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Opened 5 years ago
Closed 5 years ago
#4086 closed defect (fixed)
MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.4.0-197-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Performing matchmaker and then selecting chains
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> format session
Log from Wed Dec 23 11:34:41 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> format session
Log from Tue Dec 22 19:28:37 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> format session
Log from Mon Dec 21 18:07:04 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> format session
Log from Sun Dec 20 21:04:28 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> format session
Log from Fri Dec 18 18:45:46 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/media/datadisk1/AnalisiGAPDH
> /A8B8major/A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb"
Chain information for
A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb #1
---
Chain | Description
A E G I O Q | No description available
B D F H J L P R | No description available
C | No description available
K | No description available
> hide atoms
> show cartoons
> select #1 /Q
2740 atoms, 2789 bonds, 2 pseudobonds, 369 residues, 2 models selected
> select #1 /O
2740 atoms, 2789 bonds, 2 pseudobonds, 369 residues, 2 models selected
> select #1 /R
2588 atoms, 2633 bonds, 338 residues, 1 model selected
> select #1 /P
2588 atoms, 2633 bonds, 338 residues, 1 model selected
> color sel #1 /Q red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1 /Q red
> select clear
> color #1 /O red
> color #1 /A DARK ORANGE
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1 /A tomato
> color #1 /C tomato
> color #1 /C dark orange
> color #1 /A dark orange
> color #1 /E crimson
> color #1 /G crimson
> color #1 /I K coral
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1 /I, K coral
> color #1 /A, C crimson
> color #1 /A, C tomato
> color #1 /R,P,D,B,J,L,H,F BLUE
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1 /R,P BLUE
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1 /R,P blue
> color #1 /R,P light blue
> color #1 /R,P cyan
> color #1 /R,P blue
> color #1 /b,d,f,h,j,l blue
> ui tool show "Color Actions"
> set bgColor white
> color #1 /A, C tomato
> color #1 /A, C crimson
> color #1 /A, C tomato
> color #1 /I, K coral
> color #1 /I, K orange
> color #1 /I, K coral
> color #1 /E crimson
> color #1 /E red
> color #1 /E crimson
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
opened ChimeraX session
> lighting soft
> color #1 96/O yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1 .96/O yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1 /O:96-106 yellow
> undo
> color #1 /O:96-103,106,109,110 yellow
> color #1 /O:96-103,106,109,110,119,121-126 yellow
> color #1
> /O:96-103,106,109,110,119,121-126,141,143,148,176,179,181,183,190,191,195,215,216,219,220,222,231,341-346,349,353,356-362
> yellow
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> color #1 /C:
> 77,80.96,98,101-103,106,107,109,110,119,121,124,125,141-143,179,181,183,187-192,195,196,231,344,346,349,353-362
> yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1
> /C:77,80.96,98,101-103,106,107,109,110,119,121,124,125,141-143,179,181,183,187-192,195,196,231,344,346,349,353-362
> yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1 /C:
> 77,80.96,98,101-103,106,107,109,110,119,121,124,125,141-143,179,181,183,187-192,195,196,231,344,346,349,353-362
> yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1 /C:
> 77,80,96,98,101-103,106,107,109,110,119,121,124,125,141-143,179,181,183,187-192,195,196,231,344,346,349,353-362
> yellow
> color #1 /C:
> 77,80,96,98,101-103,106,107,109,110,119,121,124,125,141-143,179,181,183,187-192,195,196,231,344,346,349,353-362
> light green
> color #1
> /O:96-103,106,109,110,119,121-126,141,143,148,176,179,181,183,190,191,195,215,216,219,220,222,231,341-346,349,353,356-362
> light green
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
opened ChimeraX session
> .
Unknown command: .
> ..........................
Unknown command: ..........................
> ..........................
Unknown command: ..........................
> ..........................
Unknown command: ..........................
> ..........................
Unknown command: ..........................
> ..........................
Unknown command: ..........................
> ..........................
Unknown command: ..........................
