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Opened 3 months ago
Closed 3 months ago
#18602 closed defect (duplicate)
MemoryError opening mmCIF files
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "G:\\\破伤风\\\结构解析\\\20250416出图\\\T048_133\\\25-08-07 45_48_133_GT1b.cxs"
Log from Thu Aug 7 14:39:36 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "G:\\\破伤风\\\结构解析\\\20250416出图\\\T048_133\\\25-08-07 45_48_133_GT1b.cxs"
Log from Thu Aug 7 14:31:42 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "G:\\\破伤风\\\结构解析\\\20250416出图\\\T048_133\\\25-08-07 45_48_133_GT1b.cxs"
Log from Thu Aug 7 13:44:26 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "G:\\\破伤风\\\结构解析\\\20250416出图\\\T048_133\\\25-08-07 45_48_133_GT1b.cxs"
Log from Thu Aug 7 13:25:40 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open G:\\\破伤风\\\结构解析\\\20250416出图\\\T048_133\\\T048_133_GT1b.cxs
Log from Fri Apr 18 20:12:23 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open G:\\\破伤风\\\结构解析\\\20250416出图\\\T048_133\\\T048_133_GT1b.cxs
Log from Fri Apr 18 17:18:18 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open G:\\\破伤风\\\结构解析\\\20250416出图\\\T048_133\\\T048_133_GT1b.cxs
Log from Wed Apr 16 22:54:01 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open G:/破伤风/结构解析/20250416出图/T048_133/T048_133_surface.cxs
Error opening map "G:\破伤风\结构解析\20250416出图\T048_133\T048_133_surface.cxs": File
T048_133_surface.cxs, format mrc
MRC header value nsymbt (875113504) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Log from Tue Apr 15 21:43:05 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "G:\\\破伤风\\\结构解析\\\C-T048-T133\\\fitinmap-W-R口袋 .cxs"
Opened TeNT-C_T048_T133-sharp_map_3.36_zflip.mrc as #2, grid size 320,320,320,
pixel 0.856, shown at level 4.35, step 1, values float32
Log from Tue Jan 21 22:16:01 2025UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "G:\\\破伤风\\\结构解析\\\C-T048-T133\\\fitinmap-W-R口袋 .cxs"
Log from Mon Dec 16 22:53:20 2024UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "G:\\\破伤风\\\结构解析\\\C-T048-T133\\\fitinmap-W-R口袋 .cxs"
Log from Wed Jul 31 13:47:37 2024UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "G:\\\破伤风\\\结构解析\\\C-T048-T133\\\fitinmap-W-R口袋 .cxs"
Log from Tue Jul 30 22:08:47 2024UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open G:\\\破伤风\\\结构解析\\\C-T048-T133\\\fitinmap-表位图-GT1b.cxs
Log from Tue Jul 30 16:23:42 2024UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open G:\\\破伤风\\\结构解析\\\C-T048-T133\\\fitinmap-表位图-GT1b.cxs
Log from Sat Apr 20 17:27:21 2024UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open G:\\\破伤风\\\结构解析\\\C-T048-T133\\\fitinmap-表位图-GT1b.cxs
Log from Thu Jan 25 22:20:07 2024UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open G:\\\破伤风\\\结构解析\\\C-T048-T133\\\fitinmap-表位图.cxs
Log from Sun Jan 7 19:37:30 2024UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open G:\\\破伤风\\\结构解析\\\C-T048-T133\\\fitinmap.cxs
Log from Sun Jan 7 12:48:16 2024UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open G:\\\破伤风\\\结构解析\\\C-T048-T133\\\TeNT-C_T048_T133_final.pdb
Summary of feedback from opening G:\\\破伤风\\\结构解析\\\C-T048-T133\\\TeNT-
C_T048_T133_final.pdb
---
warning | Ignored bad PDB record found on line 7417
END
Chain information for TeNT-C_T048_T133_final.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
H | No description available
L | No description available
> open G:\\\破伤风\\\结构解析\\\C-T048-T133\\\TeNT-
> C_T048_T133-sharp_map_3.36_zflip.mrc
Opened TeNT-C_T048_T133-sharp_map_3.36_zflip.mrc, grid size 320,320,320, pixel
0.856, shown at level 0.111, step 2, values float32
> volume #2 level 0.2972
> volume #2 level 0.402
> hide atoms
> show cartoons
> volume #2 step 1
> transparency 50
> set bgColor white
> transparency 70
> transparency 50
> cartoon style width 2.5 thickness 1
> volume #2 level 0.6563
> volume #2 level 0.5359
