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Opened 3 years ago
Closed 3 years ago
#7918 closed defect (worksforme)
MemoryError saving session
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | chimerax-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.18363
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221025-3.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Tue Oct 25 15:43:42 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-17.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Fri Oct 14 17:25:48 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-6.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Fri Oct 14 14:23:32 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-3.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Fri Oct 14 12:43:27 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-2.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Fri Oct 14 10:35:38 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-11.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Thu Oct 13 17:27:46 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-7.cxs
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0265, step 1, values float32
Log from Thu Oct 13 16:05:18 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/PCO371_1_lg-
> coot-12.pdb
Summary of feedback from opening
E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/PCO371_1_lg-coot-12.pdb
---
warning | Cannot find consistent set of bond orders for ring system containing
atom C26 in residue LIG /L:501
Chain information for PCO371_1_lg-coot-12.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/ZLH_xwide.mrc
Opened ZLH_xwide.mrc as #2, grid size 256,256,256, pixel 0.824, shown at level
0.0147, step 1, values float32
> lighting soft
> set bgColor white
> hide atoms
> show cartoons
> hide #!2 models
> select /R
2115 atoms, 2177 bonds, 3 pseudobonds, 257 residues, 2 models selected
> color (#!1 & sel) light sea green
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel crimson
> ui tool show "Color Zone"
> color zone #2 near #1 distance 4.94
> volume splitbyzone #2
Opened ZLH_xwide.mrc 0 as #3.1, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 1 as #3.2, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 2 as #3.3, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 3 as #3.4, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 4 as #3.5, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 5 as #3.6, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
Opened ZLH_xwide.mrc 6 as #3.7, grid size 256,256,256, pixel 0.824, shown at
level 0.0147, step 1, values float32
> hide #1.1 models
> volume #3.1 style mesh
> volume #3.7 style mesh
> transparency sel 80
> help help:user/tools/colorzone.html
> volume #3.7 level 0.07364
> volume #3.7 level 0.0648
> volume #3.7 style surface
> transparency sel 90
> select clear
> transparency #3.7#!1,3 90
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> color sel byhetero
> volume #3.7 style mesh
> volume #3.7 style surface
> select /A
1950 atoms, 1989 bonds, 1 pseudobond, 235 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep pink
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-1.cxs
> volume #3.7 level 0.02943
> transparency (#!1 & sel) 30
> transparency (#!1 & sel) 10
> select clear
> transparency #3.7#!1,3 30
> transparency #3.7#!1,3 40
> transparency #3.7#!1,3 50
> transparency #3.7#!1,3 60
> surface dust #3 size 20
> undo
> surface dust #3 size 0
> surface dust #3 size 5
> surface dust #3 size 2
> surface dust #3 size 3
> select clear
> volume #3.7 style mesh
> volume #3.7 style surface
> select /B
2616 atoms, 2663 bonds, 341 residues, 1 model selected
> color sel orange
> select /N
980 atoms, 1001 bonds, 129 residues, 1 model selected
> color sel gray
> select /G
436 atoms, 442 bonds, 57 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> select clear
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-1.cxs
> lighting soft
> cartoon style width 1.5 thickness 0.3
> cartoon style width 2 thickness 0.3
> lighting soft
> lighting simple
> lighting soft
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1.8 thickness 0.3
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-2.cxs
> transparency 10 cartoons
> transparency 5 cartoons
> lighting simple
> lighting soft
> lighting full
> volume #3.7 level 0.02354
> volume #3.7 level 0.02649
> lighting soft
> transparency 2 cartoons
> transparency 0 cartoons
> transparency 10 ribbons
> lighting shadows true intensity 0.5
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> lighting full
> lighting flat
[Repeated 2 time(s)]
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting flat
[Repeated 2 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> transparency 20 ribbons
> transparency 0 ribbons
> lighting soft
[Repeated 1 time(s)]
> transparency2 ribbon
Unknown command: transparency2 ribbon
> transparency 2 ribbons
> cartoon suppressBackboneDisplay false
> ui tool show "Side View"
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-3.cxs
> lighting soft
> lighting full
> lighting simple
> lighting flat
> graphics silhouettes false
> save 20221013-PTH1R-1.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 5 ribbons
> transparency 10 ribbons
> transparency 20 ribbons
> transparency 30 ribbons
> save 20221013-PTH1R-1.tif width 2000 height 2000 supersample 3
> transparentBackground true
> lighting simple
> lighting full
> save 20221013-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 10 ribbons
> save 20221013-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 20 ribbons
> transparency 30 ribbons
> save 20221013-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 20 ribbons