> ..........................
Unknown command: ..........................
> ..........................
Unknown command: ..........................
> color #1 /Q:
> 80,98,99,101-104,106,107,110,119,121,122-124,142,143,148,176,179,181-183,188-191,195,206,207,216,222,231,344,346,350,353,356-362
> light green
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> color #1 /I:
> 77,98,99,102,103,109,121,123-126,128,140-143,148,181,183,188-192,195,215,216,219,222,224,231,346,349,353,355-362
> light green
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> color #1 /G:
> 77,80,96-99,101-103,106,107,109,110,121,123-125,143,148,176,179-181,183,187-192,195,207,208,216,231,343-346,349,350,353,354,356-362
> light green
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> color #1 /A:
> 77,95-98,102,103,106,109,123-126,140-143,179-181,183,190-192,195,216,219,222,345,346,349,350,353,354,356-359,361,362
> light green
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> color #1 /K:
> 77,80,96-98,101-103,106,107,109,110,121,122,123-125,141-143,148,179,181,183,188-191,195,346,347,350,354-362
> light green
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> color #1 /E:
> 96,98,99,102,103,106,109,110,121,122-126,141,143,179-181,183,188-191,195,216,219,222,231,343-346,348-350,352,353,355-362
> light green
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> open "/media/datadisk1/AnalisiGAPDH
> /A8B8major/A8B8GAPDH2Job303PostProcFlipped.ccp4"
Opened A8B8GAPDH2Job303PostProcFlipped.ccp4, grid size 300,300,300, pixel
1.21, shown at level 0.0145, step 2, values float32
> volume #2 step 1
> volume #2 level 0.008939
> volume appearance initial
> vop gaussian #2 sdev 3.63
> close #3
> show #!2 models
> transparency 50
> transparency 0
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting flat
> lighting soft
> graphics silhouettes false
> transparency #2 40
> transparency #2 30
> transparency #2 20
> graphics silhouettes true
> graphics silhouettes false
> transparency #2 10
> transparency #2 5
> transparency #2 5
> transparency #2 0
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
opened ChimeraX session
> transparency #2 5
> transparency #2 10
> transparency #2 15
> transparency #2 20
> hide #!2 models
> show #!2 models
> color sel #2 /Q: 333-343
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel #2 /Q: 333-343 yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> select #1 /Q: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> color sel yellow
> select clear
> hide #!2 models
> show #!2 models
> select #1 /Q: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> color sel red
> select clear
> color zone #2 near #1 /Q: 333-343 distance 3
> undo
> color zone #2 near #1 /Q: 333-343 distance 3 yellow
Expected a keyword
> color zone #2 near #1 /Q: 333-343 distance 3 palette yellow
Expected a keyword
> color zone #2 near #1 /Q: 333-343 distance 3 spec yellow
Expected a keyword
> color spec yellow zone #2 near #1 /Q: 333-343 dist 3
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color yellow
> undo
> color zone #2 near #1 /Q: 333-343 distance 3
> undo
> color zone #2 near #1 /Q: 333-343 distance 3 palette yellow
Expected a keyword
> color zone #2 near #1 /Q: 333-343 distance 3 palette: yellow
Expected a keyword
> color zone #2 near #1 /Q: 333-343 distance 3 colorname yellow
Expected a keyword
> color zone #2 near #1 /Q: 333-343 distance 3 color name yellow
Expected a keyword
> color zone #2 near #1 /Q: 333-343 distance 3, yellow
Invalid "distance" argument: Expected a number
> color zone #2 near #1 /Q: 333-343 distance 3 yellow
Expected a keyword
> color yellow
> undo
> color zone yellow #2 near #1 /Q: 333-343 dist 3
Missing or invalid "surfaces" argument: invalid surfaces specifier
> color yellow zone #2 near #1 /Q: 333-343 dist 3
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color zone #2 near #1 /Q: 333-343 distance 3
> undo
> select #1 /Q: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> transparency #2 0
> select clear
> color zone #2 near #1 /Q: 333-343 distance 2
> undo
> color zone #2 near #1 /Q: 333-343 distance 2.5
