![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#6707 closed defect (duplicate)
Problem destroying status bar
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/87a_cavity.cxs
Opened 6eid_15_1.mrc as #2, grid size 216,208,264, pixel 0.5, shown at level
5e-05, step 1, values int8
Opened 871_15_2.mrc as #3, grid size 220,216,300, pixel 0.5, shown at level
5e-05, step 1, values int8
Log from Mon Apr 25 18:58:52 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\Users\user\Documents\BCS\TMEM87a\Draft\AR_draft_220304\Figure_3\0423_cavity\87a_cavity.cxs
> format session
Opened 87a_high.mrc copy as #11, grid size 220,216,300, pixel 0.5, shown at
level 5e-05, step 1, values int8
Opened 2022.apr23.932.mrc copy as #3, grid size 204,200,280, pixel 0.5, shown
at level 5e-05, step 1, values int8
Log from Sat Apr 23 20:48:18 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\Users\user\Documents\BCS\TMEM87a\Draft\AR_draft_220304\Figure_2\Figure2a\fig2a_0420\fig2a_0422_3v.cxs
> format session
Opened 7w9w_high.mrc copy as #9, grid size 220,216,272, pixel 0.5, shown at
level 5e-05, step 1, values int8
Opened 7drt_high.mrc copy as #10, grid size 116,116,156, pixel 1, shown at
level 0.958, step 1, values int8
Opened 5yqz_high.mrc copy as #7, grid size 112,136,160, pixel 1, shown at
level 0.0342, step 1, values int8
Opened 87a_high.mrc copy as #11, grid size 220,216,300, pixel 0.5, shown at
level 5e-05, step 1, values int8
Log from Fri Apr 22 15:38:35 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
Opened 87a_high.mrc copy as #8, grid size 220,216,300, pixel 0.5, shown at
level 1, step 1, values int8
Opened 7w9w_high.mrc copy as #9, grid size 220,216,272, pixel 0.5, shown at
level 5e-05, step 1, values int8
Opened 7drt_high.mrc copy as #10, grid size 116,116,156, pixel 1, shown at
level 0.958, step 1, values int8
Opened 5yqz_high.mrc copy as #7, grid size 112,136,160, pixel 1, shown at
level 0.0342, step 1, values int8
Log from Thu Apr 21 19:41:08 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Opened 87a_high.mrc copy as #8, grid size 220,216,300, pixel 0.5, shown at
level 1, step 1, values int8
Log from Wed Apr 20 20:25:29 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Thu Apr 14 20:07:58 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/fig2a_0414.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Thu Apr 14 11:02:28 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0323/fig2a_0324.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Thu Mar 24 11:06:26 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0304/fig2a_0323.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Wed Mar 23 17:27:00 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0304/fig2a_0307.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Mon Mar 7 11:39:24 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0304/fig2a_0304.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Fri Mar 4 11:47:12 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\Users\user\Documents\BCS\TMEM87a\Draft\Han_TMEM87a_paper\ar_draft\Fig3\Fig3A\fig3a_0213.cxs
> format session
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Thu Mar 3 16:05:48 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/fig3a_0222/3a_0215.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Tue Feb 15 17:31:07 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\Users\user\Documents\BCS\TMEM87a\Draft\Han_TMEM87a_paper\ar_draft\Fig3\Fig3A\v2\3a_0214.cxs
> format session
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Mon Feb 14 21:12:11 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/fig3a_0212.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Sat Feb 12 16:19:27 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Old_figure/figure1/0209_fig1/fig1_0209.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Wed Feb 9 13:02:44 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\Users\user\Documents\BCS\TMEM87a\Draft\Old_figure\figure1\0209_fig1\fig1_0209.cxs
> format session
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Wed Feb 9 10:29:37 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Old_figure/figure1/0209_fig1/fig1_0209.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Wed Feb 9 09:59:10 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\Users\user\Documents\BCS\TMEM87a\Draft\Old_figure\figure1\Figure_1_0121\figure1_0127.cxs
> format session
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.161, step 1, values float32
Log from Thu Jan 27 15:31:58 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/figure1_0121.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.173, step 1, values float32
Log from Fri Jan 21 21:17:21 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\Users\user\Documents\BCS\TMEM87a\Draft\figure\figure1\Figure_1_0121\figure1_0121.cxs
> format session
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.173, step 1, values float32
Log from Fri Jan 21 17:11:35 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\user\Documents\BCS\TMEM87a\Draft\figure\figure1\fg1_1209.cxs
> format session
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.173, step 1, values float32
Log from Thu Dec 9 16:41:18 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/fg1_1117.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.173, step 1, values float32
Log from Wed Nov 17 13:50:39 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/tm87_v1.cxs
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.342, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.198, step 1, values float32
Log from Wed Oct 27 21:15:25 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\user\Documents\BCS\TMEM87a\Paper\figure\tm87_v1.cxs format
> session
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.318, step 1, values float32
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.15, step 2, values float32
Log from Wed Oct 27 14:21:38 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\user\Documents\BCS\TMEM87a\Paper\figure\tm87_v1.cxs format
> session
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.354, step 1, values float32
Log from Tue Oct 26 18:44:40 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\user\Documents\BCS\TMEM87a\Paper\figure\tm87_v1.cxs format
> session
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.378, step 1, values float32
Log from Mon Oct 25 19:40:21 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\user\Documents\BCS\TMEM87a\Paper\figure\tm87_v1.cxs format
> session
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.438, step 1, values float32
Log from Mon Oct 25 15:01:28 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/user/Desktop/TMEM87A_phenix/tmem87a_1025.pdb
Summary of feedback from opening
C:/Users/user/Desktop/TMEM87A_phenix/tmem87a_1025.pdb
---
warning | Ignored bad PDB record found on line 3450
END
Chain information for tmem87a_1025.pdb #1
---
Chain | Description
A | No description available
> set bgColor white
> ui mousemode right select
> select /A:124
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select clear
> select /A:375
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:412
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:408
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:412
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:415
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /A:375
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:371
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:347
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /A:351
20 atoms, 18 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /A:367
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:309
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /A:445
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /A:442
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:441
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:442
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select clear
> select clear
> open
> C:/Users/user/Desktop/TMEM87A_phenix/cryosparc_P4_J659_020_volume_map.mrc
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.15, step 2, values float32
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
> volume #2 step 1
> select clear
> volume #2 level 0.4382
> select clear
> hide #!1 models
> show #!1 models
> hide #!2 models
> select clear
> select /A:433
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:433
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select /A:432
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select /A:431
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /A:89
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /A:128
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:74
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select clear
> show #!2 models
> hide #!2 models
> select /A:74
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select clear
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
——— End of log from Mon Oct 25 15:01:28 2021 ———
opened ChimeraX session
> select clear
> select clear
> select /A:360
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A:391
8 atoms, 7 bonds, 1 residue, 1 model selected
> setattr :359-391 res ss_type 1
Assigning ss_type attribute to 33 items
> select clear
> select /A:364
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:365
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:364
11 atoms, 11 bonds, 1 residue, 1 model selected
> setattr :364-365 res ss_type 1
Assigning ss_type attribute to 2 items
> select clear
> select clear
> select clear
> select /A:423
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:424
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:419
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:424
8 atoms, 7 bonds, 1 residue, 1 model selected
> setattr :419-424 res ss_type 1
Assigning ss_type attribute to 6 items
> select clear
> setattr :419-424 res ss_type H
Assigning ss_type attribute to 6 items
Cannot set attribute 'ss_type' to 'H'
> setattr :419-424 res ss_type 1
Assigning ss_type attribute to 6 items
> select /A:421
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add /A:422
21 atoms, 21 bonds, 2 residues, 1 model selected
> select add /A:423
28 atoms, 27 bonds, 3 residues, 1 model selected
> select clear
> select clear
Alignment identifier is 1/A
> select /A:421
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add /A:422
21 atoms, 21 bonds, 2 residues, 1 model selected
> select add /A:423
28 atoms, 27 bonds, 3 residues, 1 model selected
> show sel cartoons
> select helix
1549 atoms, 1584 bonds, 189 residues, 1 model selected
> select clear
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select clear
> select clear
> select clear
> select /A:379
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:377
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add /A:379
25 atoms, 26 bonds, 2 residues, 1 model selected
> select /A:90-95,224-249,258-286,294-317,335-352,359-391,398-426,436-459
1549 atoms, 1584 bonds, 189 residues, 1 model selected
> select clear
> select clear
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
> close session
> open C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tmem87a_1025_1.pdb
Chain information for tmem87a_1025_1.pdb #1
---
Chain | Description
A | No description available
> select /A:441
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /A:442
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add /A:445
30 atoms, 29 bonds, 3 residues, 1 model selected
> hide sel atoms
> select clear
> select /A:412
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /A:415
13 atoms, 11 bonds, 2 residues, 1 model selected
> select add /A:309
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add /A:375
30 atoms, 26 bonds, 4 residues, 1 model selected
> select add /A:371
38 atoms, 33 bonds, 5 residues, 1 model selected
> hide sel atoms
> select clear
> select add /A:351
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /A:347
20 atoms, 18 bonds, 2 residues, 1 model selected
> select add /A:340
32 atoms, 30 bonds, 3 residues, 1 model selected
> select add /A:367
40 atoms, 37 bonds, 4 residues, 1 model selected
> hide sel atoms
> select clear
> select clear
> select /A:408
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:124
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /A:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A:128
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:74
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:431
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /A:89
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
> ui windowfill toggle
> ui windowfill toggle
> select clear
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
Alignment identifier is 1/A
> select clear
> select /A:90-95,224-249,258-286,294-317,328-352,360-391,398-426,436-459
1596 atoms, 1632 bonds, 195 residues, 1 model selected
> select clear
> color red
> undo
> select sequence 224-249
Nothing selected
> select sequence 224-249
Nothing selected
> select sequence 224-249
Nothing selected
> select /A:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:258-286
248 atoms, 255 bonds, 29 residues, 1 model selected
> select clear
> select /A:258-286
248 atoms, 255 bonds, 29 residues, 1 model selected
> select /A:90-95,224-249,258-286,294-317,328-352,360-391,398-426,436-459
1596 atoms, 1632 bonds, 195 residues, 1 model selected
> select clear
> select /A:224
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:224-249
218 atoms, 227 bonds, 26 residues, 1 model selected
> select /A:231
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:224-249
218 atoms, 227 bonds, 26 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel red
> select clear
> select /A:224-249
218 atoms, 227 bonds, 26 residues, 1 model selected
> ui tool show "Color Actions"
> color sel crimson
> color sel crimson
> select clear
> select /A:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:258-286
248 atoms, 255 bonds, 29 residues, 1 model selected
> color sel orange
> color sel dark orange
> select clear
> select /A:294
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:294-317
181 atoms, 180 bonds, 24 residues, 1 model selected
> color sel gold
> color sel yellow
> color sel gold
> select clear
> select /A:224
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:224-225
19 atoms, 20 bonds, 2 residues, 1 model selected
> select /A:224
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:224-249
218 atoms, 227 bonds, 26 residues, 1 model selected
> color sel red
> select clear
> select /A:328
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:328-352
187 atoms, 189 bonds, 25 residues, 1 model selected
> color sel forest green
> select clear
> select /A:360
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:360-391
258 atoms, 265 bonds, 32 residues, 1 model selected
> color sel royal blue
> select clear
> select /A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:398-426
238 atoms, 244 bonds, 29 residues, 1 model selected
> color sel midnight blue
> select clear
> select /A:436
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:436-459
209 atoms, 214 bonds, 24 residues, 1 model selected
> color sel blue violet
> select clear
> select /A:436
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:436-459
209 atoms, 214 bonds, 24 residues, 1 model selected
> color sel purple
> color sel blue violet
> color sel dark violet
> color sel dark magenta
> color sel purple
> select clear
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
> open
> C:/Users/user/Desktop/TMEM87A_phenix/cryosparc_P4_J659_020_volume_map.mrc
Opened cryosparc_P4_J659_020_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.883, shown at level 0.15, step 2, values float32
> hide #!1 models
> volume #2 step 1
> volume #2 level 0.3781
> select #2
2 models selected
> select clear
> volume #2 level 0.3781
> select clear
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
——— End of log from Mon Oct 25 19:40:21 2021 ———
opened ChimeraX session
> hide #!2 models
> show #!1 models
> show #!2 models
> show surfaces
> hide surfaces
> ui tool show "Volume Viewer"
> volume #2 color #fffce9
> surface dust #2 size 8.83
> color zone #2 near #1 distance 5.3
> color zone #2 near #1 distance 5.3
> undo
> undo
> volume show
> volume hide
> volume show
> volume style mesh
> volume style mesh
> undo
> undo
> undo
> transparency #1.2 50
> volume show
> volume style surface
> transparency 0
> transparency 50
> volume #2 level 0.354
> transparency 0
> fitmap #1 inMap #2
Fit molecule tmem87a_1025_1.pdb (#1) to map
cryosparc_P4_J659_020_volume_map.mrc (#2) using 3367 atoms
average map value = 0.672, steps = 28
shifted from previous position = 0.0128
rotated from previous position = 0.0168 degrees
atoms outside contour = 763, contour level = 0.35404
Position of tmem87a_1025_1.pdb (#1) relative to
cryosparc_P4_J659_020_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99999997 0.00020493 -0.00013135 -0.01389826
-0.00020490 0.99999997 0.00016205 0.01442828
0.00013138 -0.00016202 0.99999998 -0.00475626
Axis -0.55414339 -0.44924600 -0.70078751
Axis point 80.38781010 55.52115923 0.00000000
Rotation angle (degrees) 0.01675363
Shift along axis 0.00455291
> vop gaussian #2 sdev 2.65
Opened cryosparc_P4_J659_020_volume_map.mrc gaussian as #3, grid size
320,320,320, pixel 0.883, shown at step 1, values float32
> vop gaussian #3 sdev 2.65
Opened cryosparc_P4_J659_020_volume_map.mrc gaussian as #4, grid size
320,320,320, pixel 0.883, shown at step 1, values float32
> undo
> undo
> close #3
> close #4
> show #!1 models
> hide #!1 models
> volume #2 color #cecece
> volume style image
> undo
> undo
> volume style image
> volume style image
> volume style image
> volume style image
> volume style image
> volume style surface
> volume style mesh
> volume style surface
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
> save C:\Users\user\Desktop\image1.png supersample 3
> save C:\Users\user\Desktop\image2.png supersample 3
> save C:\Users\user\Desktop\image3.png supersample 3
> show #!1 models
> hide #!2 models
> ui mousemode right select
> select clear
> select /A:431
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /A:89
12 atoms, 10 bonds, 2 residues, 2 models selected
> color (#!1 & sel) red
> color (#!1 & sel) byhetero
> select clear
> select /A:74
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /A:128@CA
7 atoms, 5 bonds, 2 residues, 2 models selected
> color (#!1 & sel) red
> color (#!1 & sel) byhetero
> select clear
> select clear
> ui mousemode right select
> show #!2 models
> hide #!1 models
> ui mousemode right select
> ui mousemode right select
> ui mousemode right select
> select clear
> show #!1 models
> hide #!2 models
> select clear
> select clear
> show #!2 models
> hide #!1 models
> ui mousemode right rotate
> ui mousemode right rotate
> ui mousemode right select
> ui mousemode right select
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> turn y, 90