> volume #2 level 0.3752
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.6162
> cartoon style width 2 thickness 1
> hide #!2 models
> select /B:162
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
48 atoms, 47 bonds, 7 residues, 1 model selected
> select up
801 atoms, 817 bonds, 111 residues, 1 model selected
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color sel skyblue
> select clear
> select /A:21
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
55 atoms, 54 bonds, 8 residues, 1 model selected
> select up
945 atoms, 970 bonds, 121 residues, 1 model selected
> color sel lightpink
> color sel lemon chiffon
> show #!2 models
> hide #!2 models
> select clear
> show #!2 models
> hide #!2 models
> select /A:21
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
55 atoms, 54 bonds, 8 residues, 1 model selected
> select up
945 atoms, 970 bonds, 121 residues, 1 model selected
> color sel orange
> select clear
> select /C:1019
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 4 residues, 1 model selected
> select up
3787 atoms, 3711 bonds, 606 residues, 1 model selected
> color sel moccasin
> select clear
> show #!2 models
> select clear
> hide #!2 models
> select /C:1054
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 6 residues, 1 model selected
> select clear
> select /H:20
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
56 atoms, 55 bonds, 8 residues, 1 model selected
> select up
902 atoms, 925 bonds, 117 residues, 1 model selected
> color sel lightgreen
> select clear
> color sel darkseagreen
> select /H:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
36 atoms, 35 bonds, 5 residues, 1 model selected
> select up
902 atoms, 925 bonds, 117 residues, 1 model selected
> color sel darkseagreen
> select clear
> show #!2 models
> hide #!2 models
> select /C:1026
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
47 atoms, 47 bonds, 6 residues, 1 model selected
> select up
3787 atoms, 3711 bonds, 606 residues, 1 model selected
> color sel light pink
> select clear
> show #!2 models
> hide #!2 models
> select /C:1054
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 6 residues, 1 model selected
> select up
3787 atoms, 3711 bonds, 606 residues, 1 model selected
> color sel thistle
> select clear
> show #!2 models
> hide #!2 models
> select /C:1053
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 6 residues, 1 model selected
> select up
3787 atoms, 3711 bonds, 606 residues, 1 model selected
> color sel lightpink
> select clear
> show #!2 models
> transparency 0
> volume style surface
> transparency 50
> transparency 60
> transparency 65
> volume #2 level 0.4823
> volume #2 level 0.576
> save G:/破伤风/结构解析/C-T048-T133/fitinmap.cxs
opened ChimeraX session
> hide #!2 models
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> split
Split TeNT-C_T048_T133_final.pdb (#1) into 5 models
Chain information for TeNT-C_T048_T133_final.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for TeNT-C_T048_T133_final.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for TeNT-C_T048_T133_final.pdb C #1.3
---
Chain | Description
C | No description available
Chain information for TeNT-C_T048_T133_final.pdb H #1.4
---
Chain | Description
H | No description available
Chain information for TeNT-C_T048_T133_final.pdb L #1.5
---
Chain | Description
L | No description available
> select #1.1/A:1-121
945 atoms, 970 bonds, 121 residues, 1 model selected
> select clear
> select #1.5/L:1-108
836 atoms, 855 bonds, 109 residues, 1 model selected
> select #1.1/A:1-121
945 atoms, 970 bonds, 121 residues, 1 model selected
> select clear
> select #1.2/B:142-252
801 atoms, 817 bonds, 111 residues, 1 model selected
> select clear
> open G:/破伤风/pdb/5n0b_TeNT_GD1a.pdb
5n0b_TeNT_GD1a.pdb title:
Crystal structure of the tetanus neurotoxin In complex with GD1A [more
info...]