> undo
> color zone #2 near #1 /Q: 333-343 distance 3
> transparency #2 20
> undo
> transparency #2 0
> transparency #2 0
> select #1 /Q: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> color sel yellow
> hide #!2 models
> show #!2 models
> color zone #2 near #1 /Q: 333-343 distance 2.8
> undo
> toolshed show
> ui tool show "Show Volume Menu"
> volume gaussian #2 1
Expected a keyword
> volume gaussian #2 sDev 1
> volume #2 level 0.008211
> hide #!2 models
> volume #2 level 0.007605
> hide #!2 models
> hide #!2 models
> select #3
2 models selected
> volume #2 level 0.008333
> hide #!2 models
> select clear
> volume #3 sdLevel 1
> volume #3 sdLevel 2
> volume #3 sdLevel 3
> hide #!3 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
> hide #!2 models
> show #!3 models
> lighting soft
> lighting soft
> select #1 /Q: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> color sel yellow
> color zone #3 near #1 /Q: 333-343 distance 2.8
> select #1 /O: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> hide #!3 models
> color sel yellow
> show #!3 models
> color zone #3 near #1 /O: 333-343 distance 2.8
> hide #!3 models
> select #1 /C: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> color sel yellow
> select clear
> select #1 /A: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> select #1 /G: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> color sel yellow
> select clear
> select #1 /E: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> select #1 /K: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> color sel yellow
> select clear
> color zone #3 near #1 /O: 333-343,/C:333-343,/G:333-343,/K:333-343 dist 2.8
Expected a keyword
> show #!3 models
> color zone #3 near #1 /O: 333-343 /C:333-343 /G:333-343 /K:333-343 distance
> 2.8
> color zone #3 near #1 /Q: 333-343 /C:333-343 /G:333-343 /K:333-343 distance
> 2.8
> transparency #3 20
> transparency #3 10
> transparency #3 5
> transparency #3 0
> save /home/roberto/Desktop/image1.png supersample 3
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig4EM_1.tif" width
> 1299 height 880 supersample 4
> transparency #3 25
> transparency #3 50
> transparency #3 65
> ui tool show "Side View"
> transparency #3 75
> transparency #3 85
> color zone #3 near #2 /O: 333-343 /C:333-343 /G:333-343 /K:333-343 distance
> 2.8
> transparency #3 85
> select #1 /Q: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> select #1 /O: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> color sel RED
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel red
> select clear
> select clear
> select clear
> hide #!3 models
> select #1 /C: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> color sel tomato
> select clear
> show #!3 models
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig4EM_2.tif" width
> 1299 height 880 supersample 4
> select #1 /I: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> select clear
> select #1 /Q: 333-343
56 atoms, 56 bonds, 11 residues, 1 model selected
> color sel red
> select clear
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig4EM_3.tif" width
> 1299 height 880 supersample 3
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig4EM_5.tif" width
> 1299 height 880 supersample 4
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig4EM_4.tif" width
> 1299 height 880 supersample 4
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> transparency #3 75
> transparency #3 85
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig4EM_6.tif" width
> 1299 height 880 supersample 3
> hide #!3 models
> select /Q:349
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> style sel ball
Changed 12 atom styles
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #1 NAD\
Expected a keyword
> select #1 NAD
Expected a keyword
> select #1 /NAD
Nothing selected
> show atoms
> hide atoms
> select /Q:349
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /Q:355
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /Q:354
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select /Q:355
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /Q:358