Expected an axis vector or a keyword
> turn y 90
> turn y 90
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> turn y 90
> turn y 90
> volume showOutlineBox true
> transparency 50
> volume showOutlineBox false
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
——— End of log from Tue Oct 26 18:44:40 2021 ———
opened ChimeraX session
> volume hide
> show #!2 models
> volume #2 change image level -0.03296,0 level 0.1493,0.8 level 5.723,1
> volume #2 level 0.1977
> hide #!1 models
> open
> C:/Users/user/Desktop/TMEM87A_phenix/cryosparc_P4_J659_020_volume_map.mrc
Opened cryosparc_P4_J659_020_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.883, shown at level 0.15, step 2, values float32
> hide #!3 models
> volume #2 level 0.318
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
> open C:/Users/user/Desktop/TMEM87A_phenix/tmem87a_1025.pdb
Summary of feedback from opening
C:/Users/user/Desktop/TMEM87A_phenix/tmem87a_1025.pdb
---
warning | Ignored bad PDB record found on line 3450
END
Chain information for tmem87a_1025.pdb #4
---
Chain | Description
A | No description available
> hide #!4 models
> hide #!1 models
> show #!4 models
> ui mousemode right select
> select #4/A:415
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:371
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4/A:415
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #4/A:371
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4/A:415
14 atoms, 12 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select #4/A:309
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
> includeMaps true
——— End of log from Wed Oct 27 14:21:38 2021 ———
opened ChimeraX session
Drag select of 8 residues
> select clear
> hide #!4 models
> show #!1 models
> ui mousemode right select
Drag select of 102 atoms, 124 residues, 2 pseudobonds, 104 bonds
Drag select of 69 atoms, 131 residues, 2 pseudobonds, 70 bonds
Drag select of 108 atoms, 155 residues, 2 pseudobonds, 109 bonds
> color sel light slate gray
> color sel light steel blue
> color sel silver
> color sel lavender
> color sel mint cream
> color sel silver
> color sel light steel blue
> color sel light slate gray
> select clear
Drag select of 106 atoms, 138 residues, 2 pseudobonds, 108 bonds
> color sel light slate gray
> select clear
> select #1/A:433
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/A:432
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #1/A:430
22 atoms, 19 bonds, 3 residues, 2 models selected
> select add #1/A:354
26 atoms, 22 bonds, 4 residues, 2 models selected
> select add #1/A:355
31 atoms, 26 bonds, 5 residues, 2 models selected
> select add #1/A:356
40 atoms, 34 bonds, 6 residues, 2 models selected
> select add #1/A:357
47 atoms, 40 bonds, 7 residues, 2 models selected
> select add #1/A:358
55 atoms, 47 bonds, 8 residues, 2 models selected
> select add #1/A:427
66 atoms, 57 bonds, 9 residues, 2 models selected
> color sel light slate gray
> select #1/A:216
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #1/A:220
19 atoms, 18 bonds, 2 residues, 2 models selected
> select add #1/A:221
27 atoms, 25 bonds, 3 residues, 2 models selected
> select add #1/A:37
32 atoms, 29 bonds, 4 residues, 2 models selected
> select add #1/A:289
38 atoms, 34 bonds, 5 residues, 2 models selected
> select add #1/A:290
45 atoms, 40 bonds, 6 residues, 2 models selected
> select add #1/A:291
54 atoms, 48 bonds, 7 residues, 2 models selected
> select add #1/A:292
58 atoms, 51 bonds, 8 residues, 2 models selected
> select add #1/A:293
63 atoms, 55 bonds, 9 residues, 2 models selected
> color sel light slate gray
> select clear
> select #1/A:73
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:74
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/A:128
12 atoms, 10 bonds, 2 residues, 2 models selected
> color (#!1 & sel) red
> color (#!1 & sel) byhetero
> select clear
> select #1/A:431
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/A:89
12 atoms, 10 bonds, 2 residues, 2 models selected
> color (#!1 & sel) red
> color (#!1 & sel) byhetero
> select clear
> select #1/A:37
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:37-41
39 atoms, 38 bonds, 5 residues, 1 model selected
> select #1/A:37-41,46-51
81 atoms, 80 bonds, 11 residues, 1 model selected
> select #1/A:37-41,46-51,59-63
126 atoms, 125 bonds, 16 residues, 1 model selected
> select clear
> select clear
> select #1/A:473
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:220-473
2062 atoms, 2115 bonds, 254 residues, 1 model selected
> select clear
> select #1/A:37
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:37-218
1132 atoms, 1164 bonds, 2 pseudobonds, 137 residues, 2 models selected
> color sel silver
> select clear
Drag select of 86 atoms, 39 residues, 1 pseudobonds, 88 bonds
> color sel silver
> color (#!1 & sel) byhetero
> select clear
Drag select of 19 atoms, 12 residues, 1 pseudobonds, 19 bonds
> color sel light gray
> color sel silver
> color (#!1 & sel) byhetero
> select clear
> select #1/A:473
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:460-473
119 atoms, 124 bonds, 14 residues, 1 model selected
> select #1/A:427-435,460-473
195 atoms, 201 bonds, 23 residues, 1 model selected
> select #1/A:392-397,427-435,460-473
249 atoms, 254 bonds, 29 residues, 1 model selected
> color sel silver
> select clear
> select #1/A:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:357-359
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #1/A:353-359
48 atoms, 47 bonds, 7 residues, 1 model selected
> select #1/A:318-326,353-359
116 atoms, 115 bonds, 16 residues, 1 model selected
> select #1/A:287-291,318-326,353-359
151 atoms, 149 bonds, 21 residues, 1 model selected
> select #1/A:287-293,318-326,353-359
160 atoms, 158 bonds, 23 residues, 1 model selected
> select #1/A:287-293,318-326,353-359
160 atoms, 158 bonds, 23 residues, 1 model selected
> select #1/A:287-293,318-326,353-359
160 atoms, 158 bonds, 23 residues, 1 model selected
> color sel silver
> select clear
> select #1/A:327
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:327
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel silver
> select #1/A:286
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel orange
> color sel dark orange
> select clear
> select #1/A:293
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:287-293
44 atoms, 43 bonds, 7 residues, 1 model selected
> select #1/A:250-257,287-293
122 atoms, 123 bonds, 15 residues, 1 model selected
> select #1/A:214-223,250-257,287-293
206 atoms, 209 bonds, 25 residues, 1 model selected
> color sel silver
> select clear
> select clear
> select #1/A:89@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #1/A:431
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/A:89
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #1/A:74
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/A:128
12 atoms, 10 bonds, 2 residues, 2 models selected
> color sel crimson
> color sel dark red
> color sel fire brick
> color (#!1 & sel) byhetero
> select clear
> select #1/A:431
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/A:89
12 atoms, 10 bonds, 2 residues, 2 models selected
> color sel fire brick
> color (#!1 & sel) byhetero
> select clear
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!2 models
> save C:/Users/user/Desktop/TMEM87A_phenix/figure1.cxs
> show #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:37
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/A:37-219
1140 atoms, 1172 bonds, 2 pseudobonds, 138 residues, 2 models selected
> color sel orange
> color sel silver
> color sel silver
> color sel dark sea green
> hide #!2 models
> color sel gray
> color sel dark gray
> select clear
Drag select of 88 atoms, 47 residues, 2 pseudobonds, 89 bonds
> color sel silver
> color sel dark gray
> select clear
> select #4/A:473
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:220-473
2062 atoms, 2115 bonds, 254 residues, 1 model selected
> color sel dark orange
> select clear
Drag select of 19 atoms, 13 residues, 19 bonds
> color sel dark gray
> select clear
> show #!3 models
> hide #!3 models
> show #!2 models
> transparency #2.1 0
> color zone #2 near #4 distance 5.3
> transparency #2.1 50
> hide #!4 models
> show #!4 models
> hide #!4 models
> volume #2 level 0.342
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> show #!4 models
> color zone #2 near #4 distance 5.3
> hide #!4 models
> transparency #2.1 50
> show #!3 models
> volume #3 step 1
> volume #3 level 0.1977
> hide #!2 models
> show #!2 models
> transparency #2.1#3.1 0
> transparency #2.1#3.1 50
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> select #4/A:220-473
2062 atoms, 2115 bonds, 254 residues, 1 model selected
> color sel gold
> color zone #2 near sel & #4 distance 5.3
> color sel light salmon
> hide #!2 models
> show #!2 models
> color zone #2 near sel & #4 distance 5.3
> hide #!4 models
> show #!4 models
> hide #!2 models
> select clear
> select #4/A:219
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:37-219
1140 atoms, 1172 bonds, 2 pseudobonds, 138 residues, 2 models selected
> color sel steel blue
> color sel light slate gray
> select clear
Drag select of 87 atoms, 92 residues, 83 bonds
> color sel dark salmon
> color sel light salmon
> select clear
> select clear
> select clear
Drag select of 107 atoms, 120 residues, 2 pseudobonds, 108 bonds
> color sel light slate gray
> select clear
> show #!3 models
> hide #!3 models
> show #!2 models
> color zone #2 near #4 distance 5.3
> hide #!4 models
> transparency #2.1 50
> ray
Unknown command: ray
> raytraced
Unknown command: raytraced
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> image 2000, 2000
Unknown command: image 2000, 2000
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
No map chosen to save
> select #2
3 models selected
> ~select #2
Nothing selected
> save C:\Users\user\Desktop\image4.png supersample 3
> lighting simple
> lighting soft
> lighting soft
> lighting soft
> lighting simple
> lighting full
> lighting full
> lighting soft
> lighting simple
> lighting full
> set bgColor white
> save C:/Users/user/Desktop/TMEM87A_phenix/1.jpg width 703 height 571
> supersample 3
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> transparency #2.1 0
> hide #!2 models
> show #!3 models
> transparency #3.1 0
> transparency #3.1 50
> save C:/Users/user/Desktop/TMEM87A_phenix/figure1.cxs
> show #!2 models
> lighting full
> lighting full
> lighting soft
> lighting soft
> lighting soft
> lighting full
> lighting simple
> lighting simple
> hide #!3 models
> lighting full
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> turn y 90
> turn y 90
> nucleotides #!1 atoms
> style nucleic & #!1 stick
Changed 0 atom styles
> style #!1 ball
Changed 3367 atom styles
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> set bgColor Transparency
Invalid "bgColor" argument: Invalid color name or specifier
> set bgTransparency
Expected a keyword
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
No map chosen to save
> save C:/Users/user/Desktop/TMEM87A_phenix/1.png width 1000 height 812
> supersample 4 transparentBackground true
> hide #!3 models
> save C:/Users/user/Desktop/TMEM87A_phenix/2.png width 1000 height 812
> supersample 4 transparentBackground true
> hide #!2 models
> show #!3 models
> volume #3 level 0.1857
> volume #3 level 0.2218
> turn y 180
> show #!2 models
> hide #!2 models
> volume #3 level 0.1737
> volume #3 level 0.1737
> volume #3 level 0.1857
> lighting soft
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> show #!3 models
> turn y 180
> volume #3 level 0.1857
> hide #!3 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!1 models
> turn y 180
> show #!2 models
> hide #!1 models
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/figure1/1.png width
> 2000 height 1624 supersample 4 transparentBackground true
> hide #!2 models
> show #!2 models
> hide #!3 models
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/figure1/2.png width
> 2000 height 1624 supersample 4 transparentBackground true
> hide #!2 models
> show #!1 models
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/figure1/3.png width
> 2000 height 1624 supersample 4 transparentBackground true
> turn y 180
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/figure1/4.png width
> 2000 height 1624 supersample 4 transparentBackground true
> hide #!1 models
> show #!2 models
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/figure1/5.png width
> 2000 height 1624 supersample 4 transparentBackground true
> show #!3 models
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/figure1/6.png width
> 2000 height 1624 supersample 4 transparentBackground true
> hide #!3 models
> hide #!2 models
> show #!1 models
> turn y 180
> select clear
> select #1/A:74
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> undo
> select clear
> select clear
> select #1/A:127@CA
1 atom, 1 residue, 1 model selected
> select #1/A:79@CG
1 atom, 1 residue, 1 model selected
> select clear
> select #1/A:79@CB
1 atom, 1 residue, 1 model selected
> turn y 180
> select #1/A:62@CB
1 atom, 1 residue, 1 model selected
> select #1/A:62@CA
1 atom, 1 residue, 1 model selected
> select #1/A:62@CA
1 atom, 1 residue, 1 model selected
> select #1/A:79@CG
1 atom, 1 residue, 1 model selected
> select clear
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> volume #3 level 0.1977
> show #!2 models
> hide #!3 models
> show #!3 models
> save C:/Users/user/Documents/BCS/TMEM87a/Paper/figure/tm87_v1.cxs
——— End of log from Wed Oct 27 21:15:25 2021 ———
opened ChimeraX session
> show #!1 models
> hide #!2 models
> hide #!3 models
> style #!1 stick
Changed 3367 atom styles
> show #!2 models
> hide #!2 models
> ui tool show "Hide Dust"
> surface dust #2 size 8.83
> show #!2 models
> hide #!1 models
> surface dust #2 size 8.83
> surface dust #2 size 13.44
> surface dust #2 size 13.44
> show #!3 models
> hide #!2 models
> surface dust #3 size 5.3
> surface dust #3 size 19.59
> surface dust #3 size 19.59
> show #!1 models
> turn y 180
> turn y 180
> hide #!3 models
> show #!3 models
> turn y 180
> turn y 180
> turn y 180
> surface dust #3 size 14.08
> surface dust #3 size 9.96
> surface dust #3 size 9.96
> surface dust #3 size 9.96
> surface undust #3
> surface dust #3 size 8.65
> volume #3 level 0.1484
> show #!2 models
> hide #!2 models
> turn y 180
> hide #!3 models
> show #!3 models
> turn y 180
> turn y 180
> turn y 180
> turn y 180
> turn y 180
> turn y 180
> turn y 180
> turn y 180
> volume #3 level 0.1731
> turn y 180
> turn y 180
> turn y 180
> hide #!3 models
> turn y 180
> show #!3 models
> turn y 180
> turn y 180
> hide #!3 models
> save C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/tm87_1117.cxs
> save C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/model_1117.png
> width 1000 height 812 supersample 3 transparentBackground true
> show #!2 models
> hide #!1 models
> save C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/map_1117.png
> width 1000 height 812 supersample 3 transparentBackground true
> hide #!2 models
> show #!3 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/micelle_1117.png
> width 1000 height 812 supersample 3 transparentBackground true
> turn y 180
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/micelle2_1117.png
> width 1000 height 812 supersample 3 transparentBackground true
> show #!2 models
> hide #!3 models
> surface dust #2 size 15.48
> surface dust #2 size 15.48
> save C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/map2_1117.png
> width 1000 height 812 supersample 3 transparentBackground true
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/model2_1117.png
> width 1000 height 812 supersample 3 transparentBackground true
> save C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/fg1_1117.cxs
——— End of log from Wed Nov 17 13:50:39 2021 ———
opened ChimeraX session
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> setattr /A:328-334 res ss_type 3
Assigning ss_type attribute to 14 items
Drag select of 6 residues
> select add #1/A:333
52 atoms, 6 bonds, 7 residues, 2 models selected
> select add #1/A:334
59 atoms, 12 bonds, 8 residues, 2 models selected
> ui tool show "Color Actions"
> color sel silver
> select clear
> save C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/fg1_1117.cxs
> save C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/fg1_1209.cxs
——— End of log from Thu Dec 9 16:41:18 2021 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> select ::name="Y01"
168 atoms, 174 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel goldenrod
> color sel dark khaki
> color sel goldenrod
> color (#!1 & sel) byhetero
> ui mousemode right select
> select clear
Drag select of 19 residues
> select clear
> select #1/A:431
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:89
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/A:431
12 atoms, 10 bonds, 2 residues, 2 models selected
> color (#!1 & sel) byhetero
> color (#!1 & sel) byhetero
> ui tool show "Color Actions"
> color sel orange
> color sel byhetero
> select clear
> select clear
> select clear
> select #1/A:89
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel sandy brown
> color sel byhetero
> select clear
> select #1/A:431
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel sandy brown
> color sel byhetero
> select #1/A:74
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel sandy brown
> color sel byhetero
> select #1/A:128
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel sandy brown
> color sel byhetero
> select clear
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> select #1/A:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select clear
> setattr :100-110 res ss_type 1
Assigning ss_type attribute to 22 items
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/figure1_0121.cxs
> graphics silhouettes false
> select clear
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting flat
> lighting full
> lighting full
> lighting flat
> lighting full
> lighting full
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting flat
> lighting flat
> lighting flat
> lighting full
> lighting soft
> lighting soft
> lighting simple
> lighting simple
> lighting soft
> lighting flat
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting soft
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
Drag select of 14 atoms, 15 bonds
> color sel olive drab
> color sel byhetero
> color sel yellow green
> color sel byhetero
> select clear
Drag select of 12 atoms, 14 bonds
> color sel dark khaki
> color sel byhetero
> color sel yellow green
> color sel byhetero
> select clear
> select ::name="Y01"
168 atoms, 174 bonds, 2 residues, 2 models selected
> color sel dark khaki
> color sel byhetero
> color sel goldenrod
> color sel byhetero
> select clear
Drag select of 10 atoms, 9 bonds
Drag select of 14 atoms, 14 bonds
> select clear
> select ::name="NAG"
140 atoms, 144 bonds, 10 residues, 2 models selected
> color sel light green
> color sel dark sea green
> color sel byhetero
> select clear
