
1 10
Start residue of secondary structure not found: HELIX 6 6 PRO A 280 PHE A 282
1 3
Start residue of secondary structure not found: HELIX 7 7 PRO A 299 THR A 317
1 19
Start residue of secondary structure not found: HELIX 8 8 ASN A 338 TYR A 358
1 21
5 messages similar to the above omitted
Chain information for PTHrP-PTH1R-Gs
complex2-Lip-10-coot-18xuyuanjiaerliujian2.pdb #5
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> hide #!1 models
> hide #!3 models
> hide #!3.7 models
> hide #!4 models
> hide #!5 atoms
> show #!5 cartoons
> show #!4 models
> show #!1 models
> matchmaker #5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain B (#1) with PTHrP-PTH1R-Gs
complex2-Lip-10-coot-18xuyuanjiaerliujian2.pdb, chain B (#5), sequence
alignment score = 1737.9
RMSD between 338 pruned atom pairs is 0.490 angstroms; (across all 341 pairs:
0.544)
> matchmaker #5/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with PTHrP-PTH1R-Gs
complex2-Lip-10-coot-18xuyuanjiaerliujian2.pdb, chain R (#5), sequence
alignment score = 1250.6
RMSD between 188 pruned atom pairs is 0.916 angstroms; (across all 257 pairs:
2.625)
> matchmaker #4/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with PTH34-PTH1R-G112
Model2_2-coot-21xuyuanjia erliujian2.pdb, chain R (#4), sequence alignment
score = 1266
RMSD between 190 pruned atom pairs is 0.885 angstroms; (across all 257 pairs:
2.709)
> ui tool show "Side View"
> hide #4.1 models
> hide #5.1 models
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-2.cxs
——— End of log from Fri Oct 14 10:35:38 2022 ———
opened ChimeraX session
> open "E:/huawei/HaozhuoDownloads/PTH1R/mollecule/duotai/PTHrP-PTH1R-Gs
> complex2-Lip-10-coot-18xuyuanjiaerliujian.pdb"
Chain information for PTHrP-PTH1R-Gs
complex2-Lip-10-coot-18xuyuanjiaerliujian.pdb #6
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> hide #!1 models
> hide #!4 models
> hide #!5 models
> hide #!6 atoms
> show #!6 cartoons
> matchmaker #6/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with PTHrP-PTH1R-Gs
complex2-Lip-10-coot-18xuyuanjiaerliujian.pdb, chain R (#6), sequence
alignment score = 1250.6
RMSD between 188 pruned atom pairs is 0.916 angstroms; (across all 257 pairs:
2.625)
> show #!1 models
> show #!5 models
> show #!4 models
> hide #!5 models
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-2.cxs
> select #4/R
3142 atoms, 3242 bonds, 4 pseudobonds, 367 residues, 2 models selected
> color (#!4 & sel) cyan
> color (#!4 & sel) medium blue
> ui tool show "Color Actions"
> color sel slate blue
> color sel rebecca purple
> color sel royal blue
> color sel deep sky blue
> color sel royal blue
> hide #!6 models
> color sel sky blue
> lighting soft
> lighting simple
> lighting full
> transparency 0 cartoons
> cartoon style width 1.5 thickness 0.3
> color sel royal blue
[Repeated 1 time(s)]
> select #4/P
289 atoms, 294 bonds, 34 residues, 1 model selected
> color sel light coral
> select #6/R
3029 atoms, 3119 bonds, 3 pseudobonds, 369 residues, 2 models selected
> select #6/R
3029 atoms, 3119 bonds, 3 pseudobonds, 369 residues, 2 models selected
> show #!6 models
> color sel purple
> color sel light slate gray
> color sel peru
> color sel dark khaki
> color sel olive
> color sel dark khaki
> select clear
> select #6/P
302 atoms, 308 bonds, 36 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> color sel sienna
> color sel gold
> color sel sandy brown
> color sel green yellow
> color sel olive drab
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> color sel orange red
> color sel red
[Repeated 1 time(s)]