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel yellow
> select clear
> color sel red
> select clear
> select /Q:346
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /Q:349
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /Q:346
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui tool show "Build Structure"
> select #1 /I: 349,358
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1 /I: 349,358 /Q: 349,358
24 atoms, 22 bonds, 4 residues, 1 model selected
> select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C
2778 atoms, 2825 bonds, 375 residues, 1 model selected
> 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358
Unknown command: 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358
> style sel stick
Changed 2778 atom styles
> select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C
2778 atoms, 2825 bonds, 375 residues, 1 model selected
> 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358
Unknown command: 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358
> select #1 /I: 349,358, /Q: 349,358 /O: 349,358 /C;349,358 /A:349,358
> /G:349,358 /E:349,358 /K:349,358
Expected a keyword
> select #1 /I: 349,358, /Q: 349,358, /O: 349,358, /C;349,358, /A:349,358,
> /G:349,358, /E:349,358, /K:349,358
Expected a keyword
> select #1 /I: 349,358
12 atoms, 11 bonds, 2 residues, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel cartoons
> show sel cartoons
> show sel atoms
> select #1 /I: 349,358 /Q: 349,358
24 atoms, 22 bonds, 4 residues, 1 model selected
> select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C
2778 atoms, 2825 bonds, 375 residues, 1 model selected
> 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358
Unknown command: 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358
> show sel atoms
> style sel stick
Changed 2778 atom styles
> color sel yellow
> undo
> select clear
> select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C
2778 atoms, 2825 bonds, 375 residues, 1 model selected
> 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358
Unknown command: 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358
> hide sel atoms
> select clear
> select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C:349,358 /A:349,358
> /G:349,358 /E:349,358 /K:349,358
96 atoms, 88 bonds, 16 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 96 atom styles
> color sel yellow
> select clear
> color byhetero
> color bynucleotide
> select ligand
704 atoms, 768 bonds, 16 residues, 1 model selected
> show sel
> select clear
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> setattr
Missing or invalid "target" argument: Expected a text string
> setattr #1 /I: 346-352 res ss_type 1
Assigning ss_type attribute to 7 items
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
opened ChimeraX session
> show #!2 models
> volume #!2 appearance initial
> volume #2 level 0.01655
> transparency #2 50
> transparency #2 35
> volume #2 level 0.02001
> ui tool show "Side View"
> volume #2 level 0.02013
> setattr #1 /G: 344-352 res ss_type 1
Assigning ss_type attribute to 9 items
> select #1 /G: 333-362
154 atoms, 155 bonds, 30 residues, 1 model selected
> color sel crimson
> select clear
> select #1 /G: 191,77,183
33 atoms, 30 bonds, 3 residues, 1 model selected
> select clear
> select #1 /D: 191,77,183
33 atoms, 30 bonds, 3 residues, 1 model selected
> select clear
> select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C
2778 atoms, 2825 bonds, 375 residues, 1 model selected
> 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358
Unknown command: 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358
> select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C:349,358 /A:349,358
> /G:349,358 /E:349,358 /K:349,358
96 atoms, 88 bonds, 16 residues, 1 model selected
> color sel yellow
> select clear
> select #1 /G:NAD
44 atoms, 48 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #!2 models
> select clear
> select #1 /A:NAD
44 atoms, 48 bonds, 1 residue, 1 model selected
> color sel byhetero
> color sel byhetero
> select clear
> transparency #2 25
> transparency #2 15
> transparency #2 35