Drag select of 24 atoms, 24 bonds
> color sel dark sea green
> color sel byhetero
> select clear
> select ::name="NAG"
140 atoms, 144 bonds, 10 residues, 2 models selected
> color sel pale green
> color sel byhetero
> select clear
Drag select of 14 atoms, 15 bonds
> color sel pale green
> color sel byhetero
> select clear
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/figure1_0121.cxs
——— End of log from Fri Jan 21 17:11:35 2022 ———
opened ChimeraX session
> select #1/A:128
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel coral
> color sel byhetero
> color sel tomato
> color sel byhetero
> select #1/A:74
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel tomato
> color sel byhetero
> select #1/A:128
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel tomato
> color sel byhetero
> select clear
> select clear
> select #1/A:431
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel tomato
> color sel byhetero
> select clear
> select #1/A:89
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel tomato
> color sel byhetero
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.1971
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select clear
> volume #3 level 0.2092
> volume #3 level 0.1731
> hide #!3 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/figure1_0121.cxs
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/fig1d_1.tif
> width 703 height 571 supersample 3 transparentBackground true
> turn y 180
> show #!3 models
> turn y 180
> turn y 180
> turn y 180
> turn y 180
> hide #!3 models
> turn y 180
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/figure1_0121.cxs
——— End of log from Fri Jan 21 21:17:21 2022 ———
opened ChimeraX session
> select ::name="NAG"
140 atoms, 144 bonds, 10 residues, 2 models selected
> ui tool show "Color Actions"
> color sel lime
> color sel byhetero
> ui mousemode right select
> select clear
> select ::name="BMA"
22 atoms, 22 bonds, 2 residues, 2 models selected
> color (#!1 & sel) lime
> color (#!1 & sel) byhetero
> select clear
> select ::name="Y01"
168 atoms, 174 bonds, 2 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> ui tool show "Color Actions"
> color sel cyan
> color sel byhetero
> select clear
> show #!3 models
> volume #3 level 0.137
> volume #3 level 0.161
> turn y 180
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> turn y 180
> turn y 180
> show #!3 models
> turn y 180
> turn y 180
> show #!2 models
> hide #!3 models
> turn y 180
> hide #!2 models
> turn y 180
> show #!3 models
> turn y 180
> turn y 180
> hide #!3 models
> turn y 180
> show #!3 models
> turn y 180
> hide #!3 models
> show #!3 models
> turn y 180
> turn y 180
> hide #!3 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/fig1d_1.tif
> width 703 height 571 supersample 3 transparentBackground true
> show #!2 models
> hide #!1 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/fig1b_1.tif
> width 703 height 571 supersample 3 transparentBackground true
> hide #!2 models
> show #!3 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/fig1b_3.tif
> width 703 height 571 supersample 3 transparentBackground true
> hide #!3 models
> show #!1 models
> turn y 180
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/fig1d_2.tif
> width 703 height 571 supersample 3 transparentBackground true
> show #!2 models
> hide #!1 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/fig1b_2.tif
> width 703 height 571 supersample 3 transparentBackground true
> show #!3 models
> hide #!2 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/fig1b_4.tif
> width 703 height 571 supersample 3 transparentBackground true
> show #!1 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/figure/figure1/Figure_1_0121/figure1_0127.cxs
——— End of log from Thu Jan 27 15:31:58 2022 ———
opened ChimeraX session
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/87a_meeting/tmem87a_0208v2.pdb
Chain information for tmem87a_0208v2.pdb #5
---
Chain | Description
A | No description available
> hide #!3 models
> hide #!5 models
> setattr :329-334 res ss_type 0
Assigning ss_type attribute to 18 items
> show #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select
> #5/A:90-95,224-249,258-286,294-317,328,335-352,360-391,398-426,436-459
1548 atoms, 1582 bonds, 189 residues, 1 model selected
> select #5/A:224
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/A:224-249
218 atoms, 227 bonds, 26 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ffff00ff
> color sel #ff0000ff
> select #5/A:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:258-286
248 atoms, 255 bonds, 29 residues, 1 model selected
> color sel #ffff00ff
> color sel #ffdd99ff
> color sel #fd9413ff
> select
> #5/A:90-95,224-249,258-286,294-317,328,335-352,360-391,398-426,436-459
1548 atoms, 1582 bonds, 189 residues, 1 model selected
> select #5/A:294
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:294-310
129 atoms, 128 bonds, 17 residues, 1 model selected
> select #5/A:311
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:311-315
38 atoms, 37 bonds, 5 residues, 1 model selected
> select #5/A:317
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:294-317
181 atoms, 180 bonds, 24 residues, 1 model selected
> color sel #ffdd99ff
> color sel #ffffeeff
> color sel #ffe61fff
> select
> #5/A:90-95,224-249,258-286,294-317,328,335-352,360-391,398-426,436-459
1548 atoms, 1582 bonds, 189 residues, 1 model selected
> select clear
> select #5/A:294
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:294-317
181 atoms, 180 bonds, 24 residues, 1 model selected
> select #5/A:335
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:335-350
114 atoms, 115 bonds, 16 residues, 1 model selected
> select #5/A:352
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:335-352
132 atoms, 133 bonds, 18 residues, 1 model selected
> color sel #ffffeeff
> color sel #555599ff
> color sel #559555ff
> select #5/A:327
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/A:327-329
18 atoms, 17 bonds, 3 residues, 1 model selected
> hide #!1 models
> select #5/A:328
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:328
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:318-319
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/A:318-334
127 atoms, 128 bonds, 17 residues, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> setattr :326-334 res ss_type 0
Assigning ss_type attribute to 27 items
> select #5/A:224
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/A:224-249
218 atoms, 227 bonds, 26 residues, 1 model selected
> color sel #555599ff
> color sel #ffff00ff
> color sel #ff0000ff
> select #5/A:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:258-286
248 atoms, 255 bonds, 29 residues, 1 model selected
> color sel #ffff00ff
> color sel #ffdd99ff
> color sel #fd9413ff
> select #5/A:294
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:294-317
181 atoms, 180 bonds, 24 residues, 1 model selected
> color sel #ffdd99ff
> color sel #ffffeeff
> color sel #ffe61fff
> select #5/A:335
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:335-352
132 atoms, 133 bonds, 18 residues, 1 model selected
> color sel #ffffeeff
> color sel #555599ff
> color sel #559555ff
> select #5/A:360
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:360-391
258 atoms, 265 bonds, 32 residues, 1 model selected
> color sel #44cc77ff
> color sel #4c79ffff
> select #5/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:398-426
238 atoms, 244 bonds, 29 residues, 1 model selected
> color sel #11ee11ff
> color sel #1e1e85ff
> select #5/A:436
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:436-459
209 atoms, 214 bonds, 24 residues, 1 model selected
> color sel #11ee11ff
> color sel #995500ff
> color sel #950095ff
Drag select of 159 atoms, 392 residues, 2 pseudobonds, 158 bonds
Drag select of 186 atoms, 392 residues, 2 pseudobonds, 185 bonds
> hide sel atoms
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> show #!1 models
> hide #!1 models
> select #5/A:62
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:62
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:62,79
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/A:62,79,127
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel byhetero
> show #!1 models
> select clear
> hide #!1 models
> select ::name="BMA"
33 atoms, 33 bonds, 3 residues, 3 models selected
> show sel & #!5 atoms
> color sel lime
> color sel byhetero
> select ::name="NAG"
210 atoms, 216 bonds, 15 residues, 3 models selected
> show sel & #!5 atoms
> color sel byhetero
> color sel lime
> color sel byhetero
> select clear
> show #!1 models
> select #5/A:128
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:128
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:74,128
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel coral
> color sel byhetero
> hide #!1 models
> select clear
> show #!1 models
> select #5/A:89
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:89
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:89,431
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel coral
> color sel byhetero
> select clear
> hide #!1 models
No map chosen to save
> show #!3 models
> show #!2 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Old_figure/figure1/0209_fig1/fig1_0209.cxs
> includeMaps true
> select clear
> hide #!3 models
> hide #!2 models
> select ::name="CLR"
74 atoms, 77 bonds, 1 residue, 1 model selected
> show sel atoms
> select H
144 atoms, 3 residues, 3 models selected
> hide sel & #!5 atoms
> select ::name="CLR"
74 atoms, 77 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Old_figure/figure1/0209_fig1/fig1_0209.cxs
——— End of log from Wed Feb 9 09:59:10 2022 ———
opened ChimeraX session
> select ::name="CLR"
74 atoms, 77 bonds, 1 residue, 1 model selected
> color sel byhetero
> color sel byhetero
> color sel #ffff99ff
> color sel #ff94ffff
> color sel byhetero
> select clear
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Old_figure/figure1/0209_fig1/fig1_0209.cxs
——— End of log from Wed Feb 9 10:29:37 2022 ———
opened ChimeraX session
> show #!3 models
> turn y 180
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!3 models
> turn y 180
> turn y 180
> hide #!5 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Old_figure/figure1/0209_fig1/fig1_0209.cxs
> show #!5 models
> hide #!3 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Old_figure/figure1/0209_fig1/fig1dleft.png
> width 1308 height 835 supersample 3 transparentBackground true
> turn y 180
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Old_figure/figure1/0209_fig1/fig1right.png
> width 1308 height 835 supersample 3 transparentBackground true
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Old_figure/figure1/0209_fig1/fig1dleft.tif
> width 1308 height 835 supersample 3 transparentBackground true
> lighting soft
> lighting full
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting soft
> lighting soft
> setattr :100-110 res ss_type 1
Assigning ss_type attribute to 33 items
> show #!3 models
> turn y 180
> hide #!3 models
> show #!3 models
> turn y 180
> turn y 180
> turn y 180
> turn y 180
> turn y 180
> hide #!3 models
> turn y 180
> turn y 180
> turn y 180
> undo
> turn y 180
> show #!3 models
> hide #!3 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Old_figure/figure1/0209_fig1/fig1_0209.cxs
——— End of log from Wed Feb 9 13:02:44 2022 ———
opened ChimeraX session
> close #4
> close #1
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/fig3a_0212.cxs
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/7kc4_WLS.pdb
Chain information for 7kc4_WLS.pdb #1
---
Chain | Description
B | No description available
> hide atoms
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/5yqz_rhodopsin_GPCR.pdb
Chain information for 5yqz_rhodopsin_GPCR.pdb #4
---
Chain | Description
P | No description available
R | No description available
> hide atoms
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/7aky_viralrhodopsin.pdb
Chain information for 7aky_viralrhodopsin.pdb #6
---
Chain | Description
A | No description available
> show atoms
> hide atoms
> hide #1 models
> hide #!4 models
> hide #!5 models
> hide #6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/fig3a_0212.cxs
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #1 models
> hide #1 models
> show #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Destroying pre-existing alignment with identifier 5/A
Alignment identifier is 5/A
> select #5/A:37
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:37-221
1156 atoms, 1188 bonds, 2 pseudobonds, 140 residues, 2 models selected
> hide sel cartoons
> show #1 models
> ui mousemode right select
> select #1/B:39
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> select #1/B:40
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:40-226
1531 atoms, 1573 bonds, 187 residues, 1 model selected
> hide sel cartoons
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/fig3a_0212.cxs
> hide #1 models
> show #1 models
> cartoon style sel modeHelix tube sides 20
> cartoon style sel modeHelix tube sides 20
> select #5
3358 atoms, 3454 bonds, 2 pseudobonds, 399 residues, 2 models selected
> cartoon style (#!5 & sel) modeHelix tube sides 20
> select clear
> hide #!5 models
> hide #1 models
> show #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/P
Alignment identifier is 4/P
> select #4/P:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/P:2-29
236 atoms, 241 bonds, 28 residues, 1 model selected
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #4/R
Alignment identifier is 4/R
> select #4/R:27
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/R:27-109
686 atoms, 715 bonds, 83 residues, 1 model selected
> hide sel cartoons
> show #!5 models
> select #4/R:1160
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #4/R:1038-1160
938 atoms, 952 bonds, 123 residues, 1 model selected
> hide sel cartoons
> select #4/R:1037
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/R:1023-1037
88 atoms, 88 bonds, 15 residues, 1 model selected
> hide sel cartoons
> select #4/R:1022
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/R:1012-1022
73 atoms, 73 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select #4/R:1011
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/R:1002-1011
84 atoms, 84 bonds, 10 residues, 1 model selected
> select #4/R:1001
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:426-1001
17 atoms, 15 bonds, 1 pseudobond, 2 residues, 2 models selected
> hide sel cartoons
> select #4/R:1002
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:1002-1018
138 atoms, 139 bonds, 17 residues, 1 model selected
> hide sel cartoons
> select clear
> cartoon style #4-5 modeHelix tube sides 20
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!5 cartoons
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/fig3a_0212.cxs
> show #!5 models
> show #1 models
> show #6 models
> hide #!5 models
> hide #!4 models
> hide #1 models
> cartoon style #6 modeHelix tube sides 20
> show #!5 models
> show #1 models
> show #!4 models
Drag select of 1341 residues, 3 pseudobonds
> cartoon style (#1,6#!4-5 & sel) xsection oval modeHelix default
> cartoon style (#1,6#!4-5 & sel & coil) xsection oval
> cartoon style (#1,6#!4-5 & sel) xsection barbell modeHelix default
> cartoon style (#1,6#!4-5 & sel) xsection oval modeHelix default
> select clear
> hide #6 models
> hide #!4 models
> hide #1 models
> show #1 models
> hide #1 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #!5 models
> show #!5 models
> hide #6 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!4 models
> ui tool show "Color Actions"
> color dark sea green
> undo
> show #!4 models
> show #6 models
> show #1 models
> hide #6 models
> hide #!4 models
> hide #1 models
> show #6 models
> hide #!5 models
> show #!5 models
> turn x 90
> turn x 90
> turn x 90
> show #!4 models
> hide #!5 models
> hide #6 models
> hide #!4 models
> show #!5 models
> turn x 90
> show #6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #1 models
> hide #1 models
> hide #!4 models
> hide #6 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/fig3a_0212.cxs
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/3a_test1.png
> width 703 height 572 supersample 3 transparentBackground true
> show #6 models
> hide #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/3a_test2.png
> width 703 height 572 supersample 3 transparentBackground true
> show #!4 models
> hide #6 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/3a_test3.png
> width 703 height 572 supersample 3 transparentBackground true
> show #1 models
> hide #!4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/3a_test4.png
> width 703 height 572 supersample 3 transparentBackground true
> show #!4 models
> show #!5 models
> show #6 models
Drag select of 1235 residues, 3 pseudobonds
> cartoon style (#1,6#!4-5 & sel) modeHelix tube sides 20
> select clear
> hide #6 models
> hide #!4 models
> hide #1 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/3a_test1.png
> width 703 height 572 supersample 3 transparentBackground true
> show #6 models
> hide #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/3a_test2.png
> width 703 height 572 supersample 3 transparentBackground true
> hide #6 models
> show #!4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/3a_test3.png
> width 703 height 572 supersample 3 transparentBackground true
> show #1 models
> hide #!4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/3a_test4.png
> width 703 height 572 supersample 3 transparentBackground true
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #6 models
> hide #6 models
> show #!5 models
> turn y 90
> turn y 90
> hide #!5 models
> show #!5 models
> show #!3 models
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #1 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #6 models
> hide #6 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/fig3a_0212.cxs
> show #!5 models
> hide #!4 models
> turn y 90
> turn y 90
> show #!3 models
> hide #!3 models
> show #6 models
> hide #6 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/fig3a_0212.cxs
——— End of log from Sat Feb 12 16:19:27 2022 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:37
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:37-220
1148 atoms, 1180 bonds, 2 pseudobonds, 139 residues, 2 models selected
> hide sel cartoons
> select clear
> show #!4 models
Drag select of 13 residues
> hide sel atoms
> hide sel cartoons
> select clear
Drag select of 65 residues
> select clear
> hide #!5 models
Drag select of 24 residues
> select clear
Drag select of 22 residues
> select clear
Drag select of 22 residues
> hide sel cartoons
> show #!5 models
> hide #!5 models
> show #6 models
> show #1 models
> hide #1 models
> hide #!4 models
> hide #6 models
> show #!5 models
> select clear
> show #1 models
> show #!4 models
> show #6 models
> hide #6 models
> hide #!5 models
> hide #!4 models
> hide #1 models
> show #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/v2/3a_0214.cxs
——— End of log from Mon Feb 14 21:12:11 2022 ———