> color sel maroon
> color sel fire brick
> color sel brown
> color sel chocolate
> color sel coral
> color sel indian red
> color sel dark salmon
> color sel salmon
> color sel medium violet red
[Repeated 1 time(s)]
> color sel dark orchid
> color sel medium violet red
> select #6/R
3029 atoms, 3119 bonds, 3 pseudobonds, 369 residues, 2 models selected
> color sel light blue
> color sel burly wood
> color sel dark khaki
> color sel dark goldenrod
> color sel dark khaki
> color sel yellow green
> color sel dark khaki
> select clear
> select #4/A
1950 atoms, 1989 bonds, 1 pseudobond, 235 residues, 2 models selected
> color sel olive drab
> color sel dark salmon
[Repeated 3 time(s)]
> hide #!6 models
> select #4/B
2615 atoms, 2662 bonds, 341 residues, 1 model selected
> color sel olive
> color sel olive drab
> color sel khaki
> select #4/G
437 atoms, 443 bonds, 57 residues, 1 model selected
> color sel pale green
> color sel dark sea green
> select #4/N
984 atoms, 1005 bonds, 129 residues, 1 model selected
> color sel dark gray
> color sel tan
> color sel plum
> show #!6 models
> select #6/R
3029 atoms, 3119 bonds, 3 pseudobonds, 369 residues, 2 models selected
> color sel burly wood
> undo
> select #6/A
1950 atoms, 1989 bonds, 1 pseudobond, 235 residues, 2 models selected
> color sel burly wood
> color sel thistle
> color sel violet
> color sel peru
> color sel deep sky blue
> color sel chocolate
> color sel lime
> color sel pale violet red
> color sel purple
> color sel magenta
> select #6/B
2616 atoms, 2663 bonds, 341 residues, 1 model selected
> color sel tan
> color sel rosy brown
> lighting soft
> color sel dark green
> color sel forest green
> select #6/G
436 atoms, 442 bonds, 57 residues, 1 model selected
> color sel forest green
> color sel light sky blue
> lighting simple
> lighting soft
> lighting full
> color sel aquamarine
> color sel pale green
> select #6/N
983 atoms, 1005 bonds, 129 residues, 1 model selected
> color sel silver
> color sel powder blue
> color sel blue violet
> color sel slate blue
> select #6/B
2616 atoms, 2663 bonds, 341 residues, 1 model selected
> color sel rosy brown
> color sel orchid
> color sel wheat
> color sel beige
> color sel white smoke
> color sel mint cream
> color sel pink
> color sel dark violet
> color sel pale violet red
> color sel medium purple
> color sel dark magenta
[Repeated 1 time(s)]
> color sel purple
> select clear
> save 20221014-PTH1R-1.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 3 time(s)]
> transparency 10 cartoons
> save 20221014-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> ui tool show "Side View"
> save 20221014-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 5 cartoons
> save 20221014-PTH1R-3.tif width 2000 height 2000 supersample 3
> transparentBackground true
> hide #6.1 models
> save 20221014-PTH1R-3.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 4 time(s)]
> select #4/A
1950 atoms, 1989 bonds, 1 pseudobond, 235 residues, 2 models selected
> color sel orchid
> color sel blue violet
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-3.cxs
——— End of log from Fri Oct 14 12:43:27 2022 ———
opened ChimeraX session
> select clear
> hide #!6 models
> save 20221014-PTH1R-5.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 1 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-4.cxs
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/duotai/6nbfPTH1R.pdb
6nbfPTH1R.pdb title:
Cryo-em structure of parathyroid hormone receptor type 1 In complex with A
long-acting parathyroid hormone analog and G protein [more info...]