> transparency #2 50
> setattr #1 /O: 344-352 res ss_type 1
Assigning ss_type attribute to 9 items
> select #1 /O: 333-362
154 atoms, 155 bonds, 30 residues, 1 model selected
> color sel red
> select #1 /O: 349,358
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel yellow
> select clear
> volume #2 level 0.02086
> setattr #1 /C: 344-352 res ss_type 1
Assigning ss_type attribute to 9 items
> select #1 /C: 333-362
154 atoms, 155 bonds, 30 residues, 1 model selected
> color sel tomato
> select #1 /C: 349,358
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel yellow
> select clear
> select #1 /K: 333-362
154 atoms, 155 bonds, 30 residues, 1 model selected
> color sel coral
> setattr #1 /K: 344-352 res ss_type 1
Assigning ss_type attribute to 9 items
> volume #2 level 0.01964
> select #1 /K: 349,358
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel yellow
> select clear
> select #1 /E: 333-362
154 atoms, 155 bonds, 30 residues, 1 model selected
> color sel crimson
> select clear
> setattr #1 /E: 344-352 res ss_type 1
Assigning ss_type attribute to 9 items
> select #1 /E: 349,358
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel yellow
> select clear
> setattr #1 /Q: 344-352 res ss_type 1
Assigning ss_type attribute to 9 items
> select #1 /Q: 333-362
154 atoms, 155 bonds, 30 residues, 1 model selected
> color sel red
> select clear
> select #1 /Q: 349,358
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel yellow
> select clear
> volume #2 level 0.01443
> volume #2 level 0.01661
> volume #2 level 0.02061
> hide #!3 models
> volume #2 level 0.01528
> select #1 /I: 333-362
154 atoms, 155 bonds, 30 residues, 1 model selected
> color sel coral
> select clear
> select #1 /I: 349,358
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel yellow
> select clear
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> ui tool show "Build Structure"
> volume #2 level 0.01588
> volume #2 level 0.0177
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
> volume #2 sdLevel 3
> volume #2 sdLevel 2
> volume #2 sdLevel 4
> volume #2 sdLevel 5
> volume #2 sdLevel 6
> volume #2 sdLevel 7
> volume #2 sdLevel 6
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig5EM_1.tif" width
> 1299 height 880 supersample 4
> volume #2 level 0.02053
> volume #2 sdLevel 6
> volume #2 sdLevel 7
> volume #2 sdLevel 7
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig5EM_2.tif" width
> 1299 height 880 supersample 3
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig5EM_2.tif" width
> 1299 height 880 supersample 3
> volume #2 sdLevel 7
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig5EM_1.tif" width
> 1299 height 880 supersample 3
> hide #!2 models
> open "/media/datadisk1/AnalisiGAPDH /A2B2/chimeraA2B2GAPDH0Job614/2PKQ.pdb"
Summary of feedback from opening /media/datadisk1/AnalisiGAPDH
/A2B2/chimeraA2B2GAPDH0Job614/2PKQ.pdb
---
warning | Cannot find LINK/SSBOND residue CYS (349 )
2PKQ.pdb title:
Crystal structure of the photosynthetic A2B2-glyceraldehyde-3- phosphate
dehydrogenase, complexed with nadp [more info...]
Chain information for 2PKQ.pdb #4
---
Chain | Description
O Q | NADP-dependent glyceraldehydephosphate dehydrogenase subunit B
P R | NADP-dependent glyceraldehydephosphate dehydrogenase subunit A
Non-standard residues in 2PKQ.pdb #4
---
NDP — nadph dihydro-nicotinamide-adenine-dinucleotidephosphate
SO4 — sulfate ion
> select #4
10561 atoms, 10739 bonds, 6 pseudobonds, 1382 residues, 2 models selected
> ~select #4
Nothing selected
> hide #!1 models
> show #!1 models
> select #4
10561 atoms, 10739 bonds, 6 pseudobonds, 1382 residues, 2 models selected
> select #1
42627 atoms, 43384 bonds, 6 pseudobonds, 5656 residues, 2 models selected
> select #4
10561 atoms, 10739 bonds, 6 pseudobonds, 1382 residues, 2 models selected
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui tool show Matchmaker
> 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 A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain I (#1) with 2PKQ.pdb, chain O (#4), sequence alignment score = 1593.2
RMSD between 298 pruned atom pairs is 1.024 angstroms; (across all 346 pairs:
6.754)
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui tool show Matchmaker
No reference and/or match structure/chain chosen
> matchmaker #4/R#4/Q#4/P#4/O & sel to #1/R#1/Q#1/P#1/O & sel pairing ss
No 'to' chains specified
> matchmaker #4/R#4/Q#4/P#4/O to #1/R#1/Q#1/P#1/O pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain R (#1) with 2PKQ.pdb, chain R (#4), sequence alignment score = 1538.1
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain Q (#1) with 2PKQ.pdb, chain Q (#4), sequence alignment score = 1525.4
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain P (#1) with 2PKQ.pdb, chain P (#4), sequence alignment score = 1527.3
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain O (#1) with 2PKQ.pdb, chain O (#4), sequence alignment score = 1506.5
RMSD between 1252 pruned atom pairs is 1.154 angstroms; (across all 1367
pairs: 4.335)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> ui mousemode right "translate selected models"
> ui tool show Matchmaker
> matchmaker #4/O#4/P#4/Q#4/R to #1/A#1/B#1/C#1/D pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain A (#1) with 2PKQ.pdb, chain O (#4), sequence alignment score = 1578.8
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain B (#1) with 2PKQ.pdb, chain P (#4), sequence alignment score = 1500.3
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain C (#1) with 2PKQ.pdb, chain Q (#4), sequence alignment score = 1528.4
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain D (#1) with 2PKQ.pdb, chain R (#4), sequence alignment score = 1505.1
RMSD between 1252 pruned atom pairs is 1.144 angstroms; (across all 1367
pairs: 4.422)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> ~select #4
Nothing selected
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!2 models
> close #4
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> close #3
> open 2PK1
Summary of feedback from opening 2PK1 fetched from pdb
---
warning | PDB entry 2PK1 has been replaced by 3EKA
notes | Fetching compressed mmCIF 2pk1 from
http://files.rcsb.org/download/2pk1.cif
Fetching CCD ASC from http://ligand-expo.rcsb.org/reports/A/ASC/ASC.cif
2pk1 title:
Crystal Structure of the complex of hyaluranidase trimer with ascorbic acid at
3.1 A resolution reveals the locations of three binding sites [more info...]
Chain information for 2pk1 #3
---
Chain | Description
A | Hyaluronidase, phage associated
Non-standard residues in 2pk1 #3
---
ASC — ascorbic acid
2pk1 mmCIF Assemblies
---
1| author_defined_assembly
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> open 2PKQ
Summary of feedback from opening 2PKQ fetched from pdb
---
notes | Fetching compressed mmCIF 2pkq from
http://files.rcsb.org/download/2pkq.cif
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif
Fetching CCD NDP from http://ligand-expo.rcsb.org/reports/N/NDP/NDP.cif
2pkq title:
Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate
dehydrogenase, complexed with NADP [more info...]
Chain information for 2pkq #4
---
Chain | Description
O Q T | Glyceraldehyde-3-phosphate dehydrogenase B
P R S | Glyceraldehyde-3-phosphate dehydrogenase A
Non-standard residues in 2pkq #4
---
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate
SO4 — sulfate ion
2pkq mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> save "/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"
opened ChimeraX session
> open 2PKQ
2pkq title:
Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate
dehydrogenase, complexed with NADP [more info...]
Chain information for 2pkq #5
---
Chain | Description
O Q T | Glyceraldehyde-3-phosphate dehydrogenase B
P R S | Glyceraldehyde-3-phosphate dehydrogenase A
Non-standard residues in 2pkq #5
---
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate
SO4 — sulfate ion
2pkq mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select #5
15840 atoms, 16108 bonds, 5 pseudobonds, 2073 residues, 2 models selected
> close #5
> close #4
> close #3
> open 2PKQ
2pkq title:
Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate
dehydrogenase, complexed with NADP [more info...]