Chain information for 5n0b_TeNT_GD1a.pdb #3
---
Chain | Description
A | tentoxylysin
Non-standard residues in 5n0b_TeNT_GD1a.pdb #3
---
BGC — β-D-glucopyranose
GAL — β-D-galactopyranose
NGA — 2-acetamido-2-deoxy-β-D-galactopyranose
PEG — di(hydroxyethyl)ether
SIA — N-acetyl-α-neuraminic acid
ZN — zinc ion
> mmaker #3 to #1.3
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 TeNT-C_T048_T133_final.pdb C, chain C (#1.3) with
5n0b_TeNT_GD1a.pdb, chain A (#3), sequence alignment score = 2212.5
RMSD between 421 pruned atom pairs is 0.673 angstroms; (across all 437 pairs:
0.978)
> select #3/A:865-1315
3569 atoms, 3650 bonds, 4 pseudobonds, 441 residues, 2 models selected
> select #3&`sel
Expected an objects specifier or a keyword
> select #3 & `sel
Expected a keyword
> select #3 & ` sel
Expected a keyword
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3 & ~sel
7011 atoms, 7019 bonds, 4 pseudobonds, 983 residues, 3 models selected
> ~select #3.1
7011 atoms, 7019 bonds, 2 pseudobonds, 983 residues, 2 models selected
> select #3.1
2 pseudobonds, 1 model selected
> select #3.2
6 pseudobonds, 1 model selected
> select #3.1
2 pseudobonds, 1 model selected
> hide #!3 models
> show #!3 models
> select #3/A:865-1315
3569 atoms, 3650 bonds, 4 pseudobonds, 441 residues, 2 models selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select #3/A:865-1315
3569 atoms, 3650 bonds, 4 pseudobonds, 441 residues, 2 models selected
> select clear
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.2 models
> show #3.2 models
> select #3.1
2 pseudobonds, 1 model selected
> split #3
Split 5n0b_TeNT_GD1a.pdb (#3) into 2 models
Chain information for 5n0b_TeNT_GD1a.pdb A #3.1
---
Chain | Description
A | No description available
> hide #!3.1 models
> show #!3.1 models
> hide #3.2 models
> show #3.2 models
> hide #!3.1 models
> ui tool show "Side View"
> lighting soft
> select #1.3/C:865-1110
1927 atoms, 1962 bonds, 242 residues, 1 model selected
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color sel light slate grey
> select clear
> hide #1.1 models
> hide #1.2 models
> show #1.2 models
> show #1.1 models
> save G:/破伤风/结构解析/C-T048-T133/fitinmap(1).cxs
> show #!2 models
> hide #!2 models
> open "G:/破伤风/pdb/7ce2_TeNT Hc_TT0067.pdb"
7ce2_TeNT Hc_TT0067.pdb title:
The crystal structure of tent HC complexed with neutralizing antibody [more
info...]
Chain information for 7ce2_TeNT Hc_TT0067.pdb #4
---
Chain | Description
A | TENT HC
B | neutralizing antibody light chain
Z | neutralizing antibody heavy chain
> mmaker #4 to #1.3
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 TeNT-C_T048_T133_final.pdb C, chain C (#1.3) with 7ce2_TeNT
Hc_TT0067.pdb, chain A (#4), sequence alignment score = 2286.5
RMSD between 440 pruned atom pairs is 0.529 angstroms; (across all 446 pairs:
0.615)
> split #4
Split 7ce2_TeNT Hc_TT0067.pdb (#4) into 3 models
Chain information for 7ce2_TeNT Hc_TT0067.pdb A #4.1
---
Chain | Description
A | No description available
Chain information for 7ce2_TeNT Hc_TT0067.pdb B #4.2
---
Chain | Description
B | No description available
Chain information for 7ce2_TeNT Hc_TT0067.pdb Z #4.3
---
Chain | Description
Z | No description available
> hide #!4.1 models
> hide #4.2 models
> show #4.2 models
> hide #!4.3 models
> show #!4.3 models
> show #!4.1 models
> hide #!4.1 models
> select #4.1.2
Nothing selected
> select #4.2&4.3
Expected an objects specifier or a keyword
> select #4.2 4.3
Expected a keyword
> select #4.2 #4.3
3399 atoms, 3345 bonds, 2 pseudobonds, 562 residues, 3 models selected
> color sel silver
> select clear
> hide #1.1 models
> hide #1.2 models
> show #1.1 models
> show #1.2 models
> hide #!4 models
> select #4.1/A:869-1315
3619 atoms, 3701 bonds, 2 pseudobonds, 446 residues, 2 models selected
> select #4.1/A:869-1315
3619 atoms, 3701 bonds, 2 pseudobonds, 446 residues, 2 models selected
> select #1.1/A:1-121
945 atoms, 970 bonds, 121 residues, 1 model selected
> select clear
> save G:/破伤风/结构解析/C-T048-T133/fitinmap(1).cxs
opened ChimeraX session
> hide #1.1 models
> hide #1.2 models
> hide #3.2 models
> hide #1.4 models
> hide #1.5 models
> select #1.3/C:1256
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
46 atoms, 46 bonds, 5 residues, 1 model selected
> select up
3787 atoms, 3711 bonds, 606 residues, 1 model selected
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color sel gray
> color sel lihgt gray
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel light gray
> show sel surfaces