Chain information for 6nbfPTH1R.pdb #7
---
Chain | Description | UniProt
A | GS protein α subunit |
B | transducin β chain 1 | GBB1_RAT
G | G γ-I | GBG2_BOVIN
N | nanobody-35 |
P | long-acting parathyroid hormone analog |
R | parathyroid hormone/parathyroid hormone-related peptide receptor |
PTH1R_HUMAN
Non-standard residues in 6nbfPTH1R.pdb #7
---
CLR — cholesterol
PLM — palmitic acid
> hide #!1 models
> hide #!4 models
> hide #!7 atoms
> show #!7 cartoons
> matchmaker #7/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with 6nbfPTH1R.pdb, chain R
(#7), sequence alignment score = 1263.6
RMSD between 202 pruned atom pairs is 0.888 angstroms; (across all 257 pairs:
2.496)
> show #!1 models
> cartoon style width 1.5 thickness 0.3
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-5.cxs
> hide #!7 models
> show #!4 models
> save 20221014-PTH1R-6.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 10 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-6.cxs
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-7.cxs
——— End of log from Fri Oct 14 14:43:25 2022 ———
opened ChimeraX session
> select #1/B#4/B#5/B#6/B
10463 atoms, 10651 bonds, 1364 residues, 4 models selected
> hide sel & #!1,4 cartoons
> select #1/A#4/A#5/A#6/A
7800 atoms, 7956 bonds, 4 pseudobonds, 940 residues, 8 models selected
> hide sel & #!1,4 cartoons
> select #1/G#4/G#5/G#6/G
1745 atoms, 1769 bonds, 228 residues, 4 models selected
> hide sel & #!1,4 cartoons
> select #1/N#4/N#5/N#6/N
3930 atoms, 4016 bonds, 516 residues, 4 models selected
> hide sel & #!1,4 cartoons
> save 20221014-PTH1R-7.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 1 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-7.cxs
> ui tool show "Side View"
> save 20221014-PTH1R-8.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 5 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-8.cxs
> select clear
[Repeated 1 time(s)]
> select #4/R:34
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/R:34
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
120 atoms, 121 bonds, 14 residues, 1 model selected
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
Drag select of 39 residues
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
Drag select of 20 residues
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 7 residues
> hide sel cartoons
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-9.cxs
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save 20221014-PTH1R-9.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 2 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-9.cxs
——— End of log from Fri Oct 14 15:25:10 2022 ———
opened ChimeraX session
> ui tool show "Side View"
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-12.cxs
> save 20221014-PTH1R-12.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 1 time(s)]
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting full
> save 20221014-PTH1R-13.tif width 2000 height 2000 supersample 3
> transparentBackground true
> lighting simple
> lighting soft
> lighting full
> save 20221014-PTH1R-14.tif width 2000 height 2000 supersample 3
> transparentBackground true
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-13.cxs
——— End of log from Fri Oct 14 16:19:55 2022 ———
opened ChimeraX session
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221028-1.cxs
> ui tool show "Side View"
> save 20221028-PTH1R-1.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 2 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221028-1.cxs
——— End of log from Fri Oct 28 14:27:17 2022 ———
opened ChimeraX session
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221102-1.cxs
> ui tool show "Side View"
> transparency 30 ribbons
> save 20221102-1-PTH1R-24.tif width 2000 height 2000 supersample 3
> transparentBackground true
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221102-1.cxs
——— End of log from Wed Nov 2 19:29:44 2022 ———
opened ChimeraX session
> show #!6 models
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-1.cxs
> select #1/A#4/A#5/A#6/A
7800 atoms, 7956 bonds, 4 pseudobonds, 940 residues, 8 models selected
> hide sel & #!1,4,6 cartoons
> select #1/B#4/B#5/B#6/B
10463 atoms, 10651 bonds, 1364 residues, 4 models selected
> hide sel & #!1,4,6 cartoons
> select #1/G#4/G#5/G#6/G
1745 atoms, 1769 bonds, 228 residues, 4 models selected
> hide sel & #!1,4,6 cartoons
> select #1/N#4/N#5/N#6/N
3930 atoms, 4016 bonds, 516 residues, 4 models selected
> hide sel & #!1,4,6 cartoons
> select #4/P#5/P#6/P
893 atoms, 910 bonds, 106 residues, 3 models selected
> hide sel & #!4,6 cartoons
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #6/R:176
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
254 atoms, 261 bonds, 31 residues, 1 model selected
> hide sel cartoons
Drag select of 58 residues
> hide sel cartoons
Drag select of 6 residues
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-1.cxs
> lighting full
> lighting soft
> lighting simple
> lighting full
> transparency 10 ribbons
> cartoon style width 1 thickness 0.3
> ui tool show "Side View"
> cartoon style width 0.8 thickness 0.3
> cartoon style width 1 thickness 0.3
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting simple
> lighting full
> lighting soft
> lighting full
> save 20221103-1-PTH1R-24.tif width 2000 height 2000 supersample 3
> transparentBackground true
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-1.cxs
> open "E:/huawei/HaozhuoDownloads/PTH1R/mollecule/PTH1R paper2/6fj3.pdb"
6fj3.pdb title:
High resolution crystal structure of parathyroid hormone 1 receptor In complex
with A peptide agonist. [more info...]