Chain information for 2pkq #3
---
Chain | Description
O Q T | Glyceraldehyde-3-phosphate dehydrogenase B
P R S | Glyceraldehyde-3-phosphate dehydrogenase A
Non-standard residues in 2pkq #3
---
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate
SO4 — sulfate ion
2pkq mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select #3
15840 atoms, 16108 bonds, 5 pseudobonds, 2073 residues, 2 models selected
> hide #!1 models
> ui mousemode right "translate selected models"
> hide sel atoms
> show sel cartoons
> select clear
> select #3/S:333
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
32 atoms, 33 bonds, 3 residues, 1 model selected
> select up
2601 atoms, 2643 bonds, 340 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select up
50 atoms, 50 bonds, 6 residues, 1 model selected
> select up
2688 atoms, 2734 bonds, 353 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3
10551 atoms, 10731 bonds, 3 pseudobonds, 1380 residues, 2 models selected
> show #!1 models
> open 2PKQ
2pkq title:
Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate
dehydrogenase, complexed with NADP [more info...]
Chain information for 2pkq #4
---
Chain | Description
O Q T | Glyceraldehyde-3-phosphate dehydrogenase B
P R S | Glyceraldehyde-3-phosphate dehydrogenase A
Non-standard residues in 2pkq #4
---
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate
SO4 — sulfate ion
2pkq mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select #4
15840 atoms, 16108 bonds, 5 pseudobonds, 2073 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select clear
> select clear
> select clear
> select clear
> select up
37 atoms, 37 bonds, 5 residues, 1 model selected
> select up
2601 atoms, 2643 bonds, 340 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select up
31 atoms, 31 bonds, 4 residues, 1 model selected
> select up
2688 atoms, 2734 bonds, 353 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4
10551 atoms, 10731 bonds, 3 pseudobonds, 1380 residues, 2 models selected
> select #3
10551 atoms, 10731 bonds, 3 pseudobonds, 1380 residues, 2 models selected
> select #1
42627 atoms, 43384 bonds, 6 pseudobonds, 5656 residues, 2 models selected
> select #2
2 models selected
> select #1
42627 atoms, 43384 bonds, 6 pseudobonds, 5656 residues, 2 models selected
> select #4
10551 atoms, 10731 bonds, 3 pseudobonds, 1380 residues, 2 models selected
> select #3
10551 atoms, 10731 bonds, 3 pseudobonds, 1380 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #3/R#3/Q#3/P#3/O to #1/R#1/Q#1/P#1/O pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain R (#1) with 2pkq, chain R (#3), sequence alignment score = 1538.1
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain Q (#1) with 2pkq, chain Q (#3), sequence alignment score = 1525.4
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain P (#1) with 2pkq, chain P (#3), sequence alignment score = 1527.3
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain O (#1) with 2pkq, chain O (#3), sequence alignment score = 1500.5
RMSD between 1252 pruned atom pairs is 1.154 angstroms; (across all 1367
pairs: 4.269)
> matchmaker #4/O#4/P#4/Q#4/R to #1/A#1/B#1/C#1/D pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain A (#1) with 2pkq, chain O (#4), sequence alignment score = 1572.8
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain B (#1) with 2pkq, chain P (#4), sequence alignment score = 1500.3
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain C (#1) with 2pkq, chain Q (#4), sequence alignment score = 1528.4
Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb,
chain D (#1) with 2pkq, chain R (#4), sequence alignment score = 1505.1
RMSD between 1252 pruned atom pairs is 1.144 angstroms; (across all 1367
pairs: 4.366)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> hide #!1 models
> select clear
> select #3 /NADP
Nothing selected
> nucleotides #!3-4 fill
> style nucleic & #!3-4 stick
Changed 0 atom styles
> color #!3-4 bynucleotide
> show #!1 models
> hide #!1 models
> select #3
10551 atoms, 10731 bonds, 3 pseudobonds, 1380 residues, 2 models selected
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 384.130
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Hewlett-Packard
Model: HP Z800 Workstation
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
CPU: 16 Intel(R) Xeon(R) CPU X5570 @ 2.93GHz
Cache Size: 8192 KB
Memory:
total used free shared buff/cache available
Mem: 94G 2.2G 86G 47M 6.0G 91G
Swap: 13G 0B 13G
Graphics:
0f:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:119e]
Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
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: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
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: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
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
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
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: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
distro: 1.5.0
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: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted |
comment:2 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Hi Roberto,
--Eric