> select clear
> hide #!1.3 surfaces
> show #!1.3 surfaces
> select #1.3/C:1292@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
99 atoms, 100 bonds, 12 residues, 2 models selected
> select up
3787 atoms, 3711 bonds, 606 residues, 2 models selected
> color sel light gray
> select clear
> hide #!1 models
> show #!1 models
> hide #!1.3 models
> show #!1.3 models
> select #1.3:1219, 1221, 1222, 1270,1271, 1285, 1287, 1289, 1290
81 atoms, 79 bonds, 9 residues, 1 model selected
> color sel powder blue
> select #1.3:1290
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1.3:1226
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #1.5 models
> hide #1.5 models
> show #1.4 models
> hide #1.4 models
> select #1.3:1271,1289,1293,1290
46 atoms, 48 bonds, 4 residues, 1 model selected
> show #1.5 models
> hide #1.5 models
> select #1.3:1271,1289,1290,1220,1222,1272,1292,1293,1295,1296,1219,1288
111 atoms, 110 bonds, 12 residues, 1 model selected
> color sel pink
> color sel lightpink
> color sel light salmon
> color sel mistyrose
> color sel palevioletred
> select clear
> select #1.3:1271,1289,1290,1220,1222,1272,1292,1293,1295,1296,1219,1288
111 atoms, 110 bonds, 12 residues, 1 model selected
> select #1.3:1271,1289,1290，1222，1219
Expected an objects specifier or a keyword
> select #1.3:1271,1289,1290,1222,1219
52 atoms, 52 bonds, 5 residues, 1 model selected
> color sel gold
> color sel orange
> color sel dark seagreen
> select clear
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> show #1.5 models
> hide #1.5 models
> hide #1.4 models
> select #1.3/C:1295@NZ
1 atom, 1 residue, 1 model selected
> select #1.3/C:1295@CB
1 atom, 1 residue, 1 model selected
> select #1.3/C:1296@CA
1 atom, 1 residue, 1 model selected
> select #1.3:1271,1289,1290,1220,1222,1272,1292,1293,1295,1296,1219,1288,
Expected an objects specifier or a keyword
> select #1.3:1271,1289,1290,1220,1222,1272,1292,1293,1295,1296,1219,1288
111 atoms, 110 bonds, 12 residues, 1 model selected
> color sel yellow
> select #1.3:1271,1289,1290,1222,1219
52 atoms, 52 bonds, 5 residues, 1 model selected
> color sel red
> select clear
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> select #1.3:1271,1289,1290,1220,1222,1272,1292,1293,1295,1296,1219,1288
111 atoms, 110 bonds, 12 residues, 1 model selected
> color sel orange
> select #1.3:1219, 1221, 1222, 1270,1271, 1285, 1287, 1289, 1290
81 atoms, 79 bonds, 9 residues, 1 model selected
> color sel dodgerblue
> select #1.3:1271,1289,1290,1220,1222,1272,1292,1293,1295,1296,1219,1288
111 atoms, 110 bonds, 12 residues, 1 model selected
> color sel orange
> select #1.3:1271,1289,1290,1222,1219
52 atoms, 52 bonds, 5 residues, 1 model selected
> color sel light pink
> select clear
> show #1.4 models
> show #1.5 models
> hide #1.4 models
> hide #!1.3 models
> show #!1.3 models
> hide #1.5 models
> select #1.3:1271,1289,1290,1222,1219
52 atoms, 52 bonds, 5 residues, 1 model selected
> color sel red
> select clear
> select #1.3:1297
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1.3:1110–1315
Expected an objects specifier or a keyword
> select #1.3:1110-1315
1707 atoms, 1754 bonds, 206 residues, 1 model selected
> select #1.3:865-1110
1927 atoms, 1962 bonds, 242 residues, 1 model selected
> delete sel
> show #1.1 models
> show #1.2 models
> hide #1.2 models
> hide #1.1 models
> select #1.3:1271,1289,1290,1222,1219
52 atoms, 52 bonds, 5 residues, 1 model selected
> lighting soft
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> select #1.3:1219, 1221, 1222, 1270,1271, 1285, 1287, 1289, 1290
81 atoms, 79 bonds, 9 residues, 1 model selected
> color sel cornflower blue
> select #1.3:1271,1289,1290,1220,1222,1272,1292,1293,1295,1296,1219,1288,
Expected an objects specifier or a keyword
> select #1.3:1271,1289,1290,1220,1222,1272,1292,1293,1295,1296,1219,1288
111 atoms, 110 bonds, 12 residues, 1 model selected
> color sel orange
> select #1.3:1271,1289,1290,1222,1219
52 atoms, 52 bonds, 5 residues, 1 model selected
> color sel red
> select clear
> show #1.1 models
> hide #1.1 models
> show #1.4 models
> show #1.5 models
> hide #!1.3 models
> hide #1.4 models
> show #!1.3 models
> hide #1.5 models
> select #1.3:1287
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1.3:1290
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1.3:1293
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.3:1296
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.3:1222
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.3:1221