Chain information for 6fj3.pdb #8
---
Chain | Description | UniProt
A | parathyroid hormone/parathyroid hormone-related peptide
receptor,parathyroid hormone/parathyroid hormone-related peptide receptor,GLGA
glycogen synthase,parathyroid hormone/parathyroid hormone-related peptide
receptor | PTH1R_HUMAN
B | parathyroid hormone | PTHY_HORSE
Non-standard residues in 6fj3.pdb #8
---
AC5 — 1-aminocyclopentanecarboxylic acid (cyclo-leucine)
ACY — acetic acid
AIB — α-aminoisobutyric acid
BMA — β-D-mannopyranose
CL — chloride ion
FUC — α-L-fucopyranose
HRG — L-homoarginine
MAN — α-D-mannopyranose
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
NH2 — amino group
NLE — norleucine
OLA — oleic acid
PG4 — tetraethylene glycol
> matchmaker #8/R to #1/R
No molecules/chains to match specified
> hide #!8 models
> show #!8 models
> show sel cartoons
> select #8/A
4864 atoms, 4826 bonds, 1 pseudobond, 725 residues, 2 models selected
> show sel cartoons
> hide #!8 models
> show #!8 models
> matchmaker #8/A to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with 6fj3.pdb, chain A (#8),
sequence alignment score = 976.9
RMSD between 188 pruned atom pairs is 0.999 angstroms; (across all 255 pairs:
6.658)
> select clear
> hide #!1,4,6,8 atoms
> hide #!8 models
> hide #!6 models
> hide #!4 models
> hide #!1 models
> show #!8 models
> show #!1 models
> select #8/A:1223
11 atoms, 11 bonds, 1 residue, 1 model selected
> select down
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select add #8/A:1223
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #8/A:1225
19 atoms, 18 bonds, 2 residues, 1 model selected
> select add #8/A:1224
33 atoms, 33 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select add #8/A:1226
42 atoms, 41 bonds, 4 residues, 1 model selected
> select down
42 atoms, 41 bonds, 4 residues, 1 model selected
> select add #8/A:1228
54 atoms, 53 bonds, 5 residues, 1 model selected
> select subtract #8/A:1228
42 atoms, 41 bonds, 4 residues, 1 model selected
> select add #8/A:1228
54 atoms, 53 bonds, 5 residues, 1 model selected
> select add #8/A:1227
60 atoms, 58 bonds, 6 residues, 1 model selected
> select add #8/A:1229
68 atoms, 65 bonds, 7 residues, 1 model selected
> select add #8/A:1230
75 atoms, 71 bonds, 8 residues, 1 model selected
> select add #8/A:1232
81 atoms, 76 bonds, 9 residues, 1 model selected
> select subtract #8/A:1232
75 atoms, 71 bonds, 8 residues, 1 model selected
> select add #8/A:1233
86 atoms, 81 bonds, 9 residues, 1 model selected
> select add #8/A:1232
92 atoms, 86 bonds, 10 residues, 1 model selected
> hide sel cartoons
Drag select of 17 residues
> hide sel cartoons
Drag select of 98 residues
> select clear
Drag select of 63 residues
> hide sel cartoons
> select #8/A:1403
9 atoms, 8 bonds, 1 residue, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #8/A:1402
20 atoms, 18 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select add #8/A:1410
28 atoms, 25 bonds, 3 residues, 1 model selected
> select down
28 atoms, 25 bonds, 3 residues, 1 model selected
> select add #8/A:1408
39 atoms, 35 bonds, 4 residues, 1 model selected
> select add #8/A:1409
44 atoms, 39 bonds, 5 residues, 1 model selected
> select add #8/A:1406
53 atoms, 47 bonds, 6 residues, 1 model selected
> select add #8/A:1407
62 atoms, 55 bonds, 7 residues, 1 model selected
> hide sel cartoons
Drag select of 59 residues
> select up
997 atoms, 1008 bonds, 125 residues, 1 model selected
> select down
523 atoms, 55 bonds, 66 residues, 1 model selected
> hide sel cartoons
> select add #8/A:1347
532 atoms, 63 bonds, 67 residues, 1 model selected
> select up
997 atoms, 1008 bonds, 125 residues, 1 model selected
> select down
532 atoms, 63 bonds, 67 residues, 1 model selected
Drag select of 20 residues
> hide sel cartoons
Drag select of 7 residues
> select up
121 atoms, 124 bonds, 15 residues, 1 model selected
> hide sel cartoons
> select #8/A:1347
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
68 atoms, 67 bonds, 10 residues, 1 model selected
> hide sel cartoons
> select #8/A:1219
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #8/A:1221
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #8/A:1220
26 atoms, 23 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #8/A:1222
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #8/A
4864 atoms, 4826 bonds, 1 pseudobond, 725 residues, 2 models selected
> select #8/B
310 atoms, 308 bonds, 43 residues, 1 model selected
> hide sel cartoons
Drag select of 68 residues
> hide sel cartoons
Drag select of 24 residues
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
Drag select of 6 residues
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
> hide #8.1 models
> select add #8/A:1218
1160 atoms, 311 bonds, 147 residues, 1 model selected
> hide sel cartoons
> select #8/A:1411
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #8/A:1412
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #8/A:1413
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> cartoon style width 1 thickness 0.3
> show #!4 models
> show #!6 models