> save 20221013-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 10 ribbons
> save 20221013-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> save 20221013-PTH1R-3.tif width 2000 height 2000 supersample 3
> transparentBackground true
> save 20221013-PTH1R-4.tif width 2000 height 2000 supersample 3
> transparentBackground true
> lighting shadows false
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting full
> lighting shadows false
> save 20221013-PTH1R-5.tif width 2000 height 2000 supersample 3
> transparentBackground true
> size sel stickRadius 0.3
Changed 0 bond radii
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> size sel stickRadius 0.3
Changed 48 bond radii
> size sel stickRadius 0.2
Changed 48 bond radii
> volume #3.7 level 0.02649
> size sel stickRadius 0.25
Changed 48 bond radii
> size sel stickRadius 0.2
Changed 48 bond radii
> select clear
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-4.cxs
> select /R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 11 atom styles
> select clear
> color #!1,3 byhetero
> select /R:416
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> show sel atoms
> select add /R:415
15 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 15 atom styles
> select clear
> select /R:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
Drag select of 1 residues
> select clear
> select /R:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /R:413
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select /R:412
7 atoms, 6 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 7 atom styles
> select clear
> select /R:411
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select clear
> select /R:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select clear
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-5.cxs
> size sel stickRadius 0.25
Changed 0 bond radii
> size sel stickRadius 0.25
Changed 0 bond radii
> select /R:302
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select /R:302
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 9 atom styles
> select clear
> select /R:458
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select /R:459
12 atoms, 12 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 12 atom styles
> select clear
> transparency 20 cartoons
> transparency 30 cartoons
> select /R:223
10 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 10 atom styles
> select clear
> select /R:219
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 11 atom styles
> select /R:463
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select clear
> select /R:465
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 9 atom styles
> select clear
> select /A:359
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 9 atom styles
> select /A:360
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select /A:358
12 atoms, 12 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 12 atom styles
> select clear
> transparency 50 cartoons
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-6.cxs
> select /R:392
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
223 atoms, 225 bonds, 28 residues, 1 model selected
> cartoon hide sel
> select add /R:318
232 atoms, 233 bonds, 29 residues, 1 model selected
> select up
468 atoms, 480 bonds, 58 residues, 1 model selected
> hide sel cartoons
> select add /R:311
479 atoms, 491 bonds, 59 residues, 1 model selected
> select down
479 atoms, 491 bonds, 59 residues, 1 model selected
> select down
479 atoms, 491 bonds, 59 residues, 1 model selected
> select subtract /R:311
468 atoms, 480 bonds, 58 residues, 1 model selected
> select add /R:311
479 atoms, 491 bonds, 59 residues, 1 model selected
> select down
479 atoms, 491 bonds, 59 residues, 1 model selected
> select down
479 atoms, 491 bonds, 59 residues, 1 model selected
> select add /R:312
487 atoms, 498 bonds, 60 residues, 1 model selected
> select add /R:313
492 atoms, 502 bonds, 61 residues, 1 model selected
> select add /R:314
503 atoms, 513 bonds, 62 residues, 1 model selected
> select add /R:315
514 atoms, 524 bonds, 63 residues, 1 model selected
> select add /R:316
520 atoms, 529 bonds, 64 residues, 1 model selected
> hide sel cartoons
> select add /R:393
528 atoms, 536 bonds, 65 residues, 1 model selected
> hide sel cartoons
> select add /R:211
540 atoms, 548 bonds, 66 residues, 1 model selected
> select up
790 atoms, 814 bonds, 95 residues, 1 model selected
> select up
2115 atoms, 2177 bonds, 257 residues, 1 model selected
> select down
790 atoms, 814 bonds, 95 residues, 1 model selected
> hide sel cartoons
> undo
> select clear
> select /R:211
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
33 atoms, 33 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select /R:207
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
20 atoms, 19 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select /R:204
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
118 atoms, 119 bonds, 16 residues, 1 model selected
> hide sel cartoons
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-7.cxs
——— End of log from Thu Oct 13 16:05:18 2022 ———
opened ChimeraX session
> cartoon style width 1.5 thickness 0.3
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
5 hydrogen bonds found
> select clear
> color #1.2 magenta models transparency 0
> select add /R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
5 hydrogen bonds found
> select clear
> save 20221013-PTH1R-7.tif width 2000 height 2000 supersample 3
> transparentBackground
Missing "transparentBackground" keyword's argument
> save 20221013-PTH1R-7.tif width 2000 height 2000 supersample 3
> transparentBackground
Missing "transparentBackground" keyword's argument
> save 20221013-PTH1R-7.tif width 2000 height 2000 supersample 3