opened ChimeraX session
> cartoon style #5 xsection oval modeHelix default
> show #6 models
> show #!4 models
> show #1 models
> ui mousemode right select
Drag select of 1145 residues, 1 pseudobonds
> cartoon style (#1,6#!4-5 & sel) xsection oval modeHelix default
> select clear
> hide #6 models
> hide #!5 models
> hide #!4 models
> hide #1 models
> show #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/v2/3a_0215.cxs
——— End of log from Tue Feb 15 17:31:07 2022 ———
opened ChimeraX session
> select ::name="CLR"
74 atoms, 77 bonds, 1 residue, 1 model selected
> show sel atoms
> select H
46 atoms, 1 residue, 1 model selected
> hide sel atoms
> show #6 models
> hide #!5 models
> select ::name="LYR"
29 atoms, 29 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> ui mousemode right select
> select clear
> show #1 models
> hide #1 models
> show #!5 models
> show #!4 models
> show #1 models
> hide #1 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!4 models
> show #1 models
> hide #1 models
> hide #!4 models
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/7aky_vr_v2.pdb
Chain information for 7aky_vr_v2.pdb #7
---
Chain | Description
A | No description available
> hide #!5 models
> hide #6 models
Drag select of 349 atoms, 223 residues, 310 bonds
> hide sel atoms
> select clear
> show #!5 models
> hide #!5 models
> hide #7 models
> show #6 models
> close #6
> show #7 models
> select ::name="LYR"
29 atoms, 29 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> hide #7 models
> show #7 models
> select clear
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> hide #7 models
> show #7 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/fig3a_0213.cxs
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/Fig3A/fig3a_0213.cxs
——— End of log from Thu Mar 3 16:05:48 2022 ———
opened ChimeraX session
> hide #7 models
> show #!4 models
> select ::name="LYR"
29 atoms, 29 bonds, 1 residue, 1 model selected
> show #!4 atoms
> hide #!4 atoms
> show #1 models
> hide #1 models
> select ::name="LFA"
208 atoms, 187 bonds, 21 residues, 1 model selected
> show #!4 atoms
> hide #!4 models
> show #!4 models
> hide #!4 atoms
> show #1 models
> show #7 models
> show #!5 models
> hide #!5 models
> select ::name="LFA"
208 atoms, 187 bonds, 21 residues, 1 model selected
> show sel atoms
> hide sel atoms
> hide #!4 models
> hide #1 models
> show #!5 models
> hide #7 models
> turn x 90
> turn x -90
> hide #!5 models
> show #7 models
> select ::name="LYR"
29 atoms, 29 bonds, 1 residue, 1 model selected
> color sel cyan
> color sel byhetero
> ui mousemode right select
> select clear
> select #7/A:204
29 atoms, 29 bonds, 1 residue, 1 model selected
> select #7/A:204
29 atoms, 29 bonds, 1 residue, 1 model selected
> select clear
> select #7/A:204@C3
1 atom, 1 residue, 1 model selected
> select #7/A:204@C3
1 atom, 1 residue, 1 model selected
> select clear
> select #7/A:204
29 atoms, 29 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel lime
> color sel magenta
> color sel byhetero
> select clear
> select #7/A:204
29 atoms, 29 bonds, 1 residue, 1 model selected
> color sel hot pink
> color sel byhetero
> color sel light pink
> color sel pink
> color sel violet
> color sel light pink
> color sel #ffaaffff
> color sel #fac4ffff
> color sel #fad8ffff
> color sel #f6c1ffff
> color sel #f4c0ffff
> color sel #f1bbffff
> color sel #e3aaffff
> color sel #e6aaffff
> color sel #e7a9ffff
> color sel #f0a5ffff
> color sel #f1a4ffff
> color sel #f4a4ffff
> color sel #ffa1ffff
> color sel #ffa0ffff
> color sel #ffa0fdff
> color sel #ff9efdff
> color sel #ff9efaff
> color sel #ff9cf7ff
> color sel #ff9be9ff
> color sel #ff9be8ff
> color sel #ff9be1ff
> color sel #ff9ce1ff
> color sel #ff9de2ff
> color sel #ffa0e6ff
> color sel #ffaaedff
> color sel #ffb7f2ff
> color sel #ffb8f2ff
> color sel #ffb9f2ff
> color sel #ffbbf0ff
> color sel #ffbdebff
> color sel #ffbdeaff
> color sel #ffbdebff
> color sel #ffbdf0ff
> color sel #ffbbf8ff
> color sel #ffb9ffff
> color sel #ffff7fff
> color sel #ffff00ff
> color sel #ff00ffff
> color sel #ff55ffff
> color sel #fb8effff
> color sel #ffa5fbff
> color sel #ff90ffff
> color sel #ff9cfaff
> color sel #ffff7fff
> color sel #ffff00ff
> color sel #aaffffff
> color sel #c6ffffff
> color sel byhetero
> select clear
> turn x 90
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #7 models
> show #7 models
> lighting soft
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting flat
> lighting flat
> lighting full
> lighting soft
> lighting soft
> lighting simple
> lighting soft
> hide #!5 models
> select #7/A:204
29 atoms, 29 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> show #!4 models
> hide #!4 models
> show #1 models
> hide #1 models
> select #7/A:204
29 atoms, 29 bonds, 1 residue, 1 model selected
> color sel orange red
> color sel byhetero
> select clear
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #7/A:204
29 atoms, 29 bonds, 1 residue, 1 model selected
> select clear
> show #!5 models
> hide #7 models
> turn x -90
> hide #!5 models
> show #7 models
> select #7/A:204
29 atoms, 29 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel yellow
> color sel cyan
> color sel cyan
> color sel deep sky blue
> color sel pale turquoise
> color sel light blue
> color sel powder blue
> color sel aquamarine
> color sel byhetero
> select clear
> select #7/A:204
29 atoms, 29 bonds, 1 residue, 1 model selected
> color sel gold
> color sel byhetero
> select clear
> turn x -90
> turn x -90
> turn x -90
> select #7/A:204
29 atoms, 29 bonds, 1 residue, 1 model selected
> color sel plum
> color sel plum
> color sel light cyan
> color sel light pink
> color sel cyan
> color sel cyan
> color sel byhetero
> color sel #9effffff
> color sel #9dffffff
> color sel #9dfffcff
> color sel #95fdffff
> color sel #94fdffff
> color sel #93fdffff
> color sel #81fdffff
> color sel #7bfdffff
> color sel #73fff6ff
> color sel #6fffeeff
> color sel #6effeeff
> color sel #6affeeff
> color sel #53fff1ff
> color sel #47fff9ff
> color sel #40fff9ff
> color sel #2bffd5ff
> color sel #19ffa7ff
> color sel #0fff9bff
> color sel #0affa5ff
> color sel #08ffadff
> color sel #07ffd6ff
> color sel #08fff7ff
> color sel #08ffffff
> color sel #0af3ffff
> color sel #08fbffff
> color sel #07ffffff
> color sel #02ffeaff
> color sel #01ffeaff
> color sel #00ffffff
> color sel #00f2ffff
> color sel #00eaffff
> color sel #00f2ffff
> color sel #00fbffff
> color sel #00ffffff
> color sel #00ffeaff
> color sel #00ffe1ff
> color sel #00ffd5ff
> color sel #06fbffff
> color sel #05fbffff
> color sel #02fbffff
> color sel #01fbffff
> color sel #01ffffff
> color sel #00ffffff
> color sel #00fbffff
> color sel #00f2ffff
> color sel #00eaffff
> color sel byhetero
> select clear
> select #7/A:204
29 atoms, 29 bonds, 1 residue, 1 model selected
> color sel #01eaffff
> color sel #00f2ffff
> color sel #00fff7ff
> color sel #00ffeeff
> color sel #00f2ffff
> color sel #00fbffff
> color sel #00ffeeff
> color sel byhetero
> select clear
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/fig2a_0304.cxs
> show #!5 models
> hide #7 models
> turn x -90
> select clear
> select clear
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/Han_TMEM87a_paper/ar_draft/Fig3/fig2a_0304/fig2a_0304.cxs
——— End of log from Fri Mar 4 11:47:12 2022 ———
opened ChimeraX session
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> turn x -90
> turn x -90
> turn x -90
> turn x -90
> turn x 90
> show #7 models
> hide #7 models
> hide #!5 models
> show #!5 models
> turn x 90
> turn x 90
> turn x 90
> hide #!5 models
> show #7 models
> hide #7 models
> show #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0304/fig2a_0307/87a_membrane_0307.png
> width 822 height 572 supersample 3 transparentBackground true
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0304/fig2a_0307/87a_membrane_0307.png
> width 1000 height 696 supersample 3 transparentBackground true
> hide #!5 models
> show #7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:2
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #7/A:2-31
233 atoms, 237 bonds, 30 residues, 1 model selected
> ui mousemode right select
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #7/A:224
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #7/A:161-224
581 atoms, 602 bonds, 64 residues, 1 model selected
> hide sel cartoons
> select clear
> select #7/A:204@CA
1 atom, 1 residue, 1 model selected
> select #7/A:204@CA
1 atom, 1 residue, 1 model selected
> select ligand
708 atoms, 687 bonds, 44 residues, 4 models selected
> select ::name="LYR"
29 atoms, 29 bonds, 1 residue, 1 model selected
> hide sel atoms
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0304/fig2a_0307/VR_membrane_back_0304.png
> width 1000 height 696 supersample 3 transparentBackground true
> hide sel cartoons
> select clear
> select clear
> hide #7 cartoons
> select #7/A:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #7/A:161-224
581 atoms, 602 bonds, 64 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select clear
> select clear
> select #7/A:224
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #7/A:161-224
581 atoms, 602 bonds, 64 residues, 1 model selected
> hide sel atoms
> select ::name="LYR"
29 atoms, 29 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #7/A:2
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #7/A:2-31
233 atoms, 237 bonds, 30 residues, 1 model selected
> show sel cartoons
> select clear
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0304/fig2a_0307/VR_membrane_front_0304.png
> width 1000 height 696 supersample 3 transparentBackground true
> select clear
> show #7 cartoons
> select clear
> turn x -90
> turn x -90
> turn x -90
> show #!5 models
> hide #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0304/fig2a_0307/VR_membrane_vertical_0304.png
> width 1000 height 696 supersample 3 transparentBackground true
> show #!5 models
> hide #7 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0304/fig2a_0307/87a_vert_0307.png
> width 1000 height 696 supersample 3 transparentBackground true
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0304/fig2a_0307.cxs
——— End of log from Mon Mar 7 11:39:24 2022 ———
opened ChimeraX session
> cartoon style helix width 1 thickness 0.3
> select ::name="CLR"
74 atoms, 77 bonds, 1 residue, 1 model selected
> style sel ball
Changed 74 atom styles
> ui mousemode right select
> select clear
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0304/fig2a_0323.cxs
——— End of log from Wed Mar 23 17:27:00 2022 ———
opened ChimeraX session
> show #!3 models
> hide #!3 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/R
Alignment identifier is 4/R
> select #4/R:380
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/R:380-1127
1316 atoms, 1335 bonds, 1 pseudobond, 174 residues, 2 models selected
> select #4/R:1128
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/R:1128-1160
269 atoms, 276 bonds, 33 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #4/R:119-120
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #4/R:119-1017
2526 atoms, 2584 bonds, 2 pseudobonds, 323 residues, 2 models selected
> select #4/R:1018
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/R:1018-1022
24 atoms, 23 bonds, 5 residues, 1 model selected
> select #4/R:319-320
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #4/R:319-1160
2063 atoms, 2100 bonds, 1 pseudobond, 268 residues, 2 models selected
> show sel cartoons
> ui mousemode right select
> select clear
> select #4/R:1001
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #4/R:1001
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:1001-1160
1191 atoms, 1208 bonds, 160 residues, 1 model selected
> hide sel cartoons
> select clear
> show #!5 models
> hide #!5 models
> show #7 models
> hide #!4 models
> select ::name="LYR"
29 atoms, 29 bonds, 1 residue, 1 model selected
> style sel ball
Changed 29 atom styles
> select clear
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0304/fig2a_0323.cxs
> show #!5 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #1 models
> hide #1 models
> hide #7 models
> show #!4 models
> show #7 models
> hide #7 models
> hide #!4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0323/a1.png
> width 1000 height 668 supersample 3 transparentBackground true
> show #!4 models
> hide #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0323/a2.png
> width 1000 height 668 supersample 3 transparentBackground true
> hide #!4 models
> show #7 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0323/a3.png
> width 1000 height 668 supersample 3 transparentBackground true
> show #1 models
> hide #7 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0323/a4.png
> width 1000 height 668 supersample 3 transparentBackground true
> hide #1 models
> show #!5 models
> turn x 90
> undo
> show #7 models
> transparency #5 50 cartoons
> transparency #7 50 cartoons
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2d_0304/2d_0324_1.png
> width 1000 height 668 supersample 3 transparentBackground true
> transparency #7 60 cartoons
> transparency #5 60 cartoons
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2d_0304/2d_0324_1.png
> width 1000 height 668 supersample 3 transparentBackground true
> transparency #5 50 cartoons
> transparency #7 50 cartoons
> hide #1 models
> show #!4 models
> hide #!4 models
> show #!5 models
> transparency #7 40 cartoons
> transparency #5 40 cartoons
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2d_0304/1.png
> width 855 height 571 supersample 3
> transparency #5 50 cartoons
> transparency #7 50 cartoons
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2d_0304/50.png
> width 855 height 571 supersample 3
> transparency #7 60 cartoons
> transparency #5 60 cartoons
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2d_0304/60.png
> width 855 height 571 supersample 3
> transparency #5 65 cartoons
> transparency #7 65 cartoons
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2d_0304/65.png
> width 1000 height 668 supersample 3 transparentBackground true
> transparency #7 60 cartoons
> transparency #5 60 cartoons
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2d_0304/60.png
> width 855 height 571 supersample 3 transparentBackground true
> transparency #5 55 cartoons
> transparency #7 55 cartoons
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2d_0304/55.png
> width 855 height 571 supersample 3 transparentBackground true
> turn x 90
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2d_0304/55x.png
> width 855 height 571 supersample 3
> turn x -90
> hide #!3 models
> transparency #7 60 cartoons
> transparency #5 60 cartoons
> turn x 90
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2d_0304/60x.png
> width 855 height 571 supersample 3
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2d_0304/60.png
> width 855 height 571 supersample 3
> transparency #7 0 cartoons
> transparency #5 0 cartoons
> lighting soft
> lighting soft
> lighting flat
> lighting soft
> lighting simple
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> silhouettes gray 0.5
Unknown command: silhouettes gray 0.5
> graphics silhouettes gray 0.5
Expected true or false or a keyword
> graphics silhouettes true 0.5
Expected a keyword
> hide #!3 models
> graphics silhouettes width 0.5
> graphics silhouettes width 1
> graphics silhouettes width 0.7
> graphics silhouettes color gray width 1
> turn x 90
> transparency #5 60 cartoons
> transparency #7 60 cartoons
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2d_0304/60x.png
> width 855 height 571 supersample 3 transparentBackground true
> hide #!3 models
> transparency #5 0 cartoons
> transparency #7 0 cartoons
> graphics silhouettes color black width 1
> hide #1 models
> hide #7 models
> show #!5 models
> show #1 models
> show #!4 models
> show #7 models
> hide #7 models
> hide #!4 models
> hide #1 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a_0304/fig2a_0323/fig2a_0324.cxs
——— End of log from Thu Mar 24 11:06:26 2022 ———
opened ChimeraX session
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/tmem87a.pdb
Chain information for tmem87a.pdb #6
---
Chain | Description
A | No description available
> close #7
> close #4
> close #2
> close #1
> setattr :324-334 res ss_type 0
Assigning ss_type attribute to 22 items
> hide #!5 models
> setattr :100-110 res ss_type 1
Assigning ss_type attribute to 22 items
> setattr :260-286 res ss_type 1
Assigning ss_type attribute to 54 items
> setattr :260-270 res ss_type 1
Assigning ss_type attribute to 22 items
> hide #!6 atoms
> setattr :336-352 res ss_type 1
Assigning ss_type attribute to 34 items
> cartoon style #6 xsection oval modeHelix default
> cartoon style (#6 & coil) xsection oval
> cartoon style #6 xsection barbell modeHelix default
> show #!5 models
> hide #!6 models
> show #!6 models
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/5yqz_GCGR.pdb
Chain information for 5yqz_GCGR.pdb #1
---
Chain | Description
P | No description available
R | No description available
> hide #!6 models
> hide #!1,5 atoms
> hide pbonds
> hide #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R
Alignment identifier is 1/R
> select #1/R:27
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/R:27-81
435 atoms, 449 bonds, 55 residues, 1 model selected
> ui mousemode right select
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R
Alignment identifier is 1/R
> select #1/R:27
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/R:27-263
1811 atoms, 1861 bonds, 1 pseudobond, 235 residues, 2 models selected
> select #1/R:1160
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/R:389-1160
1506 atoms, 1530 bonds, 1 pseudobond, 198 residues, 2 models selected
> select clear
> select #1/R:1160
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/R:1083-1160
629 atoms, 642 bonds, 78 residues, 1 model selected
> hide sel atoms
> hide sel atoms
> hide sel atoms
> hide sel atoms
> hide sel atoms
> hide sel cartoons
> select #1/R:1082
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/R:1023-1082
397 atoms, 398 bonds, 60 residues, 1 model selected
> hide sel cartoons
> select #1/R:1022
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/R:426-1022
174 atoms, 174 bonds, 1 pseudobond, 23 residues, 2 models selected
> select
> #1/R:28-48,88-91,119-121,125-165,168-170,172-202,209-216,221-254,264-289,304-334,343-366,376-402,405-425,1002-1011,1038-1049,1059-1079,1084-1088,1092-1104,1107-1112,1114-1121,1125-1132,1136-1140,1142-1154,1157-1159
3006 atoms, 3058 bonds, 378 residues, 1 model selected
> select #1/R:426
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/R:426-1001
17 atoms, 15 bonds, 1 pseudobond, 2 residues, 2 models selected
> select clear
> select #1/R:426
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/R:426-1160
1200 atoms, 1216 bonds, 1 pseudobond, 161 residues, 2 models selected
> hide sel cartoons
> select clear
> select #1/P:25
14 atoms, 15 bonds, 1 residue, 1 model selected
> show #!6 models
> hide #!6 models
> show #!6 models
> close #6
> show #!5 models