> hide #!8 models
> save 20221103-1-PTH1R-24.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 2 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-1.cxs
——— End of log from Thu Nov 3 10:28:43 2022 ———
opened ChimeraX session
> transparency 10 ribbons
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-3.cxs
> ui tool show "Side View"
> save 20221103-4-PTH1R-24.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 7 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-4.cxs
> hide #!6 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> select #1/R:415
7 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select clear
> select #1/R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #1/R:418
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 4 atom styles
> select clear
> hide #!1 atoms
> undo
> select #1/R:418
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> show (sel-residues & sidechain) target ab
> show sel atoms
> select clear
> select #1/R:416
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select clear
> hide #!1 models
> show #!4 models
> select #4/R:418
4 atoms, 3 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 4 atom styles
> show (sel-residues & sidechain) target ab
> show sel atoms
> show (sel-residues & sidechain) target ab
> cartoon suppressBackboneDisplay false
> select clear
> hide #!4 models
> show #!6 models
> select #6/R:418
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 4 atom styles
> select clear
> select #1/R#4/R#5/R#6/R
11315 atoms, 11657 bonds, 13 pseudobonds, 1362 residues, 8 models selected
> select ~sel
40431 atoms, 41122 bonds, 16 pseudobonds, 5131 residues, 32 models selected
> hide sel & #!6 cartoons
> select clear
Drag select of 74 residues
> select up
813 atoms, 838 bonds, 99 residues, 1 model selected
> hide sel cartoons
> hide #!6 models
> show #!4 models
> show #!1 models
> select ~sel
50933 atoms, 51941 bonds, 28 pseudobonds, 6394 residues, 32 models selected
> hide sel & #!1,4 cartoons
> undo
> select ~sel
813 atoms, 838 bonds, 1 pseudobond, 99 residues, 2 models selected
> select clear
> show #!6 models
> select #1/R#4/R#5/R#6/R
11315 atoms, 11657 bonds, 13 pseudobonds, 1362 residues, 8 models selected
> select ~sel
40431 atoms, 41122 bonds, 16 pseudobonds, 5131 residues, 32 models selected
> hide sel & #!1,4,6 cartoons
> select clear
Drag select of 40 residues
> select up
728 atoms, 751 bonds, 89 residues, 1 model selected
> hide sel cartoons
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-4.cxs
> hide #!1 models
> hide #!6 models
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> color #!4 byhetero
> select #4/R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 11 atom styles
> select clear
> select #4/R:415
7 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 7 atom styles
> select #4/R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:415
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:416
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select clear
> lighting shadows false
> show #!1 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!6 models
> hide #!4 models
> hide #!1 models
> color #!6 byhetero
> select #6/R:415
7 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 7 atom styles
> select #6/R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 11 atom styles
> select #6/R:416
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select clear
> show #!4 models
> show #!1 models
> show #!8 models
> hide #!6 models
> hide #!4 models
> hide #!1 models
> select #8/A:416
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select #8/A:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #8/A:418
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel target ab
> select #8/A:415
7 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #8/A:416
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> show #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!6 models
> select #4/P#5/P#6/P
893 atoms, 910 bonds, 106 residues, 3 models selected
> show sel & #!4,6 cartoons
> hide sel & #!4,6 cartoons
> hide #!8 models
> hide #!6 models
> show #!8 models
> hide #!4 models
> ~hbonds
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-5.cxs
> hide #!8 models
> select #1/R:418
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #1/R:418
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #1/R:416
23 atoms, 21 bonds, 3 residues, 1 model selected
> select add #1/R:415
30 atoms, 28 bonds, 4 residues, 1 model selected
> ~hbonds
> select clear
> select #1/R:420
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 10 atom styles
> select clear
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-6.cxs
——— End of log from Thu Nov 3 12:21:08 2022 ———
opened ChimeraX session
> show #!4 models
> show #!6 models
> ui tool show "Side View"
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-7.cxs
> hide #!4 models
> hide #!6 models
> select #1/R:223
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel atoms
> show (sel-residues & sidechain) target ab
> select clear