> transparentBackground
Missing "transparentBackground" keyword's argument
> save 20221013-PTH1R-7.tif width 2000 height 2000 supersample 3
> transparentBackground true
> color #1.2 #550000 models transparency 0
> color #1.2 black models transparency 0
> color #1.2 #aaaaff models transparency 0
> color #1.2 #aaffff models transparency 0
> color #1.2 #ffaaff models transparency 0
> color #1.2 magenta models transparency 0
> color #1.2 #5500ff models transparency 0
> color #1.2 magenta models transparency 0
> color #1.2 #ff007f models transparency 0
> color #1.2 #550000 models transparency 0
> color #1.2 #aa0000 models transparency 0
> color #1.2 black models transparency 0
> ui mousemode right distance
> ui mousemode right "tape measure"
> ui mousemode right distance
> select /L:501@O20
1 atom, 1 residue, 1 model selected
> select /R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /R:417
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select /R:417@N
1 atom, 1 residue, 1 model selected
> select /L:501@O20
1 atom, 1 residue, 1 model selected
> select add /R:417
12 atoms, 11 bonds, 2 residues, 1 model selected
> select subtract /R:417
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> ui mousemode right "tape measure"
> ui mousemode right distance
> ui mousemode right select
> ui mousemode right distance
[Repeated 1 time(s)]
> ui mousemode right "tape measure"
> select clear
> marker segment #4 position 111.2,101.4,114.3 toPosition 115.1,97.63,99.11
> color yellow radius 0.1 label 16.09 labelHeight 1.609 labelColor yellow
> undo
[Repeated 1 time(s)]
> marker delete #4
> select clear
> select /R:212
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add /R:213
22 atoms, 21 bonds, 2 residues, 1 model selected
> select add /R:214
33 atoms, 31 bonds, 3 residues, 1 model selected
> hide sel cartoons
> save 20221013-PTH1R-7.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 3 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-8.cxs
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-9.cxs
> hide sel atoms
[Repeated 1 time(s)]
> hide sel target a
[Repeated 1 time(s)]
> show #!3.7 models
> hide #!3.7 models
> hide sel target a
> select /R
2115 atoms, 2177 bonds, 3 pseudobonds, 257 residues, 2 models selected
> hide sel atoms
> select /A
1950 atoms, 1989 bonds, 1 pseudobond, 235 residues, 2 models selected
> hide sel atoms
> select clear
> show #!3.7 models
> save 20221013-PTH1R-8.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 10 cartoons
> save 20221013-PTH1R-9.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 1 time(s)]
> show cartoons
> save 20221013-PTH1R-9.tif width 2000 height 2000 supersample 3
> transparentBackground true
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-10.cxs
> save 20221013-PTH1R-9.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 2 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221013-11.cxs
——— End of log from Thu Oct 13 17:27:46 2022 ———
opened ChimeraX session
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-1.cxs
> open "E:/huawei/HaozhuoDownloads/PTH1R/mollecule/duotai/PTH34-PTH1R-G112
> Model2_2-coot-21xuyuanjia erliujian2.pdb"
Chain information for PTH34-PTH1R-G112 Model2_2-coot-21xuyuanjia
erliujian2.pdb #4
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> matchmaker 4# to 1#
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> hide #!1 models
> hide #!4 atoms
> show #!4 cartoons
> matchmaker #4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain B (#1) with PTH34-PTH1R-G112
Model2_2-coot-21xuyuanjia erliujian2.pdb, chain B (#4), sequence alignment
score = 1755.9
RMSD between 340 pruned atom pairs is 0.504 angstroms; (across all 341 pairs:
0.518)
> show #!1 models
> hide #!2 models
> open "E:/huawei/HaozhuoDownloads/PTH1R/mollecule/duotai/PTHrP-PTH1R-Gs
> complex2-Lip-10-coot-18xuyuanjiaerliujian2.pdb"
Summary of feedback from opening
E:/huawei/HaozhuoDownloads/PTH1R/mollecule/duotai/PTHrP-PTH1R-Gs
complex2-Lip-10-coot-18xuyuanjiaerliujian2.pdb
---
warnings | End residue of secondary structure not found: HELIX 3 3 GLN A 213
PHE A 215 1 3
Start residue of secondary structure not found: HELIX 4 4 LEU A 233 TRP A 244
1 12
Start residue of secondary structure not found: HELIX 5 5 GLN A 261 ALA A 270
1 10
Start residue of secondary structure not found: HELIX 6 6 PRO A 280 PHE A 282
1 3
Start residue of secondary structure not found: HELIX 7 7 PRO A 299 THR A 317
1 19
Start residue of secondary structure not found: HELIX 8 8 ASN A 338 TYR A 358
1 21
5 messages similar to the above omitted
Chain information for PTHrP-PTH1R-Gs
complex2-Lip-10-coot-18xuyuanjiaerliujian2.pdb #5
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> hide #!1 models
> hide #!3 models
> hide #!3.7 models
> hide #!4 models
> hide #!5 atoms
> show #!5 cartoons
> show #!4 models
> show #!1 models
> matchmaker #5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain B (#1) with PTHrP-PTH1R-Gs
complex2-Lip-10-coot-18xuyuanjiaerliujian2.pdb, chain B (#5), sequence
alignment score = 1737.9
RMSD between 338 pruned atom pairs is 0.490 angstroms; (across all 341 pairs:
0.544)
> matchmaker #5/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with PTHrP-PTH1R-Gs
complex2-Lip-10-coot-18xuyuanjiaerliujian2.pdb, chain R (#5), sequence
alignment score = 1250.6
RMSD between 188 pruned atom pairs is 0.916 angstroms; (across all 257 pairs:
2.625)
> matchmaker #4/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with PTH34-PTH1R-G112
Model2_2-coot-21xuyuanjia erliujian2.pdb, chain R (#4), sequence alignment
score = 1266
RMSD between 190 pruned atom pairs is 0.885 angstroms; (across all 257 pairs:
2.709)
> ui tool show "Side View"
> hide #4.1 models
> hide #5.1 models