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/tmem87a.pdb
Chain information for tmem87a.pdb #2
---
Chain | Description
A | No description available
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!5 models
> cartoon style helix width 1 thickness 0.3
> show #!5 models
> hide #!5 models
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/P
Alignment identifier is 1/P
> select #1/P:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/P:2-29
236 atoms, 241 bonds, 28 residues, 1 model selected
> hide sel cartoons
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/7w9w_chrmine.pdb
Chain information for 7w9w_chrmine.pdb #4
---
Chain | Description
A | No description available
> hide sel atoms
> hide sel atoms
> hide sel atoms
> hide #!1 models
Drag select of 208 atoms, 270 residues, 207 bonds
> hide sel atoms
> select clear
> cartoon style helix width 1 thickness 0.3
> show #!5 models
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/7drt_wnt3a.pdb
Chain information for 7drt_wnt3a.pdb #6
---
Chain | Description
B | No description available
> hide #!5 models
> hide #4 models
> select clear
Drag select of 187 atoms, 496 residues, 186 bonds
> hide sel atoms
> select clear
> cartoon style helix width 1 thickness 0.3
> show #!5 models
> hide #!5 models
> hide #6 models
> show #!2 models
> hide #!2 models
> show #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:221
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #6/B
Alignment identifier is 6/B
> hide #!5 models
> show #6 models
> select #6/B:40
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/B:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6/B:40
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/B:40-41
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #6/B:40-226
1539 atoms, 1581 bonds, 187 residues, 1 model selected
> hide sel cartoons
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/fig2a_0414.cxs
——— End of log from Thu Apr 14 11:02:28 2022 ———
opened ChimeraX session
> hide #6 models
> show #4 models
> hide #4 models
> show #!1 models
> ui mousemode right select
> select #1/R:27
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/R:122
14 atoms, 12 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R
Alignment identifier is 1/R
> select #1/R:27
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/R:27-122
782 atoms, 815 bonds, 96 residues, 1 model selected
> hide sel cartoons
> show #6 models
> hide #6 models
> close #2
> show #!5 models
> select ::name="CLR"
158 atoms, 170 bonds, 4 residues, 3 models selected
> show sel & #!5 atoms
> select H
46 atoms, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!1 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/fig2a_0414.cxs
> show #4 models
> hide #4 models
> hide #!5 models
> show #4 models
> select ::name="RET"
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> color sel byhetero
> select clear
> show #!5 models
> hide #!5 models
> select ::name="RET"
20 atoms, 20 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark turquoise
> color sel turquoise
> color sel cyan
> hide #4 models
> show #4 models
Drag select of 20 atoms, 270 residues, 20 bonds
> ui tool show "Color Actions"
> color sel pale green
> color sel pale green
> select clear
> select ::name="RET"
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel cyan
> select clear
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/fig2a_0414.cxs
> show #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/fig2a_0414.cxs
> hide #4 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #6 models
> show #!1 models
> hide #6 models
> show #6 models
> show #4 models
> hide #!1 models
> show #!5 models
> hide #6 models
> hide #!5 models
> select ::name="RET"
20 atoms, 20 bonds, 1 residue, 1 model selected
> style sel ball
Changed 20 atom styles
> select clear
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/fig2a_0414.cxs
> show #!5 models
> show #6 models
> show #!1 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/fig2a_0414.cxs
> tile
4 models tiled
> undo
> turn y, 90
Expected an axis vector or a keyword
> turn y 90
> turn x 90
> tile
4 models tiled
> undo
Drag select of 9 residues
> select add #6/B:468
85 atoms, 8 bonds, 10 residues, 1 model selected
> hide sel cartoons
> undo
> select clear
> tile
4 models tiled
> tile
4 models tiled
> undo
> undo
> hide #4 models
> hide #!1 models
> hide #6 models
> show #!3 models
> hide #!3 models
Drag select of 23 residues
> select clear
> show #4 models
> hide #4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!5 models
> show #4 models
> hide #!1 models
> show #6 models
> hide #4 models
> show #!5 models
> show #!1 models
> show #4 models
> tile
5 models tiled
> tile
5 models tiled
> show #!3 models
> hide #!3 models
> undo
> undo
> undo
> hide #!1 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #6 models
> show #!3 models
> turn x 90
> turn x -90
> select down
Nothing selected
> turn x 90
> turn x -90
> hide #!3 models
> show #6 models
> hide #6 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #4 models
> show #6 models
> tile
5 models tiled
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_0413.tif
> width 3000 height 2188 supersample 3 transparentBackground true
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_0413.tif
> width 3000 height 1953 supersample 3 transparentBackground true
> hide #4 models
> hide #!1 models
> hide #6 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #4 models
> show #6 models
> hide #6 models
> hide #4 models
> hide #!1 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_87a.tif
> width 1000 height 651 supersample 3 transparentBackground true
> show #4 models
> hide #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_chrmine.tif
> width 1000 height 651 supersample 3 transparentBackground true
> show #!1 models
> hide #4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_gcgr.tif
> width 1000 height 651 supersample 3 transparentBackground true
> hide #!1 models
> show #6 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_wls.tif
> width 1000 height 651 supersample 3 transparentBackground true
> show #!5 models
> show #4 models
> show #!1 models
> turn x 90
> hide #6 models
> hide #!1 models
> hide #4 models
> show #4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> show #!5 models
> hide #4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_87atop.tif
> width 1000 height 651 supersample 3 transparentBackground true
> show #4 models
> hide #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_chrminetop.tif
> width 1000 height 651 supersample 3 transparentBackground true
> show #6 models
> hide #4 models
> undo
> show #!5 models
> hide #4 models
> hide #6 models
> show #6 models
> show #4 models
> show #!1 models
> hide #4 models
> hide #!5 models
> hide #6 models
> show #!5 models
> hide #!1 models
> show #4 models
> hide #4 models
> show #4 models
> hide #!5 models
> show #!5 models
> hide #4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_87atop.tif
> width 1000 height 651 supersample 3 transparentBackground true
> show #4 models
> hide #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_chrminetop.tif
> width 1000 height 651 supersample 3 transparentBackground true
> show #6 models
> hide #4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_wlstop.tif
> width 1000 height 651 supersample 3 transparentBackground true
> show #!1 models
> hide #6 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_gcgrtop.tif
> width 1000 height 651 supersample 3 transparentBackground true
> show #!5 models
> hide #!5 models
> show #!5 models
> show #4 models
> show #6 models
> hide #6 models
> hide #!5 models
> hide #4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_gcgrtop.tif
> width 1000 height 651 supersample 3 transparentBackground true
> show #4 models
> hide #!1 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_chrminetop.tif
> width 1000 height 651 supersample 3 transparentBackground true
> show #!5 models
> hide #4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_87atop.tif
> width 1000 height 651 supersample 3 transparentBackground true
> show #6 models
> hide #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/2a1_wlstop.tif
> width 1000 height 651 supersample 3 transparentBackground true
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/fig2a_0414.cxs
> show #4 models
> hide #4 models
> select #6/B:3
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/B:3
4 atoms, 3 bonds, 1 residue, 1 model selected
> show #!5 models
> select clear
> hide #!5 models
> show #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0412/fig4a_0413/fig2a_0414.cxs
——— End of log from Thu Apr 14 20:07:58 2022 ———
opened ChimeraX session
> hide #6 models
> show #!5 cartoons
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/tm87_solvent.mrc
Opened tm87_solvent.mrc as #2, grid size 68,68,88, pixel 2, shown at level
5e-05, step 1, values int8
> volume #2 level 0.2793
> ui mousemode right "map eraser"
> volume erase #2 center 141.71,155.99,89.08 radius 26.493
Opened tm87_solvent.mrc copy as #8, grid size 68,68,88, pixel 2, shown at step
1, values int8
> volume erase #8 center 122.56,142.31,92.831 radius 26.488
> volume erase #8 center 146.1,121.55,82.566 radius 26.488
> volume erase #8 center 128.51,110.24,89.508 radius 26.488
> volume erase #8 center 110.76,111.07,115.45 radius 26.488
> volume erase #8 center 102.34,149.23,133.57 radius 26.488
> volume erase #8 center 124.64,164.3,155.01 radius 26.488
> volume erase #8 center 130.62,178.61,131.18 radius 26.488
> volume erase #8 center 144.29,165.52,177.32 radius 26.488
> undo
> undo
> hide #6 models
> hide #!5 models
> show #!5 models
> volume erase #8 center 153.16,144,199.71 radius 26.488
> close #8
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/tm87_solvent.mrc
Opened tm87_solvent.mrc as #7, grid size 68,68,88, pixel 2, shown at level
5e-05, step 1, values int8
> volume erase #7 center 127.41,164.28,112.81 radius 23.558
Opened tm87_solvent.mrc copy as #9, grid size 68,68,88, pixel 2, shown at step
1, values int8
> volume erase #9 center 141.67,139.54,86.143 radius 23.496
> volume erase #9 center 120.66,130.54,97.06 radius 23.496
> volume erase #9 center 114.57,115.93,118.45 radius 23.496
> volume erase #9 center 117.98,154.89,152.24 radius 23.496
> volume erase #9 center 111.71,157.07,139.77 radius 23.496
> volume erase #9 center 160.3,165.72,143.01 radius 23.496
> volume erase #9 center 149.77,167.55,119.07 radius 23.496
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> close #7
> show #!5 cartoons
> volume erase #9 center 157.4,168.67,181.15 radius 23.496
> volume erase #9 center 144.75,132.98,197.84 radius 23.496
> volume erase #9 center 128.24,145.61,190.14 radius 23.496
> volume erase #9 center 165.09,129.16,186.31 radius 23.496
> volume erase #9 center 169.15,112.98,163.03 radius 23.496
> volume erase #9 center 162.97,120.16,140.51 radius 16.28
> volume erase #9 center 168.15,145.08,156.22 radius 16.28
> volume #9 level 0.2109
> volume erase #9 center 133.95,156.62,172.95 radius 16.28
> volume erase #9 center 136.04,117.89,167.22 radius 16.28
> volume erase #9 center 132.44,109.61,148.93 radius 16.28
> volume erase #9 center 136.38,110.16,157.02 radius 16.28
> volume erase #9 center 147.95,122.39,104.63 radius 6.512
> volume erase #9 center 139.79,114.9,115.94 radius 6.512
> volume erase #9 center 116.63,125.79,129.11 radius 6.512
> volume erase #9 center 118.69,126.25,143.87 radius 6.512
> volume erase #9 center 136.51,121.78,148.39 radius 6.512
> volume erase #9 center 144.23,142.85,162.66 radius 6.512
> volume erase #9 center 142.26,136.89,159.68 radius 6.512
> volume erase #9 center 142.35,134.1,152.31 radius 6.512
> volume erase #9 center 137.41,128.63,157.86 radius 6.512
> volume erase #9 center 157.35,131.48,137.48 radius 6.512
> volume erase #9 center 153.48,149.71,124.02 radius 6.512
> volume erase #9 center 151.39,146.1,115.69 radius 6.512
> volume erase #9 center 161.54,138.68,130.95 radius 6.512
> volume erase #9 center 161.54,138.68,130.95 radius 6.512
> volume erase #9 center 160.23,139.82,130.69 radius 6.512
> volume erase #9 center 159.72,140.02,132.11 radius 6.512
> volume erase #9 center 153.67,145.89,118.18 radius 6.512
> volume erase #9 center 153.56,144.97,118.19 radius 6.512
> volume erase #9 center 149.3,145.73,115.41 radius 6.512
> volume erase #9 center 137.35,126.97,108.35 radius 6.512
> volume erase #9 center 129.14,141.28,129.01 radius 6.512
> ui mousemode right select
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/87a_high.mrc
Opened 87a_high.mrc as #2, grid size 220,216,300, pixel 0.5, shown at level
5e-05, step 1, values int8
> hide #!9 models
> ui mousemode right "map eraser"
> volume erase #2 center 156.99,163.87,155.28 radius 13.959
Opened 87a_high.mrc copy as #8, grid size 220,216,300, pixel 0.5, shown at
step 1, values int8
> volume erase #8 center 146.92,161.88,138.67 radius 13.95
> volume erase #8 center 122.77,155.4,137.65 radius 13.95
> volume erase #8 center 129.76,158.58,155.9 radius 13.95
> volume erase #8 center 124.23,148.12,155.71 radius 13.95
> volume erase #8 center 125.3,145.96,165.31 radius 13.95
> volume erase #8 center 134.89,151.47,174.99 radius 13.95
> volume erase #8 center 141.63,162.27,172.83 radius 13.95
> volume erase #8 center 152.24,143.58,190.67 radius 13.95
> close #8
> volume erase #2 center 130.19,154.06,166.58 radius 13.95
Opened 87a_high.mrc copy as #8, grid size 220,216,300, pixel 0.5, shown at
step 1, values int8
> volume erase #8 center 128.04,155.18,148.45 radius 13.95
> volume erase #8 center 141.78,162.89,143.21 radius 13.95
> volume erase #8 center 154.88,164.57,156.45 radius 13.95
> volume erase #8 center 168.57,143.57,161.26 radius 13.95
> volume erase #8 center 139.79,159.87,180.24 radius 13.95
> volume erase #8 center 153.92,172.13,183.66 radius 13.95
> volume erase #8 center 155.19,171.16,182.57 radius 13.95
> volume erase #8 center 139.18,160.66,150.75 radius 13.95
> volume erase #8 center 139.42,119.07,180.81 radius 13.95
> volume erase #8 center 137.88,129.96,184.74 radius 13.95
> volume erase #8 center 129.6,125.02,172.3 radius 13.95
> volume erase #8 center 156.34,130.44,196.06 radius 13.95
> volume erase #8 center 151.44,123.71,181.03 radius 13.95
> volume erase #8 center 157.87,119.56,164.78 radius 13.95
> volume erase #8 center 162.06,125.07,179.2 radius 13.95
> volume erase #8 center 133.08,142.29,190.57 radius 13.95
> volume erase #8 center 171.55,161.03,166.54 radius 13.95
> volume erase #8 center 162.52,142.43,148.33 radius 13.95
> volume #8 level 0.3082
> volume #8 level 0.8764
> volume #8 level 0.6163
> volume erase #8 center 122.13,141.38,162 radius 13.95
> volume erase #8 center 119.39,140.06,156.56 radius 13.95
> volume erase #8 center 123.5,146.62,160.96 radius 13.95
> volume erase #8 center 115.48,152.15,135.25 radius 13.95
> volume erase #8 center 118.97,151.17,139.3 radius 13.95
> volume erase #8 center 115.36,144.39,118.37 radius 13.95
> volume erase #8 center 136.01,149.24,94.389 radius 13.95
> volume erase #8 center 135.54,147.53,105.2 radius 13.95
> volume erase #8 center 124.63,147.33,117.01 radius 13.95
> volume erase #8 center 112.28,133.92,121.39 radius 13.95
> volume erase #8 center 118.96,129.16,98.526 radius 13.95
> volume erase #8 center 144.84,128.82,95.415 radius 13.95
> volume erase #8 center 154.27,128.98,98.111 radius 13.95
> volume erase #8 center 148.64,140.64,96.269 radius 13.95
> volume erase #8 center 131.26,121.47,99.214 radius 13.95
> volume erase #8 center 120.59,133.06,108 radius 13.95
> volume erase #8 center 148.73,160.35,132.15 radius 6.15
> volume erase #8 center 148.73,160.35,132.15 radius 6.15
> volume erase #8 center 154.38,150.22,129.68 radius 6.15
> volume erase #8 center 156.34,147.87,136.86 radius 6.15
> volume erase #8 center 152.76,125.33,141.39 radius 6.15
> volume erase #8 center 154.18,125.77,146.77 radius 6.15
> volume erase #8 center 147.66,121.11,152 radius 6.15
> volume erase #8 center 149.91,117.83,146.44 radius 6.15
> volume erase #8 center 142.4,125.33,165.17 radius 6.15
> volume erase #8 center 143.35,131.73,174.83 radius 6.15
> volume erase #8 center 156.94,141.79,167.11 radius 4.725
> transparency #5,7-8 50
> volume erase #8 center 154.86,147.81,124.05 radius 7.425
> volume erase #8 center 154.86,147.81,124.05 radius 7.425
> volume erase #8 center 154.86,147.81,124.05 radius 7.425
> volume erase #8 center 153.77,142.07,117.58 radius 7.425
> volume erase #8 center 152.73,141.03,116.06 radius 7.425
> volume erase #8 center 138.62,138.33,106.62 radius 7.425
> volume erase #8 center 138.61,149.82,129.41 radius 7.425
> volume erase #8 center 140.29,150.63,132.02 radius 7.425
> volume erase #8 center 142.7,147.5,131.34 radius 4.575
> volume erase #8 center 127.98,117.58,122.2 radius 7.425
> volume erase #8 center 129.55,119.15,122.3 radius 7.425
> volume erase #8 center 128.34,116.77,125.41 radius 7.425
> volume erase #8 center 122.94,122.62,125.08 radius 7.425
> volume erase #8 center 122.36,121.35,127.87 radius 7.425
> volume erase #8 center 122.36,121.35,127.87 radius 7.425
> volume erase #8 center 125.95,125.89,120.57 radius 7.425
> volume erase #8 center 124.99,123.97,124.69 radius 7.425
> volume erase #8 center 122.05,122.74,128.4 radius 7.425
> volume erase #8 center 123.49,131.08,136.45 radius 7.425
> volume erase #8 center 139.8,120.35,159.62 radius 7.425
> volume erase #8 center 139.8,120.35,159.62 radius 7.425
> volume erase #8 center 140.02,120.55,161.69 radius 7.425
> volume erase #8 center 140.02,120.55,161.69 radius 7.425
> volume erase #8 center 132.64,122.87,161 radius 7.425
> volume erase #8 center 136.99,122.93,162.89 radius 7.425
> volume erase #8 center 130.8,121.81,158.6 radius 7.425
> volume erase #8 center 127.28,120.91,152.9 radius 7.425
> volume erase #8 center 123.73,120.86,145.9 radius 7.425
> volume erase #8 center 123.01,122.17,141.64 radius 7.425
> volume erase #8 center 122.79,118.53,133.5 radius 7.425
> volume erase #8 center 129.52,116.89,124.59 radius 7.425
> volume erase #8 center 133.97,116.99,115.05 radius 4.125
> volume #8 level 1
> volume erase #8 center 149.03,142.65,117.46 radius 4.125
> volume erase #8 center 146.92,141.7,116.92 radius 4.125
> close #2
> close #9
> volume erase #8 center 155.7,113.95,132.56 radius 11.991
> volume erase #8 center 151.6,110.95,131.61 radius 10.304
> volume erase #8 center 150.59,112.17,131.21 radius 10.304
> volume erase #8 center 140.72,110.8,135.44 radius 10.304
> volume erase #8 center 128.28,117.66,144.91 radius 7.1102
> volume erase #8 center 125.14,125.52,152.99 radius 7.1102
> volume erase #8 center 146.87,119.48,151.74 radius 7.1102
> volume erase #8 center 127.22,126.22,158.75 radius 7.1102
> volume erase #8 center 127.88,126.01,158.14 radius 7.1102
> volume erase #8 center 158.13,150.85,126.53 radius 11.972
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
——— End of log from Wed Apr 20 20:25:29 2022 ———
opened ChimeraX session
> hide #!8 models
> hide #!5 models