8 atoms, 7 bonds, 1 residue, 1 model selected
> save G:/破伤风/结构解析/C-T048-T133/fitinmap-表位图.cxs
opened ChimeraX session
> hide #!1 models
> show #!1 models
> hide #!1.3 models
> show #!1.3 models
> show #1.1 models
> hide #1.1 models
> select #1.3
1860 atoms, 1748 bonds, 364 residues, 2 models selected
> color sel #d3d3d3
> select clear
> select #1.3:1147,1214,1216,1219,1222,1226,1229,1270,1271，
Expected an objects specifier or a keyword
> select #1.3/C:1147,1214,1216,1219,1222,1226,1229,1270,1271，
Expected an objects specifier or a keyword
> select #1.3/C:1147,1214,1216,1219,1222,1226,1229,1270,1271
80 atoms, 74 bonds, 9 residues, 1 model selected
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> select #1.3/C:1147,1214,1216,1226,1229,1270,
Expected an objects specifier or a keyword
> select clear
> select #1.3/C:1147,1214,1216,1226,1229,1270
54 atoms, 49 bonds, 6 residues, 1 model selected
> color sel thistle
> select clear
> select #1.3/C:1220,1272,1288,1289,1290,1292,1293,1295,1296
85 atoms, 84 bonds, 9 residues, 1 model selected
> color sel navajo white
> color sel bisque
> color sel khaki
> select clear
> select #1.3/C:1219,1222,1271
26 atoms, 24 bonds, 3 residues, 1 model selected
> color sel royalblue
> select clear
> save G:/破伤风/结构解析/C-T048-T133/fitinmap-表位图-GT1b.cxs
opened ChimeraX session
> hide #!1.3 models
> show #!1.3 models
> select #1.3/C:1220@ND2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
236 atoms, 242 bonds, 30 residues, 2 models selected
> select up
1860 atoms, 1748 bonds, 364 residues, 2 models selected
> color sel #d3d3d3
> Sel #1.3/C:1289,1271,1290
Unknown command: Sel #1.3/C:1289,1271,1290
> select clear
> Sel #1.3/C:1289,1271,1290
Unknown command: Sel #1.3/C:1289,1271,1290
> select #1.3/C:1289,1271,1290
36 atoms, 38 bonds, 3 residues, 1 model selected
> color sel thistle
> select clear
> select #1.3/C:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color sel dark sea green
> select clear
> show #1.1 models
> show #1.2 models
> hide #1.2 models
> hide #1.1 models
> show #1.4 models
> show #1.5 models
> hide #1.4 models
> hide #1.5 models
> show #1.4 models
> show #1.5 models
> hide #1.4 models
> hide #1.5 models
> select #1.3/C:1271,1289,1290
36 atoms, 38 bonds, 3 residues, 1 model selected
> show #1.5 models
> show #1.4 models
> hide #1.4 models
> hide #1.5 models
> select #1.3/C:1271,1289,1290,1222,1218,1293
65 atoms, 66 bonds, 6 residues, 1 model selected
> color sel thistle
> select clear
> select #1.3/C:1271,1289,1290
36 atoms, 38 bonds, 3 residues, 1 model selected
> color sel light steel blue
> color sel royalblue
> color sel red
> select clear
> select #1.3/C:1271,1289,1290
36 atoms, 38 bonds, 3 residues, 1 model selected
> color sel dark sea green
> select clear
> select #1.3/C:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> color sel light steel blue
> select clear
> select #1.3/C:1271,1289,1290
36 atoms, 38 bonds, 3 residues, 1 model selected
> color sel yellow
> color sel gold
> color sel orange
> select clear
> save G:/破伤风/结构解析/C-T048-T133/fitinmap-表位图-GT1b.cxs
> select #1.3/C:1271,1289,1290
36 atoms, 38 bonds, 3 residues, 1 model selected
> color sel khaki
> select clear
> hide #!1 models
> show #!1 models
> show #1.1 models
> hide #1.1 models
> show #1.2 models
> hide #1.2 models
> save G:/破伤风/结构解析/C-T048-T133/fitinmap-表位图-GT1b.cxs
opened ChimeraX session
> select #1.3/C:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> select clear
> color sel khaki
> select #1.3/C:1271,1289,1290
36 atoms, 38 bonds, 3 residues, 1 model selected
> color sel thistle
> select clear
> select #1.3/C:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> color sel #d3d3d3
> select clear
> select #1.3/C:1271,1289,1290,1222,1218,1293
65 atoms, 66 bonds, 6 residues, 1 model selected
> select clear
> select #1.3/C:1271,1289,1290
36 atoms, 38 bonds, 3 residues, 1 model selected
> color sel khaki
> select clear
> select #1.3/C:1219,1220,1222,1272,1288,1292,1293,1295,1296
75 atoms, 70 bonds, 9 residues, 1 model selected
> select #1.3/C:1289,1271,1290,1222,1293
54 atoms, 55 bonds, 5 residues, 1 model selected
> color sel khaki
> select #1.3/C:1219,1220, 1272,1288, 1292, 1295,1296
57 atoms, 52 bonds, 7 residues, 1 model selected
> color sel light steel blue
> select clear
> select #1.3/C:1218
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> save G:/破伤风/结构解析/C-T048-T133/fitinmap-表位图-GT1b.cxs
opened ChimeraX session
> select #1.3/C:1293@CE1