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-2.cxs
——— End of log from Fri Oct 14 10:35:38 2022 ———
opened ChimeraX session
> open "E:/huawei/HaozhuoDownloads/PTH1R/mollecule/duotai/PTHrP-PTH1R-Gs
> complex2-Lip-10-coot-18xuyuanjiaerliujian.pdb"
Chain information for PTHrP-PTH1R-Gs
complex2-Lip-10-coot-18xuyuanjiaerliujian.pdb #6
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
P | No description available
R | No description available
> hide #!1 models
> hide #!4 models
> hide #!5 models
> hide #!6 atoms
> show #!6 cartoons
> matchmaker #6/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with PTHrP-PTH1R-Gs
complex2-Lip-10-coot-18xuyuanjiaerliujian.pdb, chain R (#6), sequence
alignment score = 1250.6
RMSD between 188 pruned atom pairs is 0.916 angstroms; (across all 257 pairs:
2.625)
> show #!1 models
> show #!5 models
> show #!4 models
> hide #!5 models
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-2.cxs
> select #4/R
3142 atoms, 3242 bonds, 4 pseudobonds, 367 residues, 2 models selected
> color (#!4 & sel) cyan
> color (#!4 & sel) medium blue
> ui tool show "Color Actions"
> color sel slate blue
> color sel rebecca purple
> color sel royal blue
> color sel deep sky blue
> color sel royal blue
> hide #!6 models
> color sel sky blue
> lighting soft
> lighting simple
> lighting full
> transparency 0 cartoons
> cartoon style width 1.5 thickness 0.3
> color sel royal blue
[Repeated 1 time(s)]
> select #4/P
289 atoms, 294 bonds, 34 residues, 1 model selected
> color sel light coral
> select #6/R
3029 atoms, 3119 bonds, 3 pseudobonds, 369 residues, 2 models selected
> select #6/R
3029 atoms, 3119 bonds, 3 pseudobonds, 369 residues, 2 models selected
> show #!6 models
> color sel purple
> color sel light slate gray
> color sel peru
> color sel dark khaki
> color sel olive
> color sel dark khaki
> select clear
> select #6/P
302 atoms, 308 bonds, 36 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> color sel sienna
> color sel gold
> color sel sandy brown
> color sel green yellow
> color sel olive drab
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> color sel orange red
> color sel red
[Repeated 1 time(s)]
> color sel maroon
> color sel fire brick
> color sel brown
> color sel chocolate
> color sel coral
> color sel indian red
> color sel dark salmon
> color sel salmon
> color sel medium violet red
[Repeated 1 time(s)]
> color sel dark orchid
> color sel medium violet red
> select #6/R
3029 atoms, 3119 bonds, 3 pseudobonds, 369 residues, 2 models selected
> color sel light blue
> color sel burly wood
> color sel dark khaki
> color sel dark goldenrod
> color sel dark khaki
> color sel yellow green
> color sel dark khaki
> select clear
> select #4/A
1950 atoms, 1989 bonds, 1 pseudobond, 235 residues, 2 models selected
> color sel olive drab
> color sel dark salmon
[Repeated 3 time(s)]
> hide #!6 models
> select #4/B
2615 atoms, 2662 bonds, 341 residues, 1 model selected
> color sel olive
> color sel olive drab
> color sel khaki
> select #4/G
437 atoms, 443 bonds, 57 residues, 1 model selected
> color sel pale green
> color sel dark sea green
> select #4/N
984 atoms, 1005 bonds, 129 residues, 1 model selected
> color sel dark gray
> color sel tan
> color sel plum
> show #!6 models
> select #6/R
3029 atoms, 3119 bonds, 3 pseudobonds, 369 residues, 2 models selected
> color sel burly wood
> undo
> select #6/A
1950 atoms, 1989 bonds, 1 pseudobond, 235 residues, 2 models selected
> color sel burly wood
> color sel thistle
> color sel violet
> color sel peru
> color sel deep sky blue
> color sel chocolate
> color sel lime
> color sel pale violet red
> color sel purple
> color sel magenta
> select #6/B
2616 atoms, 2663 bonds, 341 residues, 1 model selected
> color sel tan
> color sel rosy brown
> lighting soft
> color sel dark green
> color sel forest green
> select #6/G
436 atoms, 442 bonds, 57 residues, 1 model selected
> color sel forest green
> color sel light sky blue
> lighting simple
> lighting soft
> lighting full
> color sel aquamarine
> color sel pale green
> select #6/N
983 atoms, 1005 bonds, 129 residues, 1 model selected
> color sel silver
> color sel powder blue
> color sel blue violet
> color sel slate blue
> select #6/B
2616 atoms, 2663 bonds, 341 residues, 1 model selected
> color sel rosy brown
> color sel orchid
> color sel wheat
> color sel beige
> color sel white smoke
> color sel mint cream
> color sel pink
> color sel dark violet
> color sel pale violet red
> color sel medium purple
> color sel dark magenta
[Repeated 1 time(s)]
> color sel purple
> select clear
> save 20221014-PTH1R-1.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 3 time(s)]
> transparency 10 cartoons
> save 20221014-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> ui tool show "Side View"
> save 20221014-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 5 cartoons
> save 20221014-PTH1R-3.tif width 2000 height 2000 supersample 3
> transparentBackground true
> hide #6.1 models
> save 20221014-PTH1R-3.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 4 time(s)]
> select #4/A
1950 atoms, 1989 bonds, 1 pseudobond, 235 residues, 2 models selected
> color sel orchid
> color sel blue violet
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-3.cxs
——— End of log from Fri Oct 14 12:43:27 2022 ———
opened ChimeraX session
> select clear
> hide #!6 models
> save 20221014-PTH1R-5.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 1 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-4.cxs
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/duotai/6nbfPTH1R.pdb
6nbfPTH1R.pdb title:
Cryo-em structure of parathyroid hormone receptor type 1 In complex with A
long-acting parathyroid hormone analog and G protein [more info...]