> select #1/R:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> show #!4 models
> hide #!1 models
> select #4/R:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> select #1/R:299@CA
1 atom, 1 residue, 1 model selected
> select subtract #1/R:299
Nothing selected
> select add #1/R:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-7.cxs
> hbonds sel reveal true
11 hydrogen bonds found
> ~hbonds
> style sel stick
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> select clear
[Repeated 1 time(s)]
> style #!1 stick
Changed 8141 atom styles
> select #1/R:295
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/R:303
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/R:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show (sel-residues & sidechain) target ab
> select clear
> show #!8 models
> select #8/A:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> hide sel atoms
> hide #!8 models
> select #1/R:302
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #1/R:410
7 atoms, 6 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #1/R:459
12 atoms, 12 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select clear
> hide #!1 models
> show #!4 models
> style #!4 stick
Changed 9417 atom styles
> select #4/R:303
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/R:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/R:302
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #4/R:223
10 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> show #!1 models
> hide #!1 models
> select #4/R:459
12 atoms, 12 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> show #!4 models
> select #4/R:410
7 atoms, 6 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #1/R:299@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide #!4 models
> select #1/R:299@CG1
1 atom, 1 residue, 1 model selected
> select #1/R:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!1 models
> show #!1 models
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-8.cxs
> select #1/R:219
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #1/R:405
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #1/R:465
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #1/R:463
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select clear
> hide #!1 models
> show #!4 models
> select #4/R:405
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #4/R:463
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #4/R:465
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #4/R:219
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!8 models
> select #8/A:465
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #8/A:405
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #8/A:410
7 atoms, 6 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #8/A:302
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #8/A:219
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #8/A:223
10 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #8/A:459
12 atoms, 12 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> show #!1 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> select #8/A:463
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select clear
> show #!1 models
> show #!4 models
> hide #!8 models
> hide #!4 models
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-9.cxs
> select #1/R:233
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #1/R:421
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/R:451
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select clear
> select #1/R:295
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> hide #!1 models
> show #!4 models
> select #4/R:295
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #4/R:420
10 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #4/R:233
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #4/R:451
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select clear
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!8 models
> select #8/A:451
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #8/A:420
10 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #8/A:233
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #8/A:295
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show (sel-residues & sidechain) target ab
> select clear
> show #!1 models
> hide #!8 models
> show #!4 models
> hide #!1 models
> hide #!4 models
> show #!6 models
> style #!6 stick
Changed 9710 atom styles
> select #6/R:295
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show (sel-residues & sidechain) target ab
> select #6/R:303
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #6/R:302
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #6/R:223
10 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #6/R:410
7 atoms, 6 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #6/R:459
12 atoms, 12 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select clear
> select #6/R:219
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #6/R:405
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #6/R:463