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/7drt_high.mrc
Opened 7drt_high.mrc as #2, grid size 212,216,292, pixel 0.5, shown at level
1, step 1, values int8
> close #2
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/2022.apr20.099.mrc
Opened 2022.apr20.099.mrc as #2, grid size 220,216,272, pixel 0.5, shown at
level 5e-05, step 1, values int8
> close #2
> show #4 models
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/7w9w_high.mrc
Opened 7w9w_high.mrc as #2, grid size 220,216,272, pixel 0.5, shown at level
5e-05, step 1, values int8
> ui mousemode right "map eraser"
> volume erase #2 center 160.55,162.26,159.83 radius 10.18
Opened 7w9w_high.mrc copy as #9, grid size 220,216,272, pixel 0.5, shown at
step 1, values int8
> volume erase #9 center 167.01,147.84,157.95 radius 10.132
> volume erase #9 center 165.07,140.78,159.4 radius 10.132
> volume erase #9 center 161.07,146.82,145.35 radius 10.132
> volume erase #9 center 156.54,154.91,136.29 radius 10.132
> volume erase #9 center 156.5,158.13,147.02 radius 10.132
> volume erase #9 center 137.29,153.54,176.7 radius 10.132
> volume erase #9 center 145.61,134.6,195.92 radius 10.132
> volume erase #9 center 130.94,125.15,152.82 radius 10.132
> volume erase #9 center 133.73,126.77,162.04 radius 10.132
> volume erase #9 center 156.13,120.2,166.12 radius 10.132
> volume erase #9 center 159.46,121.43,156.95 radius 10.132
> volume erase #9 center 158.34,121.39,152.17 radius 10.132
> volume erase #9 center 168.88,144.74,165.6 radius 10.132
> volume erase #9 center 157.79,129.41,184.48 radius 10.132
> volume erase #9 center 141.04,132.47,180.53 radius 10.132
> volume erase #9 center 149.66,133.65,179.4 radius 10.132
> volume erase #9 center 127.58,136.08,157.23 radius 10.132
> volume erase #9 center 128.35,138.53,156.92 radius 10.132
> volume erase #9 center 126.2,126.95,142.67 radius 10.132
> volume erase #9 center 145.75,131.79,158.86 radius 10.132
> volume erase #9 center 153.91,121.46,133.03 radius 10.132
> volume erase #9 center 153.91,121.46,133.03 radius 10.132
> volume erase #9 center 153.93,126.82,136.72 radius 10.132
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume erase #9 center 166,168.3,170.01 radius 10.132
> volume erase #9 center 167.16,155.08,184.12 radius 10.132
> volume erase #9 center 169.1,141.77,176.62 radius 10.132
> volume erase #9 center 168.29,144.02,179.18 radius 10.132
> close #2
> show #!5 models
> hide #!9 models
> hide #4 models
> hide #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
> show #6 models
> show #6 cartoons
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/2022.apr20.942.mrc
Opened 2022.apr20.942.mrc as #2, grid size 116,116,156, pixel 1, shown at
level 5e-05, step 1, values int8
> close #2
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/7drt_high.mrc
Opened 7drt_high.mrc as #2, grid size 116,116,156, pixel 1, shown at level
5e-05, step 1, values int8
> volume erase #2 center 126.31,143.07,168.35 radius 13.408
Opened 7drt_high.mrc copy as #10, grid size 116,116,156, pixel 1, shown at
step 1, values int8
> volume erase #10 center 125.79,165.03,161.6 radius 13.338
> volume erase #10 center 131.77,159.2,165.38 radius 13.338
> volume erase #10 center 155.72,166.19,160.72 radius 13.338
> volume erase #10 center 146.89,164.45,147.25 radius 13.338
> volume erase #10 center 131.72,162.17,152.2 radius 13.338
> volume erase #10 center 150.55,163.67,178.9 radius 13.338
> volume erase #10 center 146.83,146.56,181.14 radius 13.338
> volume erase #10 center 160.38,131.93,183.8 radius 13.338
> volume erase #10 center 163.47,124.82,174.61 radius 13.338
> volume erase #10 center 148.35,124.49,184.5 radius 13.338
> volume erase #10 center 157.77,118.78,169.65 radius 13.338
> volume erase #10 center 166.46,126.78,156.35 radius 13.338
> volume erase #10 center 167.67,151.01,168.63 radius 18.564
> volume erase #10 center 166.52,146.68,151.35 radius 18.564
> volume erase #10 center 159.81,153.72,123.21 radius 18.564
> volume erase #10 center 151.62,158.8,118.49 radius 18.564
> volume erase #10 center 150.19,145.27,96.538 radius 18.564
> volume erase #10 center 125.86,139.85,95.821 radius 18.564
> volume erase #10 center 135.89,117.32,92.459 radius 18.564
> volume erase #10 center 155.09,111.86,103.78 radius 18.564
> volume erase #10 center 168.79,129.6,119.88 radius 18.564
> volume erase #10 center 166.32,128.95,120.64 radius 18.564
> volume erase #10 center 146.8,100.26,110.24 radius 18.564
> volume erase #10 center 145.81,102.63,111.7 radius 18.564
> volume erase #10 center 160.33,109.34,111.65 radius 18.564
> volume erase #10 center 157.5,123.77,99.468 radius 18.564
> volume erase #10 center 117.16,141.22,103.18 radius 18.564
> volume erase #10 center 118.97,158.24,104.26 radius 18.564
> volume erase #10 center 124.12,128.21,98.745 radius 18.564
> volume erase #10 center 124.98,132.81,100.9 radius 18.564
> volume erase #10 center 127.13,150.08,183.61 radius 18.564
> volume erase #10 center 109.96,136.7,155.49 radius 18.564
> volume erase #10 center 130.32,147.65,160.54 radius 7.878
> volume erase #10 center 123.81,141.74,150.45 radius 7.878
> volume erase #10 center 128.47,142.78,121.91 radius 7.878
> volume erase #10 center 128.89,149.62,127.65 radius 7.878
> transparency #6-7,10 50
> volume erase #10 center 109.32,132.85,136.95 radius 7.878
> volume erase #10 center 110.97,133.48,136.63 radius 7.878
> volume erase #10 center 114.29,146.61,129.47 radius 7.878
> volume erase #10 center 119.37,151.87,130.98 radius 7.878
> volume erase #10 center 116.93,150.92,138.59 radius 7.878
> volume erase #10 center 118.49,150.28,123.22 radius 7.878
> volume erase #10 center 118.99,149.94,123.98 radius 7.878
> volume erase #10 center 126.15,124.09,110.75 radius 7.878
> volume erase #10 center 126.11,114.35,115.99 radius 7.878
> volume erase #10 center 125.87,117.58,115.04 radius 7.878
> volume erase #10 center 123.17,120.03,115.13 radius 7.878
> volume #2 level 0.09784
> close #2
> volume #10 level 0.9576
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
> hide #!10 models
> hide #6 models
> show #!1 models
> show #!1 cartoons
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/5yqz_GCGR.pdb
Chain information for 5yqz_GCGR.pdb #2
---
Chain | Description
R | No description available
> close #1
> show #!5 models
> hide #!5 models
> hide pbonds
> show #4 models
> hide #4 models
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/2022.apr20.80c.mrc
Opened 2022.apr20.80c.mrc as #1, grid size 112,136,160, pixel 1, shown at
level 5e-05, step 1, values int8
> close #1
> close #3
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/5yqz_high.mrc
Opened 5yqz_high.mrc as #1, grid size 112,136,160, pixel 1, shown at level
5e-05, step 1, values int8
> volume #1 level 0.03423
> transparency #1-2 50
> volume erase #1 center 143.66,145.48,184.46 radius 19.772
Opened 5yqz_high.mrc copy as #7, grid size 112,136,160, pixel 1, shown at step
1, values int8
> volume erase #7 center 140.91,173.53,160.89 radius 19.76
> volume erase #7 center 160.17,141.33,179.64 radius 19.76
> volume erase #7 center 162.97,146.65,158.15 radius 19.76
> volume erase #7 center 158.49,130.54,159.08 radius 9.28
> volume erase #7 center 131.15,147.3,152.96 radius 9.28
> volume erase #7 center 127.04,144.27,159.04 radius 9.28
> volume erase #7 center 133.07,159.77,135.74 radius 9.28
> volume erase #7 center 129.53,148.8,90.62 radius 17.36
> volume erase #7 center 137.16,126.83,90.877 radius 17.36
> volume erase #7 center 134.62,149.69,94.872 radius 17.36
> volume erase #7 center 162.04,156.47,115.3 radius 17.36
> volume erase #7 center 169.4,143.27,126.97 radius 17.36
> volume erase #7 center 155.69,124.11,118.24 radius 17.36
> volume erase #7 center 160.02,139.09,127.42 radius 13.44
> volume erase #7 center 153.26,145.26,101.17 radius 13.44
> volume erase #7 center 153.26,145.26,101.17 radius 13.44
> volume erase #7 center 152.28,148.97,115.47 radius 13.44
> volume erase #7 center 113.42,132.89,111.49 radius 13.44
> volume erase #7 center 156.05,117.01,136.1 radius 13.44
> volume erase #7 center 151.96,120.12,134.19 radius 13.44
> volume erase #7 center 149.94,117.31,152.88 radius 13.44
> volume erase #7 center 123.09,139.85,102.45 radius 13.44
> volume erase #7 center 143.06,154.99,104.68 radius 13.44
> volume erase #7 center 135.38,120.22,108.71 radius 13.227
> ui mousemode right select
> cartoon style helix width 1 thickness 0.3
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
> show #!8 models
> ui mousemode right "map eraser"
> volume erase #8 center 142.36,117.96,148.12 radius 8.242
> volume erase #8 center 137.16,117.58,145.09 radius 8.242
> volume erase #8 center 143.46,114.34,139.08 radius 8.242
> volume erase #8 center 134.51,117.6,146.16 radius 8.242
> volume erase #8 center 131.55,121.7,149.79 radius 8.242
> volume erase #8 center 133.77,121.2,156.72 radius 7.4599
> volume erase #8 center 143.12,119.84,156.03 radius 7.4599
> volume erase #8 center 138.82,125.62,147.94 radius 3.0682
> volume erase #8 center 144.91,142.75,150.91 radius 3.0682
> volume erase #8 center 169.81,143.48,184.73 radius 3.0682
> volume erase #8 center 169.81,143.48,184.73 radius 3.0682
> volume erase #8 center 166.04,144.02,184.89 radius 3.0682
> volume erase #8 center 164.58,143.14,189.62 radius 3.0682
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
> show #!9 models
> show #!10 models
> hide #!9 models
> hide #!8 models
> show #!2 models
> hide #!5 models
> hide #!10 models
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0304/5yqz_rhodopsin_GPCR.pdb
Chain information for 5yqz_rhodopsin_GPCR.pdb #3
---
Chain | Description
P | No description available
R | No description available
> show #!7 models
> hide #!7 models
> close #3
> show #!7 models
> hide #!2 models
> show #4 models
> close #1
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
> hide #!7 models
> hide #4 models
> show #!5 models
> show #!8 models
> show #4 models
> hide #!8 models
> hide #!5 models
> show #!9 models
> hide #!9 models
> hide #4 models
> show #!5 models
> show #!8 models
> volume erase #8 center 143.4,135.8,152.5 radius 5.7152
> volume erase #8 center 143.46,135.75,150.49 radius 5.7152
> volume erase #8 center 142.14,133.36,154.03 radius 5.7152
> volume erase #8 center 137.76,128.95,154.14 radius 5.7152
> volume erase #8 center 143.64,129.2,152.12 radius 5.7152
> volume erase #8 center 145.78,133.32,151.4 radius 5.7152
> volume erase #8 center 146.39,132.87,150.85 radius 5.7152
> volume erase #8 center 139.31,136.8,153.71 radius 5.7152
> volume erase #8 center 139.31,136.8,153.71 radius 5.7152
> volume erase #8 center 139.38,131.99,161.14 radius 5.7152
> volume erase #8 center 137.32,127.98,158.4 radius 5.7152
> volume erase #8 center 143.91,126.26,164.48 radius 5.7152
> volume erase #8 center 143.04,127.23,162.59 radius 5.7152
> volume erase #8 center 141.06,129.51,158.2 radius 5.7152
> volume erase #8 center 140.13,129.75,168.74 radius 5.7152
> volume erase #8 center 141.4,140.37,152.09 radius 5.7152
> volume erase #8 center 133.08,136.79,158.07 radius 5.7152
> volume erase #8 center 138.27,132.55,165.42 radius 5.7152
> volume erase #8 center 143.7,130.8,166.55 radius 5.7152
> volume erase #8 center 142.65,128.93,160.13 radius 5.7152
> volume erase #8 center 143.23,128.64,162.38 radius 5.7152
> volume erase #8 center 138.38,137.46,160.54 radius 1.6243
> volume erase #8 center 138.2,138.14,159.2 radius 1.6243
> volume erase #8 center 141.6,129.24,161.77 radius 1.6243
> volume erase #8 center 143.17,128.76,163 radius 1.6243
> volume erase #8 center 143.17,128.76,163 radius 1.6243
> volume erase #8 center 156.05,139.29,188.06 radius 6.9786
> volume erase #8 center 163.18,137.8,187.8 radius 6.9786
> volume erase #8 center 155.17,142.3,192.1 radius 6.9786
> volume erase #8 center 161.04,143.82,191.79 radius 6.9786
> volume erase #8 center 145.06,141.97,185.76 radius 6.9786
> volume erase #8 center 145.44,141.23,184.06 radius 6.9786
> volume erase #8 center 169.89,148.7,171.96 radius 6.1965
> volume erase #8 center 162.78,154.76,168.87 radius 4.3316
> volume erase #8 center 163.7,151.56,168.18 radius 4.3316
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/87a_c.png
> width 703 height 577 supersample 3 transparentBackground true
> hide #!8 models
> show #!7 models
> show #!2 models
> hide #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/gcgr_c.png
> width 703 height 577 supersample 3 transparentBackground true
> hide #!2 models
> hide #!7 models
> show #!9 models
> show #4 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/chrmine_c.png
> width 703 height 577 supersample 3 transparentBackground true
> hide #!9 models
> hide #4 models
> show #6 models
> show #!10 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/wls_c.png
> width 703 height 577 supersample 3 transparentBackground true
> hide #!10 models
> hide #6 models
> show #6 models
> show #!5 models
> hide #6 models
> show #!8 models
> volume erase #8 center 138.87,118.41,109.57 radius 11.972
> volume erase #8 center 143.03,131.3,107.98 radius 11.972
> volume erase #8 center 146.17,121.2,114.68 radius 9.5053
> volume erase #8 center 147.52,139.16,112.77 radius 6.738
> volume erase #8 center 147.81,136.74,113.03 radius 6.738
> volume erase #8 center 144.86,137.74,112.89 radius 6.738
> volume erase #8 center 158.09,137.43,132.21 radius 6.738
> volume erase #8 center 150.94,118.45,131.59 radius 6.738
> volume erase #8 center 152.23,122.41,130.53 radius 6.738
> volume erase #8 center 139.42,116.47,121.5 radius 6.738
> volume erase #8 center 136.38,138.24,115.33 radius 6.738
> volume erase #8 center 137.67,135.77,114.38 radius 6.738
> volume erase #8 center 135.49,131.99,114.51 radius 6.738
> volume erase #8 center 139.46,128.46,114.13 radius 6.738
> hide #!5 models
> hide #!8 models
> show #!9 models
> show #4 models
> volume erase #9 center 141.09,138.43,125.77 radius 3.6258
> volume erase #9 center 135.37,141.17,134.28 radius 3.6258
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
> volume erase #9 center 134.4,133.11,138.78 radius 3.6258
> volume erase #9 center 133.47,133.7,139.37 radius 3.6258
> volume erase #9 center 136.89,127.72,134.61 radius 3.6258
> volume erase #9 center 135.47,128.16,136.41 radius 3.6258
> volume erase #9 center 132.58,131,140.3 radius 3.6258
> volume erase #9 center 133.01,133.95,136.77 radius 3.6258
> volume erase #9 center 146.23,136.37,131.04 radius 3.6258
> hide #!8 models
> volume erase #9 center 140.78,132.62,128.43 radius 3.604
> volume erase #9 center 142.74,129.1,129.21 radius 3.604
> volume erase #9 center 137.92,126.52,133.87 radius 3.604
> volume erase #9 center 135.37,128.85,135.87 radius 3.604
> volume erase #9 center 135.66,130.13,136.55 radius 3.604
> volume erase #9 center 136.16,131.74,136.62 radius 3.604
> volume erase #9 center 133.41,136.47,137.63 radius 3.604
> volume erase #9 center 137.82,128.23,133.44 radius 3.604
> volume erase #9 center 138.02,125.82,134.12 radius 3.604
> volume erase #9 center 137.91,125.39,137.03 radius 4.5543
> volume erase #9 center 138.75,126.73,137.02 radius 4.5543
> volume erase #9 center 137.71,123.08,132.69 radius 4.5543
> volume erase #9 center 140.42,128.65,128.24 radius 4.5543
> volume erase #9 center 143.8,129.47,130.72 radius 2.9625
> volume erase #9 center 141.72,130.28,136.34 radius 2.9625
> volume erase #9 center 139.72,128.22,132.43 radius 2.9625
> volume erase #9 center 134.85,136.45,138.24 radius 2.8741
> volume erase #9 center 135.68,133.21,137.03 radius 2.8741
> volume erase #9 center 138.93,142.12,131.92 radius 2.8741
> volume erase #9 center 139.76,131.56,140.21 radius 2.8741
> volume erase #9 center 134.65,138.9,135.83 radius 3.8911
> volume erase #9 center 139.36,135.77,128.17 radius 3.8911
> volume erase #9 center 143.53,134.57,127.58 radius 3.8911
> volume erase #9 center 137.61,130.91,131.53 radius 3.8911
> volume erase #9 center 141.53,129.36,130.23 radius 3.8911
> volume erase #9 center 138.77,130.22,130.76 radius 3.8911
> transparency #4,9 20
> show #!8 models
> show #!10 models
> show #!7 models
> transparency #4,7-10 0
> transparency #4,7-10 30
> show #!2 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #4 models
> show #4 models
> show #!5 models
> show #6 models
> hide #4 models
> hide #!5 models
> hide #6 models
> hide #!2 models
> hide #!7 models
> show #6 models
> show #!10 models
> hide #!10 models
> show #!5 models
> hide #6 models
> show #!8 models
> show #!2 models
> show #6 models
> hide #6 models
> hide #!5 models
> hide #!2 models
> show #!5 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/87a_c.png
> width 1000 height 821 supersample 3 transparentBackground true
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/87a_c.png
> width 1000 height 821 supersample 3 transparentBackground true
> hide #!8 models
> hide #!5 models
> show #!2 models
> show #!7 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/gcgr_c.png
> width 1000 height 821 supersample 3 transparentBackground true
> show #!9 models
> hide #!7 models
> show #4 models
> hide #!2 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/chrmine_c.png
> width 1000 height 821 supersample 3 transparentBackground true
> hide #4 models
> show #6 models
> hide #!9 models
> show #!10 models
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/wls_c.png
> width 1000 height 821 supersample 3 transparentBackground true
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0420_3v.cxs
——— End of log from Thu Apr 21 19:41:08 2022 ———
opened ChimeraX session
> hide #!10 models
> hide #6 models
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/87a_high.mrc
Opened 87a_high.mrc as #1, grid size 220,216,300, pixel 0.5, shown at level
5e-05, step 1, values int8
> show #!5 models
> ui mousemode right select
> ui mousemode right "map eraser"
> volume erase #1 center 122.53,145.22,102.9 radius 12.748
Opened 87a_high.mrc copy as #11, grid size 220,216,300, pixel 0.5, shown at
step 1, values int8
> close #8
> close #1
> volume erase #11 center 144,133.56,96.62 radius 13.875
> volume erase #11 center 130.78,127.39,101.05 radius 13.875
> volume erase #11 center 141.33,145.72,94.034 radius 13.875
> volume erase #11 center 125.05,150.94,109.87 radius 13.875
> volume erase #11 center 129.96,153.4,105.78 radius 13.875
> volume erase #11 center 114.78,127.33,121.82 radius 13.875
> volume erase #11 center 118.08,118.06,125.4 radius 13.875
> volume erase #11 center 129.33,160,131.88 radius 13.875
> volume erase #11 center 116.49,148.01,133.78 radius 13.875
> volume erase #11 center 125.31,151.4,148.7 radius 13.875
> volume erase #11 center 128.84,151.16,165.24 radius 13.875
> volume erase #11 center 125.61,150.1,157.12 radius 13.875
> volume erase #11 center 128.58,157.94,169.91 radius 13.875
> volume erase #11 center 138.38,159.55,178.99 radius 13.875
> volume erase #11 center 137.69,160.88,166.5 radius 9.15
> volume erase #11 center 156.68,158.59,155.76 radius 9.15
> volume erase #11 center 156.68,158.59,155.76 radius 12.45
> volume erase #11 center 152.91,163.52,136.59 radius 12.45