Chain information for 6nbfPTH1R.pdb #7
---
Chain | Description | UniProt
A | GS protein α subunit |
B | transducin β chain 1 | GBB1_RAT
G | G γ-I | GBG2_BOVIN
N | nanobody-35 |
P | long-acting parathyroid hormone analog |
R | parathyroid hormone/parathyroid hormone-related peptide receptor |
PTH1R_HUMAN
Non-standard residues in 6nbfPTH1R.pdb #7
---
CLR — cholesterol
PLM — palmitic acid
> hide #!1 models
> hide #!4 models
> hide #!7 atoms
> show #!7 cartoons
> matchmaker #7/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with 6nbfPTH1R.pdb, chain R
(#7), sequence alignment score = 1263.6
RMSD between 202 pruned atom pairs is 0.888 angstroms; (across all 257 pairs:
2.496)
> show #!1 models
> cartoon style width 1.5 thickness 0.3
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-5.cxs
> hide #!7 models
> show #!4 models
> save 20221014-PTH1R-6.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 10 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-6.cxs
——— End of log from Fri Oct 14 14:23:32 2022 ———
opened ChimeraX session
> select #1/B#4/B#5/B#6/B
10463 atoms, 10651 bonds, 1364 residues, 4 models selected
> cartoon hide (#!1,4 & sel)
> select #1/G#4/G#5/G#6/G
1745 atoms, 1769 bonds, 228 residues, 4 models selected
> cartoon hide (#!1,4 & sel)
> save 20221014-PTH1R-17.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 4 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-16.cxs
[Repeated 1 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221014-17.cxs
——— End of log from Fri Oct 14 17:25:48 2022 ———
opened ChimeraX session
> hide #!4 models
> help help:user
[Repeated 3 time(s)]
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> help help:user
[Repeated 1 time(s)]
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> help help:user
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221025-1.cxs
> select #1/R:411
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/R:412
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #1/R:413
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #1/R:414
31 atoms, 27 bonds, 4 residues, 1 model selected
> select add #1/R:415
38 atoms, 34 bonds, 5 residues, 1 model selected
> select add #1/R:416
46 atoms, 41 bonds, 6 residues, 1 model selected
> select add #1/R:417
57 atoms, 52 bonds, 7 residues, 1 model selected
> color sel blue
> color sel orange
> ui tool show "Color Actions"
> color sel lime
> color sel forest green
> color sel medium purple
> color sel dark blue
> color sel navy
> color sel indigo
[Repeated 1 time(s)]
> color sel navy
> color sel rebecca purple
> color sel orchid
> color sel light sky blue
> color sel indian red
> color sel coral
> show #!4 models
> color sel brown
> color sel blue violet
> color sel dark orchid
> color sel dark magenta
> color sel lime
> color sel chartreuse
> color sel spring green
> color sel forest green
> color sel lime
> color sel yellow green
> color sel purple
[Repeated 1 time(s)]
> color sel dark turquoise
> color sel magenta
> color sel yellow
> color sel gold
> color sel orange
> color sel dark orange
> hide #!4 models
> select #1/R:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select #1/R:302
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select #1/R:458
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select #1/R:463
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select #1/R:459
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel dark orange
> select #1/R:465
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel dark orange
> select #1/R:219
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel dark orange
> select #1/R:223
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel dark orange
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting shadows true
> graphics silhouettes true
> lighting shadows false
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> select #1/A:359
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel dark orange
> select #1/A:360
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel dark orange
> select #1/A:358
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel dark orange
> select clear
> show #!4 models
> hide #!1 models
> select #4/R:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel lime
> show #!1 models
> color sel chartreuse
> color sel lawn green
> color sel yellow green
> color sel lime
> hide #!1 models
> select #4/R:425
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:424
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:427
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:364
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:367
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:444
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:445
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:233
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:292
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> show #!1 models
> hide #!1 models
> select #4/R:289
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:288
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:429
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:440
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:441
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:437
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:184
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:355
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:354
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:353
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:360
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:181
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:195
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel lime
> select clear
> show #!1 models
> hide #!1 models
> select #4/R:31
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:33
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/R:32
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #4/R:33
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:32
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:34
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:37
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:38
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:138
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel lime
> select clear
> select #4/R:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:135
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:136
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:171
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:167
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:144
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/R:114
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:115
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:162
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:161
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #4/R:163
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel lime
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!1 models
> show #!4 models
> save 20221025-PTH1R-1.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 4 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221025-2.cxs
> transparency 10 cartoons
[Repeated 1 time(s)]
> transparency 10 ribbons
> save 20221025-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 20 ribbons
> transparency 30 ribbons
> save 20221025-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> transparency 20 ribbons
> save 20221025-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting full
> transparency 0 cartoons
> transparency 10 cartoons
> hide #!4 models
> hide #!1 models
> show #!4 models
> save 20221025-PTH1R-2.tif width 2000 height 2000 supersample 3
> transparentBackground true
[Repeated 5 time(s)]
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221025-3.cxs
——— End of log from Tue Oct 25 15:43:42 2022 ———
opened ChimeraX session
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221028-2.cxs
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221029-1.cxs
> select #4/R
3142 atoms, 3242 bonds, 4 pseudobonds, 367 residues, 2 models selected
> color (#!4 & sel) byhetero
> ui tool show "Color Actions"
> color sel royal blue
> hide #!4 models
> show #!1 models
> open "E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/6ORV TT-OAD2.pdb"
Chain information for 6ORV TT-OAD2.pdb #8
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> hide #!1 models
> hide #!8 atoms
> show #!8 cartoons
> show #!1 models
> hide #!1 models
> matchmaker #8/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with 6ORV TT-OAD2.pdb, chain
R (#8), sequence alignment score = 607.5
RMSD between 152 pruned atom pairs is 0.900 angstroms; (across all 251 pairs:
4.459)
> show #!1 models
> hide #!8 models
> show #!4 models
> hide #!4 models
> show #!8 models
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/7c2eRGT1383.pdb
7c2eRGT1383.pdb title:
GLP-1R-GS complex structure with A small molecule full agonist [more info...]