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #6/R:465
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #6/R:233
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #6/R:420
10 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #6/R:451
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select clear
> show #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!8 models
> hide #!6 models
> hide #!4 models
> show #!4 models
> hide #!8 models
> show #!6 models
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-9.cxs
——— End of log from Thu Nov 3 13:06:47 2022 ———
opened ChimeraX session
> ui tool show "Side View"
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-9.cxs
——— End of log from Thu Nov 3 16:58:28 2022 ———
opened ChimeraX session
Drag select of 28 atoms, 58 residues, 24 bonds
> hide sel atoms
Drag select of 3 atoms, 18 residues, 3 bonds
> hide sel atoms
Drag select of 11 residues, 4 atoms, 2 bonds
> hide sel atoms
> select clear
> ui tool show "Side View"
Drag select of 9 atoms, 22 residues, 10 bonds
> hide sel atoms
Drag select of 12 atoms, 27 residues, 6 bonds
> hide sel atoms
Drag select of 7 atoms, 6 residues, 3 bonds
> hide sel atoms
Drag select of 4 atoms, 5 residues, 1 bonds
> hide sel atoms
Drag select of 19 atoms, 28 residues, 17 bonds
> hide sel atoms
Drag select of 59 residues, 16 atoms, 13 bonds
> hide sel atoms
Drag select of 16 atoms, 73 residues, 15 bonds
> hide sel atoms
> select clear
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-16.cxs
——— End of log from Thu Nov 3 18:04:27 2022 ———
opened ChimeraX session
> save 20221103-8-PTH1R-24.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 15 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-17.cxs
——— End of log from Thu Nov 3 18:16:52 2022 ———
opened ChimeraX session
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-22.cxs
> hide #!1,4,6 atoms
> ui tool show "Side View"
> select #1/A#4/A#5/A#6/A
7800 atoms, 7956 bonds, 4 pseudobonds, 940 residues, 8 models selected
> select #1/A#4/A#5/A#6/A
7800 atoms, 7956 bonds, 4 pseudobonds, 940 residues, 8 models selected
> show sel & #!1,4,6 cartoons
> select clear
> select #1/B#4/B#5/B#6/B
10463 atoms, 10651 bonds, 1364 residues, 4 models selected
> select #1/B#4/B#5/B#6/B
10463 atoms, 10651 bonds, 1364 residues, 4 models selected
> show sel & #!1,4,6 cartoons
> select clear
> select #1/G#4/G#5/G#6/G
1745 atoms, 1769 bonds, 228 residues, 4 models selected
> show sel & #!1,4,6 cartoons
> select clear
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-23.cxs
> select #6/A
1950 atoms, 1989 bonds, 1 pseudobond, 235 residues, 2 models selected
> ui tool show "Color Actions"
> color sel olive
> color sel indigo
> color sel pale violet red
> color sel dark slate gray
> color sel light steel blue
> color sel powder blue
> color sel silver
> color sel honeydew
> color sel dark sea green
> color sel rosy brown
[Repeated 1 time(s)]
> color sel dark slate blue
> color sel slate blue
> color sel cadet blue
> color sel steel blue
> color sel goldenrod
> color sel green yellow
> color sel yellow green
> color sel spring green
> color sel navy
> color sel magenta
> color sel dark violet
> color sel dodger blue
> color sel slate gray
> color sel cadet blue
> color sel saddle brown
> color sel sienna
> color sel goldenrod
> color sel sandy brown
> color sel light goldenrod yellow
> color sel old lace
> color sel light pink
> color sel light coral
> color sel aquamarine
> color sel sky blue
> color sel burly wood
> color sel violet
> color sel plum
> color sel lavender
> color sel azure
> color sel light goldenrod yellow
> color sel old lace
> color sel pink
> color sel peach puff
> color sel navy
> select clear
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> cartoon style width 1.5 thickness 0.3
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> save 20221103-13-PTH1R-24.tif width 2000 height 2000 supersample 3
> transparentBackground true
> cartoon style width 1.2 thickness 0.3
[Repeated 8 time(s)]
> save 20221103 PTH1R-1.tif width 2000 height 2000 supersample 3
> transparentBackground true
Cannot determine format for '20221103'
> save 20221103PTH1R-1.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 4 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-23.cxs
Traceback (most recent call last):
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 624, in save
fserialize(stream, data)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 302, in msgpack._cmsgpack.Packer.pack
MemoryError
MemoryError
File "msgpack\\_packer.pyx", line 302, in msgpack._cmsgpack.Packer.pack
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "D:\Program Files (x86)\ChimeraX 1.3\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:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 624, in save
fserialize(stream, data)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 302, in msgpack._cmsgpack.Packer.pack
MemoryError
MemoryError
File "msgpack\\_packer.pyx", line 302, in msgpack._cmsgpack.Packer.pack
See log for complete Python traceback.