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> select up
99 atoms, 100 bonds, 12 residues, 2 models selected
> select up
1860 atoms, 1748 bonds, 364 residues, 2 models selected
> color sel #d3d3d3
> select clear
> select #1.3/C:1289,1271,1290,1222,1218,1293
65 atoms, 66 bonds, 6 residues, 1 model selected
> color sel royalblue
> color sel light steel blue
> select #1.3/C:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> color sel thistle
> select clear
> show #1.4 models
> show #1.5 models
> volume #2 level 0.8292
> volume #2 level 3.479
> volume #2 level 3.854
> volume #2 level 3.493
> hide #!1 models
> show #!1 models
> hide #!2 models
> volume #2 level 3.761
> hide #!2 models
> volume #2 level 4.216
> save "G:/WR pocket.png" width 701 height 557 supersample 3
> hide #1.4 models
> hide #1.5 models
> show #1.5 models
> hide #1.5 models
> set bgColor white
> save C:\Users\fanka\Desktop\image1.png supersample 3
> show #1.1 models
> show #1.2 models
> hide #1.2 models
> hide #1.1 models
> show #!3.1 models
> show #3.2 models
> hide #!3.1 models
> hide #3.2 models
> save "G:/破伤风/结构解析/C-T048-T133/fitinmap-W-R口袋 .cxs"
> show #1.4 models
> show #1.5 models
> volume #2 level 3.814
> ui tool show "Side View"
> select #1.5/L:21
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
43 atoms, 42 bonds, 6 residues, 1 model selected
> select up
836 atoms, 855 bonds, 109 residues, 1 model selected
> show sel surfaces
> select #1.4/H:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
36 atoms, 35 bonds, 5 residues, 1 model selected
> select up
902 atoms, 925 bonds, 117 residues, 1 model selected
> show sel surfaces
> select clear
> select #1.4/H:25@OG
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
58 atoms, 58 bonds, 9 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> color sel khaki
> select clear
> select #1.5/L:56@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
64 atoms, 64 bonds, 9 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> color sel khaki
> transparency sel 50
> transparency sel 70
> hide sel cartoons
> show sel cartoons
> show sel cartoons
> select clear
> select #1.4/H:74@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
28 atoms, 28 bonds, 4 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> transparency sel 70
> transparency sel 40
> select clear
> select #1.5/L:79@OE1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
34 atoms, 33 bonds, 4 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> transparency sel 40
> select clear
> hide #!1.3-5 surfaces
> show #!1.3-5 surfaces
> hide #!1.3-5 surfaces
> select #1.5/L:36
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
57 atoms, 59 bonds, 6 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> color sel orange
> select clear
> select #1.4/H:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
36 atoms, 35 bonds, 5 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> color sel orange
> select clear
> show #!1.3-5 surfaces
> select #1.5/L:57@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
64 atoms, 64 bonds, 9 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> transparency sel 40
> select clear
> select #1.4/H:28@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
58 atoms, 58 bonds, 9 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> transparency sel 40
> select clear
> select #1.4/H:27@N
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
58 atoms, 58 bonds, 9 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> transparency sel 40
> select #1.5/L:45@NH2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
35 atoms, 34 bonds, 4 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> transparency sel 40
> select clear
> select #1.4/H:28@CA
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
58 atoms, 58 bonds, 9 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> color sel dark sea green
> select #1.5/L:39@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
41 atoms, 42 bonds, 6 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> color sel dark sea green
> transparency sel 40
> select #1.4/H:76@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
28 atoms, 28 bonds, 4 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> transparency sel 40
> select clear
> select #1.4/H:29@N
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
58 atoms, 58 bonds, 9 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> color sel khaki
> transparency sel 40
> select clear