Chain information for 7c2eRGT1383.pdb #9
---
Chain | Description | UniProt
A | guanine nucleotide-binding protein G(S) subunit α isoforms short |
B | transducin β chain 1 | GBB1_HUMAN
G | G γ-I | GBG2_HUMAN
N | nanobody 35|lama glama |
R | GLP-1R | GLP1R_HUMAN
Non-standard residues in 7c2eRGT1383.pdb #9
---
FFR — 2-[[4-[6-[(4-cyano-2-fluoranyl-
phenyl)methoxy]pyridin-2-yl]-3,6-dihydro-2~{H}-pyridin-1-yl]methyl]-3-[[(2~{S})-oxetan-2-yl]methyl]imidazo[4,5-B]pyridine-5-carboxylic
acid
> hide #!1 models
> hide #!8 models
> hide #!9 atoms
> show #!9 cartoons
> matchmaker #9/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with 7c2eRGT1383.pdb, chain R
(#9), sequence alignment score = 694
RMSD between 163 pruned atom pairs is 0.950 angstroms; (across all 252 pairs:
4.145)
> show #!7 models
> hide #!7 models
> hide #!9 models
> open
> E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/6x1aPF-06882961.pdb
6x1aPF-06882961.pdb title:
Non peptide agonist PF-06882961, bound to glucagon-like peptide-1 (GLP-1)
receptor [more info...]
Chain information for 6x1aPF-06882961.pdb #10
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN
B | transducin β chain 1 | GBB1_HUMAN
G | G γ-I | GBG2_HUMAN
N | NANOBODY35 |
R | GLP-1R | GLP1R_HUMAN
Non-standard residues in 6x1aPF-06882961.pdb #10
---
UK4 —
2-[(4-{6-[(4-cyano-2-fluorophenyl)methoxy]pyridin-2-yl}piperidin-1-yl)methyl]-1-{[(2S)-oxetan-2-yl]methyl}-1H-benzimidazole-6-carboxylic
acid
> hide #!10 atoms
> show #!10 cartoons
> matchmaker #10/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with 6x1aPF-06882961.pdb,
chain R (#10), sequence alignment score = 718.8
RMSD between 167 pruned atom pairs is 1.023 angstroms; (across all 255 pairs:
4.024)
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/6x19CHU-128.pdb
6x19CHU-128.pdb title:
Non peptide agonist chu-128, bound to glucagon-like peptide-1 (GLP-1) receptor
[more info...]
Chain information for 6x19CHU-128.pdb #11
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN
B | transducin β chain 1 | GBB1_HUMAN
G | G γ-I | GBG2_HUMAN
N | NANOBODY35 |
R | GLP-1R | GLP1R_HUMAN
Non-standard residues in 6x19CHU-128.pdb #11
---
UK1 —
3-{(1S)-1-[5-(2,2-dimethylmorpholin-4-yl)-2-{(4S)-2-(4-fluoro-3,5-dimethylphenyl)-3-[3-(4-fluoro-1-methyl-1H-indazol-5-yl)-2-oxo-2,3-dihydro-1H-imidazol-1-yl]-4-methyl-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-C]pyridine-5-carbonyl}-1H-indol-1-yl]butyl}-1,2,4-oxadiazol-5(4H)-one
> hide #!10 models
> hide #!11 atoms
> show #!11 cartoons
> matchmaker #11/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with 6x19CHU-128.pdb, chain R
(#11), sequence alignment score = 737.6
RMSD between 165 pruned atom pairs is 1.003 angstroms; (across all 255 pairs:
3.932)
> hide #!11 models
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/6xoxLY3502970.pdb
6xoxLY3502970.pdb title:
Cryo-em of human GLP-1R bound to non-peptide agonist LY3502970 [more info...]