> volume erase #11 center 146.61,163.65,138.1 radius 12.45
> volume erase #11 center 164.47,162.84,166.06 radius 12.45
> volume erase #11 center 162.71,142.07,158.74 radius 9
> volume erase #11 center 163.82,144.67,165.12 radius 9
> volume erase #11 center 166.57,144.4,169.85 radius 9
> volume erase #11 center 139.3,140.87,193.58 radius 9
> volume erase #11 center 142.06,131.26,186.83 radius 9
> volume erase #11 center 137.82,141.38,182.82 radius 9
> volume erase #11 center 139.18,136.47,178.98 radius 9
> volume erase #11 center 158.31,131.36,178.84 radius 9
> volume erase #11 center 158.78,129.45,161.93 radius 9
> volume erase #11 center 154.17,124.36,142.9 radius 6.15
> volume erase #11 center 155.06,149.98,133.02 radius 6.15
> volume erase #11 center 151.89,147.99,125.7 radius 6.15
> volume erase #11 center 151.89,147.99,125.7 radius 6.15
> volume erase #11 center 127.22,131.03,113.19 radius 6.15
> volume erase #11 center 145.7,144.89,116.02 radius 6.15
> volume erase #11 center 141.81,154.33,125.69 radius 8.4
> volume erase #11 center 159.68,165.91,174.38 radius 8.4
> volume erase #11 center 160.45,163.74,179.91 radius 8.4
> volume erase #11 center 152.12,132.31,190.87 radius 8.4
> volume erase #11 center 167.48,139.22,189.43 radius 8.4
> volume erase #11 center 162.23,131.76,189.49 radius 8.4
> volume erase #11 center 154.79,126.05,168.63 radius 8.4
> volume erase #11 center 156.67,122.78,157.34 radius 8.4
> volume erase #11 center 152.96,118.59,149.28 radius 8.4
> volume erase #11 center 151.6,119.06,149.67 radius 8.4
> volume erase #11 center 157.32,128.02,140.53 radius 8.4
> volume erase #11 center 158.47,131.05,141.92 radius 8.4
> volume erase #11 center 129.22,122.24,121.01 radius 8.4
> volume erase #11 center 142.29,124.08,112.28 radius 8.4
> volume erase #11 center 151.47,125.84,114.3 radius 8.4
> volume erase #11 center 157.6,125.9,134.37 radius 8.4
> volume erase #11 center 151.06,115.6,128.54 radius 8.4
> volume erase #11 center 154.45,120.94,127.02 radius 8.4
> volume erase #11 center 147.11,112.62,130.98 radius 8.4
> volume erase #11 center 139.35,118,117.09 radius 8.4
> volume erase #11 center 153.55,148.16,126.91 radius 8.4
> volume erase #11 center 154.73,144.59,114.97 radius 8.4
> volume erase #11 center 146.25,137.09,105.69 radius 8.4
> volume erase #11 center 137.3,132.81,106.64 radius 8.4
> volume erase #11 center 141.93,130.2,106.91 radius 8.4
> volume erase #11 center 147.38,135.37,107.92 radius 8.4
> volume erase #11 center 149.75,120.88,124.34 radius 8.4
> volume erase #11 center 152.12,122.61,130.82 radius 8.4
> volume erase #11 center 138.85,124.12,114.24 radius 8.4
> volume erase #11 center 141.4,134.4,110.23 radius 8.4
> volume erase #11 center 156.7,140.76,135.65 radius 8.4
> volume erase #11 center 158.15,139.45,132.08 radius 8.4
> volume erase #11 center 146.33,146.14,116.64 radius 8.4
> volume erase #11 center 150.42,139.27,112.12 radius 8.4
> volume erase #11 center 150.42,139.27,112.12 radius 8.4
> volume erase #11 center 150.07,137.85,113.86 radius 8.4
> volume erase #11 center 141.18,129.86,111.28 radius 8.4
> volume erase #11 center 141.18,129.86,111.28 radius 8.4
> volume erase #11 center 118.52,127,108.03 radius 8.4
> volume erase #11 center 135.24,153.21,125.95 radius 8.4
> volume erase #11 center 139.99,152.4,134.36 radius 8.4
> volume erase #11 center 141.36,151.05,130.2 radius 8.4
> volume erase #11 center 142.57,145.09,132.62 radius 4.425
> volume erase #11 center 146.28,138.32,116.69 radius 4.425
> volume erase #11 center 147.31,133.14,117.11 radius 4.425
> volume erase #11 center 148.36,127.98,117.27 radius 4.425
> volume erase #11 center 145.35,125.24,118.28 radius 4.425
> volume erase #11 center 142.09,124,117.93 radius 4.425
> volume erase #11 center 143.74,118.99,125.12 radius 4.425
> volume erase #11 center 145.64,119.7,129.3 radius 4.425
> volume erase #11 center 147.75,121.1,134.99 radius 4.425
> volume erase #11 center 144.7,127.25,172.03 radius 6
> volume erase #11 center 138.22,126.57,167.73 radius 6
> volume erase #11 center 135.5,126.21,164.43 radius 6
> volume erase #11 center 130.38,125.13,158.66 radius 6
> volume erase #11 center 127.28,125.35,154.21 radius 6
> volume erase #11 center 129.35,123.55,149.59 radius 6
> volume erase #11 center 126.75,119.41,144.45 radius 6
> volume erase #11 center 127.22,120.03,140.44 radius 6
> volume erase #11 center 133.04,113.14,134.43 radius 6
> volume erase #11 center 141.45,120.91,128.02 radius 6
> volume erase #11 center 140.84,119.39,133.19 radius 6
> volume erase #11 center 141.79,116.93,141.62 radius 6
> volume erase #11 center 140.02,120.02,155.26 radius 6
> volume erase #11 center 140.02,120.02,155.26 radius 6
> volume erase #11 center 143.06,117.12,148.2 radius 6
> volume erase #11 center 138.13,116.08,143.13 radius 6
> volume erase #11 center 140,122.67,162.14 radius 6
> volume erase #11 center 141.26,123.58,165.97 radius 6
> volume erase #11 center 135.65,119.9,160.57 radius 6
> volume erase #11 center 128.18,124.17,154.32 radius 6
> volume erase #11 center 123.7,121.06,137.73 radius 6
> volume erase #11 center 125.45,120.07,130.89 radius 6
> volume erase #11 center 137.28,119.08,143.94 radius 6
> volume erase #11 center 132.23,120.23,144.08 radius 6
> volume erase #11 center 134.1,119.69,150.81 radius 6
> volume erase #11 center 129.21,122.68,151.82 radius 6
> volume erase #11 center 132.14,122.68,156.1 radius 6
> volume erase #11 center 136.88,123.42,161.68 radius 6
> volume erase #11 center 136.88,123.42,161.68 radius 6
> volume erase #11 center 135.36,120.21,157.4 radius 6
> volume erase #11 center 129.69,122.15,148.3 radius 6
> volume erase #11 center 130.68,122.61,147.47 radius 6
> volume erase #11 center 133.15,122.57,151.79 radius 6
> volume erase #11 center 133.45,123.26,156.73 radius 6
> volume erase #11 center 135.87,119.19,145.13 radius 6
> volume erase #11 center 139.47,118.72,150.95 radius 6
> volume erase #11 center 159.12,131.07,144.21 radius 6
> volume erase #11 center 142.02,154.51,151.9 radius 6
> volume erase #11 center 152.56,124.91,148.17 radius 6
> volume erase #11 center 127.89,145.79,140.62 radius 6
> volume erase #11 center 137.63,151.82,156.6 radius 6
> volume erase #11 center 154.35,141.32,166.42 radius 2.85
> volume erase #11 center 145.04,147.9,179.14 radius 2.85
> volume erase #11 center 147.75,149.92,175.99 radius 2.85
> volume erase #11 center 156.04,143.98,167.18 radius 2.85
> volume erase #11 center 141.23,132.17,112.18 radius 8.175
> volume erase #11 center 139.58,127.24,114.35 radius 8.175
> volume erase #11 center 136.07,128.83,118.78 radius 8.175
> volume erase #11 center 132.26,118.91,123.54 radius 8.175
> volume erase #11 center 128.12,118.55,127.29 radius 8.175
> volume erase #11 center 124.86,121.85,133.48 radius 8.175
> volume erase #11 center 143.34,121.44,117.77 radius 8.175
> volume erase #11 center 165.14,155.49,183.17 radius 8.175
> volume erase #11 center 162.92,151.8,182.86 radius 8.175
> volume erase #11 center 162.36,147,184.76 radius 6.975
> volume erase #11 center 169.13,142.1,178.13 radius 6.975
> volume erase #11 center 169.44,154.79,170.79 radius 6.975
> volume erase #11 center 170.38,141.05,176.15 radius 6.975
> volume erase #11 center 166.91,140.72,179.86 radius 6.975
> volume erase #11 center 164.99,134.1,183.34 radius 6.975
> volume erase #11 center 132.23,128.6,130 radius 3.1943
> volume erase #11 center 135.9,120.45,128.5 radius 3.1943
> volume erase #11 center 134.2,120.02,130.63 radius 3.1943
> volume erase #11 center 132.59,123.32,127.1 radius 3.1943
> volume erase #11 center 133.62,124.21,131.5 radius 3.1943
> volume erase #11 center 145.76,122,137.94 radius 3.1943
> volume erase #11 center 145.99,122.64,135.55 radius 3.1943
> volume erase #11 center 140.86,117.54,144.03 radius 3.1943
> volume erase #11 center 134.39,125.04,144.91 radius 3.1943
> volume erase #11 center 138.53,123.13,142.92 radius 3.1943
> volume erase #11 center 134.72,116.83,153.83 radius 11.994
> volume erase #11 center 137.28,120.28,146.68 radius 6.4488
> volume erase #11 center 139.4,125.54,164.2 radius 6.4488
> volume erase #11 center 139.88,121.58,156.93 radius 6.4488
> volume erase #11 center 149.14,117.53,121.05 radius 11.994
> volume erase #11 center 147.77,122.68,115.07 radius 11.994
> volume erase #11 center 146.93,116.7,120.65 radius 11.994
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_2/Figure2a/fig2a_0420/fig2a_0422_3v.cxs
——— End of log from Fri Apr 22 15:38:35 2022 ———
opened ChimeraX session
> close #9
> close #10
> close #7
> close #6
> close #4
> close #2
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/87a_cavity.cxs
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 5/A
> select /A:258-259
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:258-286
248 atoms, 255 bonds, 29 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select /A:294
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:294-317
181 atoms, 180 bonds, 24 residues, 1 model selected
> show sel atoms
> color sel byhetero
> ui mousemode right select
> select clear
> select #11
2 models selected
> select clear
> select /A:279@CG
1 atom, 1 residue, 1 model selected
> select /A:279
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:279
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select /A:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:258-263
54 atoms, 56 bonds, 6 residues, 1 model selected
> hide sel atoms
> select /A:265
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:265-271
54 atoms, 54 bonds, 7 residues, 1 model selected
> hide sel atoms
> select clear
> select /A:273
9 atoms, 8 bonds, 1 residue, 1 model selected
> select
> /A:90-95,100-110,224-249,258-286,294-317,335-352,360-391,398-426,436-459
1638 atoms, 1673 bonds, 199 residues, 1 model selected
> select clear
> select clear
> select clear
> select /A:274
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:275
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:275
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:274
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:274-276
23 atoms, 23 bonds, 3 residues, 1 model selected
> select /A:274
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:274-275
12 atoms, 11 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /A:278
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:279
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:279-280
20 atoms, 20 bonds, 2 residues, 1 model selected
> select
> /A:90-95,100-110,224-249,258-286,294-317,335-352,360-391,398-426,436-459
1638 atoms, 1673 bonds, 199 residues, 1 model selected
> select /A:278
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:278
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:277
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:281
9 atoms, 8 bonds, 1 residue, 1 model selected
> select
> /A:90-95,100-110,224-249,258-286,294-317,335-352,360-391,398-426,436-459
1638 atoms, 1673 bonds, 199 residues, 1 model selected
> select /A:281
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:281-286
57 atoms, 57 bonds, 6 residues, 1 model selected
> hide sel atoms
> select clear
> select #11
2 models selected
> select clear
> select /A:294
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:294
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:294-304
81 atoms, 80 bonds, 11 residues, 1 model selected
> select /A:303
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:294-303
72 atoms, 71 bonds, 10 residues, 1 model selected
> select /A:294
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:294-300
54 atoms, 53 bonds, 7 residues, 1 model selected
> hide sel atoms
> select clear
> select /A:302
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:303
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:303
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:302
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:302-303
12 atoms, 11 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /A:301
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select /A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:307-308
13 atoms, 12 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /A:306
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /A:310
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:310-312
22 atoms, 21 bonds, 3 residues, 1 model selected
> hide sel atoms
> select /A:313
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:313-315
23 atoms, 22 bonds, 3 residues, 1 model selected
> hide sel atoms
> select /A:317
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide sel atoms
> select /A:263
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:263-264
9 atoms, 8 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select /A:224
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:224-249
218 atoms, 227 bonds, 26 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select /A:224
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:224-236
109 atoms, 112 bonds, 13 residues, 1 model selected
> hide sel atoms
> select /A:237
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:237-249
109 atoms, 114 bonds, 13 residues, 1 model selected
> hide sel atoms
> select clear
> select /A:436-437
20 atoms, 19 bonds, 2 residues, 1 model selected
> select /A:436-459
209 atoms, 214 bonds, 24 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select /A:436
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:436
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:436-438
28 atoms, 27 bonds, 3 residues, 1 model selected
> hide sel atoms
> select /A:439
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:439-440
21 atoms, 22 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /A:222
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:222-223
17 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select /A:444@CA
1 atom, 1 residue, 1 model selected
> select /A:443
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:443-444
13 atoms, 12 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /A:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:447-448
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:447-448
16 atoms, 15 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /A:447
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:447-449
27 atoms, 27 bonds, 3 residues, 1 model selected
> hide sel atoms
> select /A:450
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:450-459
79 atoms, 79 bonds, 10 residues, 1 model selected
> hide sel atoms
> select clear
> select /A:301
6 atoms, 5 bonds, 1 residue, 1 model selected
> select
> /A:90-95,100-110,224-249,258-286,294-317,335-352,360-391,398-426,436-459
1638 atoms, 1673 bonds, 199 residues, 1 model selected
> select /A:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select /A:407
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:406
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:398-406
81 atoms, 83 bonds, 9 residues, 1 model selected
> show sel atoms
> select /A:407
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:407-411
36 atoms, 35 bonds, 5 residues, 1 model selected
> show sel atoms
> select /A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:398-411
117 atoms, 119 bonds, 14 residues, 1 model selected
> color sel byhetero
> select /A:411
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:408-411
29 atoms, 28 bonds, 4 residues, 1 model selected
> hide sel atoms
> select /A:412
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:412-418
49 atoms, 49 bonds, 7 residues, 1 model selected
> select /A:411
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:404-411
62 atoms, 62 bonds, 8 residues, 1 model selected
> hide sel atoms
> select /A:403
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:402-403
21 atoms, 21 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /A:399-400
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /A:398-400
22 atoms, 21 bonds, 3 residues, 1 model selected
> hide sel atoms
> select /A:387
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:392
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:392-397
54 atoms, 53 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hide sel atoms
> select clear
> select /A:318
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:318-319
16 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:318-320
20 atoms, 20 bonds, 3 residues, 1 model selected
> show sel atoms
> show sel atoms
> color sel byhetero
> select clear
> select /A:373
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:370
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:370-382
111 atoms, 115 bonds, 13 residues, 1 model selected
> select
> /A:90-95,100-110,224-249,258-286,294-317,335-352,360-391,398-426,436-459
1638 atoms, 1673 bonds, 199 residues, 1 model selected
> select /A:370-371
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:370-385
134 atoms, 138 bonds, 16 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select /A:370
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:370
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:372
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:373
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:373-374
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:372
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:372-375
26 atoms, 25 bonds, 4 residues, 1 model selected
> hide sel atoms
> select /A:376-377
28 atoms, 31 bonds, 2 residues, 1 model selected
> select /A:376-380
55 atoms, 59 bonds, 5 residues, 1 model selected
> hide sel atoms
> select /A:381
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:381-384
30 atoms, 29 bonds, 4 residues, 1 model selected
> hide sel atoms
> select clear
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/87a_cavity.cxs
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/2022.apr23.932.mrc
Opened 2022.apr23.932.mrc as #1, grid size 204,200,280, pixel 0.5, shown at
level 5e-05, step 1, values int8
> hide #!11 models
> select clear
> ui mousemode right "map eraser"
> volume erase #1 center 127.37,120.32,118.66 radius 11.991
Opened 2022.apr23.932.mrc copy as #3, grid size 204,200,280, pixel 0.5, shown
at step 1, values int8
> volume erase #3 center 143.55,126.18,108.21 radius 11.97
> volume erase #3 center 148.99,117.46,126.28 radius 11.97
> volume erase #3 center 159.86,122.44,142.8 radius 11.97
> volume erase #3 center 159.09,120.89,161.61 radius 11.97
> volume erase #3 center 161.43,138.37,169.56 radius 11.97
> volume erase #3 center 153.95,140.35,181.33 radius 11.97
> volume erase #3 center 157.4,157.56,177.89 radius 11.97
> volume erase #3 center 145.71,152.49,179.17 radius 11.97
> volume erase #3 center 154.72,161.41,156.19 radius 11.97
> volume erase #3 center 123.61,151.5,141.54 radius 11.97
> ui mousemode right select
> select clear
> ui mousemode right "map eraser"
> volume erase #3 center 133.71,123.07,168.71 radius 12.008
> volume erase #3 center 133.71,123.07,168.71 radius 12.008
> volume erase #3 center 130.53,123.95,136.92 radius 4.8034