> select #1.5/L:57@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
64 atoms, 64 bonds, 9 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> color sel khaki
> transparency sel 40
> transparency sel 30
> transparency sel 50
> select clear
> select #1.5/L:61@NH2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
64 atoms, 64 bonds, 9 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> hide sel surfaces
> show sel surfaces
> select clear
> select #1.5/L:56@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
64 atoms, 64 bonds, 9 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> graphics silhouettes true
> select clear
> select #1.5/L:54@NH1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
64 atoms, 64 bonds, 9 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> color sel dark sea green
> transparency sel 50
> select clear
> graphics silhouettes false
> select #1.4/H:76@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
28 atoms, 28 bonds, 4 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> color sel khaki
> lighting soft
> lighting soft
> transparency sel 50
> select clear
> select #1.4/H:29@CG1
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 2 models selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
58 atoms, 58 bonds, 9 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> transparency sel 20
> hide sel surfaces
> color gold
> color sel gold
> select clear
> select #1.4/H:23
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
56 atoms, 55 bonds, 8 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> show sel surfaces
> transparency sel 50
> select clear
> select #1.4/H:5@O
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
36 atoms, 35 bonds, 5 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> color sel orange
> transparency sel 50
> select clear
> save "G:/破伤风/结构解析/C-T048-T133/fitinmap-W-R口袋 .cxs"
opened ChimeraX session
> show #1.1 models
> show #1.2 models
> select #1.1 #1.3
2805 atoms, 2718 bonds, 485 residues, 2 models selected
> select #1.1 #1.2
1746 atoms, 1787 bonds, 232 residues, 2 models selected
> show sel surfaces
> transparency sel 70
> transparency sel 60
> select clear
> select #1.1
945 atoms, 970 bonds, 121 residues, 1 model selected
> color sel #ffa500 target s
> select #1.2
801 atoms, 817 bonds, 111 residues, 1 model selected
> color sel #87ceeb target s
> select clear
> select #1.2
801 atoms, 817 bonds, 111 residues, 1 model selected
> select #1.2 #1.1
1746 atoms, 1787 bonds, 232 residues, 2 models selected
> transparency sel 60
> select clear
> save "G:/破伤风/结构解析/C-T048-T133/fitinmap-W-R口袋 .cxs"
opened ChimeraX session
> open C:/Users/fanka/Desktop/C_T154/C_T154_model.pdb
Summary of feedback from opening
C:/Users/fanka/Desktop/C_T154/C_T154_model.pdb
---
warning | Ignored bad PDB record found on line 5451
END
Chain information for C_T154_model.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> mmaker #5 to #1.3
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 TeNT-C_T048_T133_final.pdb C, chain C (#1.3) with C_T154_model.pdb,
chain C (#5), sequence alignment score = 1950.5
RMSD between 205 pruned atom pairs is 0.000 angstroms; (across all 205 pairs:
0.000)
> split #5
Split C_T154_model.pdb (#5) into 3 models
Chain information for C_T154_model.pdb A #5.1
---
Chain | Description
A | No description available
Chain information for C_T154_model.pdb B #5.2
---
Chain | Description
B | No description available
Chain information for C_T154_model.pdb C #5.3
---
Chain | Description
C | No description available
> hide #5.2 models
> show #5.2 models
> hide #5.3 models
> show #5.3 models
> hide #5.1 models
> show #5.1 models
> hide #5.2 models
> show #5.2 models
> hide #5.3 models
> select #5.1/A:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
41 atoms, 40 bonds, 5 residues, 1 model selected
> select up
939 atoms, 964 bonds, 123 residues, 1 model selected
> show sel surfaces
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color sel misty rose
> color sel lavender
> color sel light pink
> color sel #bcbddd target surface
Invalid "target" argument: Character 'u' is not an allowed target, must be one
of acrsbpfl
> color sel #bcbddd target s
> color sel #bcbddd target c
> transparency sel 70
> select clear
> select #5.2/B:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 4 residues, 1 model selected
> select up
817 atoms, 834 bonds, 107 residues, 1 model selected
> show sel surfaces
> color sel #fcb93e target s
> color sel #ff6b62 target s
> color sel #ff6b62 target c