Chain information for 6xoxLY3502970.pdb #12
---
Chain | Description | UniProt
A | α subunit of GS with N-terminus swapped with equivalent residues In
gi,guanine nucleotide-binding protein G(S) subunit α isoforms xlas |
GNAS1_HUMAN
B | transducin β chain 1 | GBB1_HUMAN
E | single-chain variable fragment SCFV16 |
G | G γ-I | GBG2_HUMAN
N | nanobody 35 |
R | GLP-1R | GLP1R_HUMAN
Non-standard residues in 6xoxLY3502970.pdb #12
---
V6G —
3-[(1S,2S)-1-(5-[(4S)-2,2-dimethyloxan-4-yl]-2-{(4S)-2-(4-fluoro-3,5-dimethylphenyl)-3-[3-(4-fluoro-1-methyl-1H-indazol-5-yl)-2-oxo-2,3-dihydro-1H-imidazol-1-yl]-4-methyl-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-C]pyridine-5-carbonyl}-1H-indol-1-yl)-2-methylcyclopropyl]-1,2,4-oxadiazol-5(4H)-one
> hide #!12 models
> matchmaker #12/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with 6xoxLY3502970.pdb, chain
R (#12), sequence alignment score = 713.8
RMSD between 163 pruned atom pairs is 0.961 angstroms; (across all 252 pairs:
3.528)
> matchmaker #12/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with 6xoxLY3502970.pdb, chain
R (#12), sequence alignment score = 713.8
RMSD between 163 pruned atom pairs is 0.961 angstroms; (across all 252 pairs:
3.528)
> show #!1 models
> show #!12 models
> hide #!1 models
> hide #!12 atoms
> show #!12 cartoons
> show #!1 models
> hide #!1 models
> open "E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/compound
> 2-bound.pdb"
compound 2-bound.pdb title:
Cryo-em structure of the compound 2-bound human GLP-1 receptor-GS complex
[more info...]
Chain information for compound 2-bound.pdb #13
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN
B | transducin β chain 1 | GBB1_RAT
G | G γ-I | GBG2_BOVIN
N | nanobody-35 |
R | glucagon-like peptide 1 receptor | GLP1R_HUMAN
Non-standard residues in compound 2-bound.pdb #13
---
CLR — cholesterol
HNO — N-tert-butyl-6,7-bis(chloranyl)quinoxalin-2-amine
> hide #!12 models
> hide #!13 atoms
> show #!13 cartoons
> matchmaker #13/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with compound 2-bound.pdb,
chain R (#13), sequence alignment score = 722.8
RMSD between 175 pruned atom pairs is 1.010 angstroms; (across all 256 pairs:
2.934)
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/7x8rBoc5.pdb
7x8rBoc5.pdb title:
Cryo-em structure of the BOC5-bound HGLP-1R-GS complex [more info...]
Chain information for 7x8rBoc5.pdb #14
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN
B | transducin β chain 1 | GBB1_RAT
G | G γ-I | GBG2_HUMAN
N | nanobody 35 |
R | glucagon-like peptide 1 receptor | GLP1R_HUMAN
Non-standard residues in 7x8rBoc5.pdb #14
---
BYI — 2,4-bis(3-methoxy-4-thiophen-2-ylcarbonyloxy-
phenyl)-1,3-bis[[4-[(2-methylpropan-2-yl)oxycarbonylamino]phenyl]carbonylamino]cyclobutane-1,3-dicarboxylic
acid
> hide #!13 models
> hide #!14 atoms
> show #!14 cartoons
> matchmaker #14/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with 7x8rBoc5.pdb, chain R
(#14), sequence alignment score = 718
RMSD between 172 pruned atom pairs is 0.960 angstroms; (across all 250 pairs:
3.809)
> open E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/7x8sWB4-24.pdb
7x8sWB4-24.pdb title:
Cryo-em structure of the WB4-24-bound HGLP-1R-GS complex [more info...]
Chain information for 7x8sWB4-24.pdb #15
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN
B | transducin β chain 1 | GBB1_RAT
G | G γ-I | GBG2_HUMAN
N | nanobody-35 |
R | glucagon-like peptide 1 receptor | GLP1R_HUMAN
Non-standard residues in 7x8sWB4-24.pdb #15
---
WB2 — 2,4-bis(3-methoxy-4-thiophen-2-ylcarbonyloxy-
phenyl)-1,3-bis[[4-(2-methylpropanoylamino)phenyl]carbonylamino]cyclobutane-1,3-dicarboxylic
acid
> hide #!14 models
> hide #!15 atoms
> show #!15 cartoons
> matchmaker #15/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCO371_1_lg-coot-12.pdb, chain R (#1) with 7x8sWB4-24.pdb, chain R
(#15), sequence alignment score = 697.3
RMSD between 172 pruned atom pairs is 0.970 angstroms; (across all 252 pairs:
3.806)
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221029-1.cxs
Failed to make context current.