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-23.cxs
Traceback (most recent call last):
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
s['array'] = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x0000023A29756460> ->
<chimerax.surface.dust.Redust object at 0x0000023A14627670> ->
<chimerax.map.volume.VolumeSurface object at 0x0000023A19DF3BB0> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000023A57B8D5B0> 'ZLH_xwide.mrc 6' ->
<chimerax.map.session.GridDataState object at 0x0000023A2D1E1370>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x0000023A29756460> ->
<chimerax.surface.dust.Redust object at 0x0000023A14627670> ->
<chimerax.map.volume.VolumeSurface object at 0x0000023A19DF3BB0> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000023A57B8D5B0> 'ZLH_xwide.mrc 6' ->
<chimerax.map.session.GridDataState object at 0x0000023A2D1E1370>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x0000023A29756460> ->
<chimerax.surface.dust.Redust object at 0x0000023A14627670> ->
<chimerax.map.volume.VolumeSurface object at 0x0000023A19DF3BB0> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000023A57B8D5B0> 'ZLH_xwide.mrc 6' ->
<chimerax.map.session.GridDataState object at 0x0000023A2D1E1370>
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'ZLH_xwide.mrc 6' -> : Error while saving session data for '_surface_updaters'
-> -> -> 'surface' -> 'ZLH_xwide.mrc 6' ->
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
s['array'] = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x0000023A29756460> ->
<chimerax.surface.dust.Redust object at 0x0000023A14627670> ->
<chimerax.map.volume.VolumeSurface object at 0x0000023A19DF3BB0> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000023A57B8D5B0> 'ZLH_xwide.mrc 6' ->
<chimerax.map.session.GridDataState object at 0x0000023A2D1E1370>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "D:\Program Files (x86)\ChimeraX 1.3\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:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x0000023A29756460> ->
<chimerax.surface.dust.Redust object at 0x0000023A14627670> ->
<chimerax.map.volume.VolumeSurface object at 0x0000023A19DF3BB0> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000023A57B8D5B0> 'ZLH_xwide.mrc 6' ->
<chimerax.map.session.GridDataState object at 0x0000023A2D1E1370>: Error while
saving session data for '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x0000023A29756460> ->
<chimerax.surface.dust.Redust object at 0x0000023A14627670> ->
<chimerax.map.volume.VolumeSurface object at 0x0000023A19DF3BB0> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000023A57B8D5B0> 'ZLH_xwide.mrc 6' ->
<chimerax.map.session.GridDataState object at 0x0000023A2D1E1370>
ValueError: error processing: '_surface_updaters' -> -> -> 'surface' ->
'ZLH_xwide.mrc 6' -> : Error while saving session data for '_surface_updaters'
-> -> -> 'surface' -> 'ZLH_xwide.mrc 6' ->
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> color light sea green
[Repeated 1 time(s)]
> undo
[Repeated 1 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221103-23.cxs
Traceback (most recent call last):
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 620, in save
fserialize(stream, mgr.bundle_infos())
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 298, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 295, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack\\_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap
File "_serialize.pyx", line 209, in chimerax.core._serialize._encode_ext
File "_serialize.pyx", line 196, in chimerax.core._serialize._pack_as_array
File "msgpack\\_packer.pyx", line 120, in msgpack._cmsgpack.Packer.__cinit__
MemoryError: Unable to allocate internal buffer.
MemoryError: Unable to allocate internal buffer.
File "msgpack\\_packer.pyx", line 120, in msgpack._cmsgpack.Packer.__cinit__
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "D:\Program Files (x86)\ChimeraX 1.3\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:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 620, in save
fserialize(stream, mgr.bundle_infos())
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 298, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 295, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack\\_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap
File "_serialize.pyx", line 209, in chimerax.core._serialize._encode_ext
File "_serialize.pyx", line 196, in chimerax.core._serialize._pack_as_array
File "msgpack\\_packer.pyx", line 120, in msgpack._cmsgpack.Packer.__cinit__
MemoryError: Unable to allocate internal buffer.
MemoryError: Unable to allocate internal buffer.
File "msgpack\\_packer.pyx", line 120, in msgpack._cmsgpack.Packer.__cinit__
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 513.29
OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 20L6A09YCD
OS: Microsoft Windows 10 家庭中文版 (Build 18363)
Memory: 17,027,555,328
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
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: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
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: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
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: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
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: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 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: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
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: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving session |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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