> volume erase #3 center 132,123.18,137.71 radius 4.8034
> volume erase #3 center 138.64,123.12,130.49 radius 4.8034
> volume erase #3 center 139.28,122.3,121.02 radius 4.8034
> volume erase #3 center 139.77,123.58,119.25 radius 4.8034
> volume erase #3 center 138.32,119.73,124.86 radius 4.8034
> hide #2 models
> ui mousemode right select
> close #1
> transparency #3,5 50
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/87a_cavity.cxs
> select /A:279
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:272
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:304
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/87a_cavity.cxs
——— End of log from Sat Apr 23 20:48:18 2022 ———
opened ChimeraX session
> hide #!3 models
> show #!11 models
> hide #!11 models
> close #11
> close #3
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/6eid_1124.pdb
Chain information for 6eid_1124.pdb #1
---
Chain | Description
A | No description available
> hide #!5 models
> hide #1 atoms
> select ::name="LYR"
29 atoms, 29 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right select
> select clear
> show #!5 models
> cartoon style helix width 1 thickness 0.3
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/2022.apr25.2ea.mrc
Opened 2022.apr25.2ea.mrc as #2, grid size 216,208,264, pixel 0.5, shown at
level 5e-05, step 1, values int8
> close #2
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/6eid_10_3.mrc
Opened 6eid_10_3.mrc as #2, grid size 196,192,248, pixel 0.5, shown at level
5e-05, step 1, values int8
> volume #2 level 0.3298
> close #2
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/6eid15_2.mrc
Opened 6eid15_2.mrc as #2, grid size 216,208,264, pixel 0.5, shown at level
5e-05, step 1, values int8
> hide #!5 models
> hide #!2 models
> show #!2 models
> open C:/Users/user/Downloads/2022.apr25.0dd.mrc
Opened 2022.apr25.0dd.mrc as #3, grid size 216,208,264, pixel 0.5, shown at
level 5e-05, step 1, values int8
> hide #!2 models
> volume #3 level 0.3352
> transparency #1,3 50
> close #3
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/6eid_15_1.mrc
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/87a_15_1.mrc
Opened 6eid_15_1.mrc as #3.1, grid size 216,208,264, pixel 0.5, shown at level
5e-05, step 1, values int8
Opened 87a_15_1.mrc as #3.2, grid size 220,216,300, pixel 0.5, shown at level
1, step 1, values int8
> close #2
> hide #!3.2 models
> transparency #1#3.1#!3 50
> hide #!3.1 models
> show #!3.2 models
> show #!5 models
> close #3.2
> close #3
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/87a_15_1.mrc
Opened 87a_15_1.mrc as #2, grid size 220,216,300, pixel 0.5, shown at level 1,
step 1, values int8
> close #2
> hide #!5 models
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/6eid_15_1.mrc
Opened 6eid_15_1.mrc as #2, grid size 216,208,264, pixel 0.5, shown at level
5e-05, step 1, values int8
> transparency #1-2 50
> hide #!2 models
> open C:/Users/user/Downloads/2022.apr25.48c.mrc
Opened 2022.apr25.48c.mrc as #3, grid size 220,216,300, pixel 0.5, shown at
level 1, step 1, values int8
> hide #!3 models
> show #!3 models
> volume #3 level 0.1046
> transparency #1,3 50
> close #3
> open
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/871_15_2.mrc
Opened 871_15_2.mrc as #3, grid size 220,216,300, pixel 0.5, shown at level
5e-05, step 1, values int8
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/87a_cavity.cxs
——— End of log from Mon Apr 25 18:58:52 2022 ———
opened ChimeraX session
> hide #1 models
> show #!5 models
> transparency #3,5 50
> ui mousemode right "map eraser"
> volume erase #3 center 127.15,123.7,105.59 radius 12.748
Opened 871_15_2.mrc copy as #6, grid size 220,216,300, pixel 0.5, shown at
step 1, values int8
> volume erase #6 center 149.17,135.25,97.539 radius 12.75
> volume erase #6 center 141.5,137.53,95.054 radius 12.75
> volume erase #6 center 141.5,137.53,95.054 radius 12.75
> volume erase #6 center 137.93,122.33,98.328 radius 12.75
> volume erase #6 center 146.4,127.02,96.526 radius 12.75
> volume erase #6 center 122.76,148.5,110.37 radius 12.75
> volume erase #6 center 134.79,152.13,104.29 radius 12.75
> volume erase #6 center 112.46,131.88,114.25 radius 12.75
> volume erase #6 center 116.16,146.68,138.86 radius 12.75
> volume erase #6 center 126.63,147.06,163.72 radius 12.75
> volume erase #6 center 129.48,150.29,174.38 radius 12.75
> volume erase #6 center 131.96,157.59,154.31 radius 12.75
> volume erase #6 center 127.13,157.66,135.48 radius 12.75
> volume erase #6 center 123.49,148.77,148.17 radius 12.75
> volume erase #6 center 125.21,149.92,151.62 radius 12.75
> volume erase #6 center 133.09,160.24,163.1 radius 12.75
> volume erase #6 center 140.69,155.52,177.19 radius 9.45
> volume erase #6 center 152.98,168.08,179.7 radius 9.45
> volume erase #6 center 149.38,169.4,171.14 radius 9.45
> volume erase #6 center 153.77,162.63,154.54 radius 9.45
> volume erase #6 center 157.83,163.7,160.68 radius 9.45
> volume erase #6 center 158.41,159.28,160.52 radius 9.45
> volume erase #6 center 158.41,159.28,160.52 radius 9.45
> volume erase #6 center 140.38,158.07,141.05 radius 9.45
> volume erase #6 center 153.06,161.68,144.83 radius 9.45
> volume erase #6 center 158.21,124.37,141.6 radius 9.45
> volume erase #6 center 157.46,125.93,144.68 radius 9.45
> volume erase #6 center 156.75,127.72,144.54 radius 9.45
> volume erase #6 center 158.96,123.63,162.34 radius 9.45
> volume erase #6 center 145.84,115.38,145.05 radius 9.45
> volume erase #6 center 149.06,114.94,156.54 radius 9.45
> volume erase #6 center 156.19,125.53,164.32 radius 9.45
> volume erase #6 center 156.19,125.53,164.32 radius 9.45
> volume erase #6 center 153.63,116.55,156.27 radius 9.45
> volume erase #6 center 138.25,130.37,177.31 radius 9.45
> volume erase #6 center 141.38,133.71,189.12 radius 9.45
> volume erase #6 center 138.62,141.96,187.53 radius 9.45
> volume erase #6 center 144.19,151.75,178.85 radius 5.7
> volume erase #6 center 158.8,166.51,177.19 radius 5.7
> volume erase #6 center 163.15,159.23,167.64 radius 5.7
> volume erase #6 center 152.51,133.01,187.51 radius 4.725
> volume erase #6 center 150.31,133.35,186.25 radius 4.725
> volume erase #6 center 159.02,140.65,151.69 radius 4.725
> volume erase #6 center 164.86,134.47,161.07 radius 2.85
> volume erase #6 center 164.16,137.05,158.92 radius 2.85
> volume erase #6 center 161.81,134.43,158.77 radius 2.85
> volume erase #6 center 142.67,117.22,167.18 radius 7.575
> volume erase #6 center 144.35,120.89,166.06 radius 7.575
> volume erase #6 center 139.63,119.32,159.21 radius 7.575
> volume erase #6 center 138.23,123.04,169.63 radius 7.575
> volume erase #6 center 137.59,123.35,166.86 radius 9
> volume erase #6 center 136.25,122.47,161.4 radius 9
> volume erase #6 center 132.36,120.35,154.33 radius 9
> volume erase #6 center 125.88,119.17,145.33 radius 9
> volume erase #6 center 141.11,121.04,154.71 radius 4.725
> volume erase #6 center 139.27,122.06,151.02 radius 4.725
> volume erase #6 center 136.77,121,145.39 radius 4.725
> volume erase #6 center 137.66,121.11,141.61 radius 4.725
> volume erase #6 center 135.88,121.45,147.82 radius 5.7
> volume erase #6 center 130.17,124.77,142.5 radius 5.7
> volume erase #6 center 131.18,125.46,144.33 radius 4.725
> volume erase #6 center 131.03,125.14,148.34 radius 4.725
> volume erase #6 center 132.99,127.53,155.43 radius 4.725
> volume erase #6 center 132.81,128.88,157.72 radius 4.725
> volume erase #6 center 133.27,130.93,160.7 radius 4.725
> volume erase #6 center 134.11,131.79,161.53 radius 4.725
> volume erase #6 center 134.11,131.79,161.53 radius 4.725
> volume erase #6 center 144.19,124.66,158.04 radius 4.725
> volume erase #6 center 142.37,122.97,155.81 radius 4.725
> volume erase #6 center 141.09,123.13,154.26 radius 4.725
> volume erase #6 center 143.99,125.5,162.92 radius 4.725
> volume erase #6 center 151.3,125.74,174.25 radius 4.725
> volume erase #6 center 154.28,127.41,179.72 radius 4.725
> volume erase #6 center 154.15,126.96,170.17 radius 4.725
> volume erase #6 center 158.74,127,171.42 radius 4.725
> volume erase #6 center 162.15,127.66,172.7 radius 4.725
> volume erase #6 center 168.17,128.14,174.46 radius 4.725
> volume erase #6 center 168.17,128.14,174.46 radius 4.725
> volume erase #6 center 169.67,131.88,176.19 radius 4.725
> volume erase #6 center 166.48,128.08,175.59 radius 4.725
> volume erase #6 center 158.95,126.78,172.23 radius 4.725
> volume erase #6 center 155.36,126.7,172.8 radius 4.725
> volume erase #6 center 150.76,126.41,176.8 radius 4.725
> volume erase #6 center 148.74,128.18,171.48 radius 4.725
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/87a_cavity.cxs
> volume erase #6 center 152.04,127.8,172.16 radius 4.725
> volume erase #6 center 151.4,127.17,181.78 radius 4.725
> volume erase #6 center 150.32,139,192.91 radius 4.725
> volume erase #6 center 151.9,141.13,192.85 radius 4.725
> volume erase #6 center 153.42,136.76,192.07 radius 4.725
> volume erase #6 center 155.35,134.87,190.21 radius 4.725
> volume erase #6 center 157.68,130,187.4 radius 4.725
> volume erase #6 center 157.64,131.92,187.66 radius 4.725
> volume erase #6 center 167.99,142.87,185.09 radius 4.725
> volume erase #6 center 165.37,143.26,190.86 radius 4.725
> volume erase #6 center 162.19,142.24,194.62 radius 4.725
> volume erase #6 center 155.09,136.77,196.04 radius 4.725
> volume erase #6 center 118.45,136.05,123.29 radius 8.55
> volume erase #6 center 120.72,122.63,128.18 radius 8.55
> volume erase #6 center 129,123.44,121.31 radius 8.55
> volume erase #6 center 138.64,127.82,111.13 radius 8.55
> volume erase #6 center 123.24,130.84,114.23 radius 8.55
> volume erase #6 center 136.48,136.33,107.96 radius 8.55
> volume erase #6 center 141.63,122.88,111.78 radius 8.55
> volume erase #6 center 151.47,144.75,116.57 radius 8.55
> volume erase #6 center 156.6,147.39,124.09 radius 8.55
> volume erase #6 center 162.11,143.88,130.21 radius 8.55
> volume erase #6 center 158.28,149.87,132.42 radius 8.55
> volume erase #6 center 152.6,154.84,131.46 radius 8.55
> volume erase #6 center 152.57,134.57,109.95 radius 8.55
> volume erase #6 center 147.97,135.03,114.66 radius 3.3
> volume erase #6 center 148.07,138.06,114.65 radius 3.3
> volume erase #6 center 147.8,139.19,117.75 radius 3.3
> volume erase #6 center 146.9,139.9,117.62 radius 3.3
> volume erase #6 center 150.03,139.86,121.1 radius 3.3
> volume erase #6 center 152.29,140.51,128.89 radius 3.3
> volume erase #6 center 154.33,140.78,129.65 radius 3.3
> volume erase #6 center 154.98,137.9,133.54 radius 3.3
> volume erase #6 center 154.86,140.32,131.88 radius 3.3
> volume erase #6 center 151.11,143.06,126.73 radius 3.3
> volume erase #6 center 151.08,141.72,125.79 radius 3.3
> volume erase #6 center 149.47,142.19,123.26 radius 3.3
> volume erase #6 center 150.36,138.75,122.06 radius 3.3
> volume erase #6 center 147.39,137.99,118.89 radius 3.3
> volume erase #6 center 148.29,135.28,116.04 radius 3.3
> volume erase #6 center 143.91,134.82,112.38 radius 3.3
> volume erase #6 center 145.18,125.76,116.41 radius 3.3
> volume erase #6 center 144.97,122.95,117.48 radius 4.725
> volume erase #6 center 145.13,119.57,121.69 radius 4.725
> volume erase #6 center 142.63,119.48,122.64 radius 4.725
> volume erase #6 center 143.78,118.46,128.41 radius 4.725
> volume erase #6 center 144.95,118.11,130.2 radius 4.725
> volume erase #6 center 148.94,120.35,128.5 radius 4.725
> volume erase #6 center 146.96,119.22,138.13 radius 4.725
> volume erase #6 center 150.37,119.38,131.37 radius 4.725
> volume erase #6 center 150.84,122.33,131.28 radius 4.725
> volume erase #6 center 139.94,117.24,128.42 radius 4.725
> volume erase #6 center 137.35,150.42,123.12 radius 4.725
> volume erase #6 center 137.95,147.18,127.49 radius 4.725
> volume erase #6 center 133.29,150.35,124.48 radius 4.725
> volume erase #6 center 122.57,147.19,127.01 radius 4.725
> volume erase #6 center 129.01,148.96,135.91 radius 4.725
> ui tool show "Volume Viewer"
> close #3
> volume #6 level 1
> volume erase #6 center 155.29,141.65,131.84 radius 4.725
> volume erase #6 center 149.12,138.13,122.82 radius 4.725
> volume erase #6 center 144.01,138.44,117.36 radius 4.725
> volume erase #6 center 142.64,134.16,114.01 radius 4.725
> volume erase #6 center 146.23,129.67,115.04 radius 4.725
> volume erase #6 center 146.76,131.54,116.95 radius 4.725
> volume erase #6 center 148.44,134.5,119.19 radius 4.725
> volume erase #6 center 154.08,135.76,134.77 radius 4.725
> volume erase #6 center 126.88,121.54,135.07 radius 4.725
> volume erase #6 center 131.62,120.04,135.74 radius 4.725
> volume erase #6 center 129.84,120.92,131.13 radius 4.725
> volume erase #6 center 130.32,122.83,132.12 radius 4.725
> volume erase #6 center 135.39,120.29,136.73 radius 4.725
> volume erase #6 center 139.31,120.18,137.78 radius 4.725
> volume erase #6 center 142.23,120.4,138.49 radius 4.725
> volume erase #6 center 141.88,121.93,132.3 radius 4.725
> volume erase #6 center 136.89,121.9,131.85 radius 4.725
> volume erase #6 center 138.21,122.39,127.9 radius 4.725
> volume erase #6 center 149.25,123.42,129.98 radius 4.725
> volume erase #6 center 148.35,126.96,127.52 radius 4.725
> volume erase #6 center 146.5,123.56,124.42 radius 4.725
> volume erase #6 center 145.21,124.34,117.67 radius 4.725
> volume erase #6 center 143.04,121.17,126.55 radius 4.725
> volume erase #6 center 153.73,142.55,131.03 radius 4.725
> volume erase #6 center 154.17,138.8,131.35 radius 4.725
> volume erase #6 center 154.52,139.35,136.77 radius 4.725
> volume erase #6 center 152.29,136.53,132.13 radius 4.725
> volume erase #6 center 145.95,124.83,130.43 radius 3.3
> volume erase #6 center 139.33,121.67,124.31 radius 3.3
> volume erase #6 center 136.74,125.87,152.47 radius 3.3
> volume erase #6 center 133.74,125.45,150.1 radius 3.3
> volume erase #6 center 129.8,123.68,134.93 radius 3.3
> volume erase #6 center 161.28,139.25,154.82 radius 6.3
> volume erase #6 center 164.13,139.58,157.83 radius 6.3
> volume erase #6 center 160.44,132.65,159.17 radius 6.3
> volume erase #6 center 164.48,132.16,164.49 radius 6.3
> volume erase #6 center 169.75,139.01,169.06 radius 6.3
> volume erase #6 center 166.77,142.8,167.21 radius 4.575
> volume erase #6 center 166.2,139.1,161.65 radius 4.575
> volume erase #6 center 167.18,146.59,160.35 radius 4.575
> volume erase #6 center 159.2,143.46,159.14 radius 1.875
> volume erase #6 center 159.2,143.46,159.14 radius 1.875
> volume erase #6 center 159.36,143.14,158.55 radius 1.875
> volume erase #6 center 157.87,142.02,159.22 radius 1.875
> volume erase #6 center 159.4,138.59,159.55 radius 1.875
> volume erase #6 center 157.88,138.65,159.57 radius 1.875
> volume erase #6 center 164.72,139.4,165.46 radius 1.875
> volume erase #6 center 164.75,140.15,167.77 radius 1.875
> volume erase #6 center 164.76,140.75,169.61 radius 1.875
> volume erase #6 center 163.04,141.23,170.78 radius 1.875
> volume erase #6 center 163.53,144.91,165.13 radius 1.875
> volume erase #6 center 162.47,146.49,163.45 radius 1.875
> volume erase #6 center 150.77,141.44,132.86 radius 1.875
> volume erase #6 center 150.71,141.17,135.2 radius 1.875
> volume erase #6 center 150.1,143.03,134.28 radius 1.875
> volume erase #6 center 164.6,153,169.87 radius 4.125
> volume erase #6 center 168.13,145.09,174.97 radius 4.125
> volume erase #6 center 167.7,149.35,174.47 radius 4.125
> volume erase #6 center 166.38,146.57,171.36 radius 4.125
> volume erase #6 center 166.67,148.35,173.58 radius 4.125
> volume erase #6 center 162.97,156.13,174.46 radius 4.125
> volume erase #6 center 160.48,156.47,175.45 radius 4.125
> volume erase #6 center 160.08,154.11,180.29 radius 4.125
> volume erase #6 center 156.08,154.45,176.91 radius 4.125
> volume erase #6 center 152.77,154.47,183.08 radius 4.125
> volume erase #6 center 152.77,154.47,183.08 radius 4.125
> volume erase #6 center 150.38,153.3,186.93 radius 4.125
> volume erase #6 center 149.76,152.97,184.78 radius 4.125
> volume erase #6 center 150.87,151.46,186.03 radius 4.125
> volume erase #6 center 147.79,149.86,183.2 radius 4.125
> volume erase #6 center 149.15,149.1,183.29 radius 4.125
> volume erase #6 center 156.14,155.66,184.78 radius 4.125
> volume erase #6 center 164.79,129.36,175.74 radius 4.125
> volume erase #6 center 165.51,130.16,179.29 radius 4.125
> volume erase #6 center 166.81,134.38,178.56 radius 4.125
> volume erase #6 center 166.23,135.25,181.4 radius 4.125
> volume erase #6 center 161.44,146.68,184.76 radius 4.125
> volume erase #6 center 162.42,150.59,180.57 radius 4.125
> volume erase #6 center 167.17,143.3,180.18 radius 4.125
> volume erase #6 center 165.94,144.96,182.45 radius 4.125
> volume erase #6 center 165.11,152.88,175.8 radius 4.125
> volume erase #6 center 162.51,154.39,174.61 radius 4.125
> volume erase #6 center 162.45,153.34,171.86 radius 4.125
> volume erase #6 center 159.47,153.06,186.11 radius 4.125
> volume erase #6 center 131.69,125.6,128.61 radius 4.125
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/87a_cavity.cxs
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/87a_15_2_0426.mrc
> models #6
> save
> C:/Users/user/Documents/BCS/TMEM87a/Draft/AR_draft_220304/Figure_3/0423_cavity/87a_cavity.cxs
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 932, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 652, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 252, in reset_state
alignment._destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 603, in _destroy
self._notify_observers(self.NOTE_DESTROYED, None)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 652, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 474, in alignment_notification
self.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 512, in delete
ToolInstance.delete(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 154, in delete
self.session.ui.remove_tool(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 345, in remove_tool
self.main_window.remove_tool(tool_instance)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 725, in remove_tool
tw._destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2049, in _destroy
self.__toolkit.destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2189, in destroy
sbar.destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\statusbar.py", line 51, in destroy
v.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 438, in delete
self.make_current()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 99, in make_current
qc = self._initialize_context()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 27.20.100.8853
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Manufacturer: LG Electronics
Model: 17ZD95N-GX76K
OS: Microsoft Windows 10 Pro (Build 19044)
Memory: 16,890,650,624
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
OSLanguage: ko-KR
Locale: ('ko_KR', 'cp949')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem destroying status bar |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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