> show #!15 atoms
> hide #!15 atoms
> select ::name="N2V"
61 atoms, 68 bonds, 1 residue, 1 model selected
> show #!15 atoms
> show #!14 models
> show #!13 models
> hide #!13-15 atoms
> show #!13-15 cartoons
> show #!11 models
> show #!12 models
> show #!10 models
> show #!9 models
> show #!8 models
> show #!1 models
> select ::name="BYI"
76 atoms, 82 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="CLR"
961 atoms, 1054 bonds, 31 residues, 5 models selected
> show sel & #!13 atoms
> select ::name="CLR"
961 atoms, 1054 bonds, 31 residues, 5 models selected
> hide sel & #!13 atoms
> select ::name="FFR"
41 atoms, 46 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/G#4/G#5/G#6/G#8/G
2181 atoms, 2211 bonds, 285 residues, 5 models selected
> hide sel & #!1,8 cartoons
> select #1/B#4/B#5/B#6/B#8/B
13063 atoms, 13298 bonds, 1702 residues, 5 models selected
> hide sel & #!1,8 cartoons
> select #1/G#4/G#5/G#6/G#8/G
2181 atoms, 2211 bonds, 285 residues, 5 models selected
> hide sel & #!1,8 cartoons
> select #1/N#4/N#5/N#6/N#8/N
4891 atoms, 4997 bonds, 642 residues, 5 models selected
> hide sel & #!1,8 cartoons
> select #7/G#9/G#10/G#11/G#12/G#13/G#14/G#15/G
3468 atoms, 3516 bonds, 452 residues, 8 models selected
> hide sel & #!9-15 cartoons
> select #10/N#11/N
1930 atoms, 1966 bonds, 260 residues, 2 models selected
> hide sel cartoons
> select #10/A#11/A#13/A#14/A#15/A
11621 atoms, 11804 bonds, 10 pseudobonds, 1447 residues, 10 models selected
> hide sel cartoons
> select #9/A
1637 atoms, 1670 bonds, 4 pseudobonds, 193 residues, 2 models selected
> hide sel cartoons
> select #12/N#14/N
1927 atoms, 1971 bonds, 254 residues, 2 models selected
> hide sel cartoons
> select #9/N
961 atoms, 983 bonds, 126 residues, 1 model selected
> hide sel cartoons
> select #7/N#13/N#15/N
2883 atoms, 2949 bonds, 378 residues, 3 models selected
> hide sel & #!13,15 cartoons
> select #12/E
1783 atoms, 1829 bonds, 1 pseudobond, 232 residues, 2 models selected
> hide sel cartoons
> select #12/E
1783 atoms, 1829 bonds, 1 pseudobond, 232 residues, 2 models selected
> hide sel cartoons
> select #7/B#9/B#10/B#11/B#12/B#13/B#14/B#15/B
20839 atoms, 21158 bonds, 2761 residues, 8 models selected
> hide sel & #!9-15 cartoons
> select #12/A
1792 atoms, 1824 bonds, 5 pseudobonds, 220 residues, 2 models selected
> hide sel cartoons
> select #10/A#11/A#13/A#14/A#15/A
11621 atoms, 11804 bonds, 10 pseudobonds, 1447 residues, 10 models selected
> select #1/A#4/A#5/A#6/A#8/A
9454 atoms, 9643 bonds, 8 pseudobonds, 1135 residues, 10 models selected
> hide sel & #!1,8 cartoons
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221029-2.cxs
> hide #15.1 models
> hide #14.1 models
> hide #12.1 models
> hide #11.1 models
> hide #10.1 models
> hide #9.1 models
> hide #8.1 models
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221029-2.cxs
> cartoon style width 1.5 thickness 0.3
> select ::name="HNO"
17 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="HOH"
159 atoms, 159 residues, 2 models selected
> show sel atoms
> select ::name="HOH"
159 atoms, 159 residues, 2 models selected
> hide sel atoms
> select ::name="N2V"
61 atoms, 68 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="LIG"
44 atoms, 48 bonds, 1 residue, 1 model selected
> select ::name="N2V"
61 atoms, 68 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select ::name="UK1"
65 atoms, 74 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="UK4"
41 atoms, 46 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="V6G"
65 atoms, 75 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="WB2"
72 atoms, 78 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221029-2.cxs
> hide #13.1 models
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221029-2.cxs
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> show #!14 models
> show #!13 models
> show #!12 models
> lighting soft
> lighting simple
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting simple
[Repeated 1 time(s)]
> lighting full
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting full
> graphics silhouettes true
> lighting shadows false
> lighting full
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting full
> lighting simple
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows false
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting simple
> lighting soft
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting full
[Repeated 1 time(s)]
> graphics silhouettes false
> lighting shadows false
> lighting full
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> graphics silhouettes false
> lighting full
[Repeated 1 time(s)]
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows false
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> show #!8 models
> select #8/R
2390 atoms, 2464 bonds, 1 pseudobond, 282 residues, 2 models selected
> ui tool show "Color Actions"
> color sel steel blue
> color sel light coral
> color sel sky blue
> color sel light green
> color sel dark sea green
> show #!9 models
> show #!14 models
> show #!15 models
> show #!13 models
> show #!12 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!12 models
> hide #!14 models
> hide #!13 models
> hide #!15 models
> hide #!6 models
> show #!8 models
> color (#!8 & sel) orange
> ui tool show "Color Actions"
> color sel burly wood
[Repeated 1 time(s)]
> select clear
> select ::name="N2V"
61 atoms, 68 bonds, 1 residue, 1 model selected
> color sel purple
> ui tool show "Color Actions"
> color sel dark magenta
> color sel dark orchid
> color sel byhetero
> color sel dark orchid
> select clear
> undo
> color sel byhetero
> save E:/huawei/HaozhuoDownloads/PTH1R/mollecule/xiaofenzi/20221029-2.cxs
Traceback (most recent call last):
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 624, in save
fserialize(stream, data)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 694, in write
compressed = self._compressor.compress(data)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 624, in save
fserialize(stream, data)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 694, in write
compressed = self._compressor.compress(data)
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "D:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 513.29
OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 20L6A09YCD
OS: Microsoft Windows 10 家庭中文版 (Build 18363)
Memory: 17,027,555,328
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving session |
comment:2 by , 3 years ago
| Resolution: | → worksforme |
|---|---|
| Status: | assigned → closed |
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