> transparency sel 70
> select clear
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.4 models
> hide #!1.5 models
> select #5.2/B:57@O
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
90 atoms, 91 bonds, 13 residues, 2 models selected
> select up
817 atoms, 834 bonds, 107 residues, 2 models selected
> color sel #f4eeac target c
> color sel #f4eeac target s
> transparency sel 70
> select clear
> select #5.2/B:57@O
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
90 atoms, 91 bonds, 13 residues, 2 models selected
> select up
817 atoms, 834 bonds, 107 residues, 2 models selected
> color sel #f6c8a8 target s
> color sel #f6c8a8 target c
> transparency sel 70
> select clear
> select #5.2/B:61@NH2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
90 atoms, 91 bonds, 13 residues, 2 models selected
> select up
817 atoms, 834 bonds, 107 residues, 2 models selected
> color sel #dea3a2 target c
> color sel #dea3a2 target c
> color sel #dea3a2 target s
> transparency sel 70
> select clear
> show #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> hide #!1.4 models
> select #5.2/B:60@N
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
90 atoms, 91 bonds, 13 residues, 2 models selected
> select up
817 atoms, 834 bonds, 107 residues, 2 models selected
> select #5.1/A:75@O
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
30 atoms, 29 bonds, 4 residues, 2 models selected
> select up
939 atoms, 964 bonds, 123 residues, 2 models selected
> transparency sel 50
> select clear
> select #5.2/B:57@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
90 atoms, 91 bonds, 13 residues, 2 models selected
> select up
817 atoms, 834 bonds, 107 residues, 2 models selected
> transparency sel 50
> select clear
> show #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> hide #!1.4 models
> show #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> hide #!1.4 models
> show #!1.1 models
> show #!1.2 models
> show #!1.4 models
> show #!1.5 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!1.1 models
> hide #!1.2 models
> select #5.2/B:77@O
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
29 atoms, 28 bonds, 4 residues, 2 models selected
> select up
817 atoms, 834 bonds, 107 residues, 2 models selected
> color sel #fadcb4 target s
> color sel #fadcb4 target c
> transparency sel 50
> select clear
> color sel #e8d3d2 target c
> select #5.2/B:61@CD
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
90 atoms, 91 bonds, 13 residues, 2 models selected
> select up
817 atoms, 834 bonds, 107 residues, 2 models selected
> color sel #e8d3d2 target c
> color sel #e8d3d2 target s
> transparency sel 50
> select clear
> select #5.2/B:58@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
90 atoms, 91 bonds, 13 residues, 2 models selected
> select up
817 atoms, 834 bonds, 107 residues, 2 models selected
> color sel #faed9b target s
> color sel #faed9b target c
> transparency sel 50
> select clear
> show #!1.1 models
> show #!1.2 models
> show #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> hide #!1.4 models
> hide #!1.1 models
> hide #!1.2 models
> select #5.2/B:54@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
90 atoms, 91 bonds, 13 residues, 2 models selected
> select up
817 atoms, 834 bonds, 107 residues, 2 models selected
> color sel #fdd741 target c
> color sel #fdd741 target s
> transparency sel 50
> select clear
> select #5.2/B:59@CD
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
90 atoms, 91 bonds, 13 residues, 2 models selected
> select up
817 atoms, 834 bonds, 107 residues, 2 models selected
> color sel #c5f0a4 target s
> color sel #c5f0a4 target c
> transparency sel 50
> select clear
> volume #2 level 4.348
> select #5.1/A:28@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
44 atoms, 44 bonds, 7 residues, 2 models selected
> select up
939 atoms, 964 bonds, 123 residues, 2 models selected
> color sel #b8aeeb target c
> color sel #b8aeeb target s
> transparency sel 50
> select #5.2/B:59@CG
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
90 atoms, 91 bonds, 13 residues, 2 models selected
> select up
817 atoms, 834 bonds, 107 residues, 2 models selected
> color sel #f2b56f target s
> color sel #f2b56f target c
> transparency sel 50
> select clear
> save "G:/破伤风/结构解析/C-T048-T133/fitinmap-W-R口袋 .cxs"
——— End of log from Tue Jan 21 22:16:01 2025 ———
opened ChimeraX session
> show #!1.1 models
> show #!1.2 models
> show #!1.5 models
> show #!1.4 models
> color #5.2 #e1b6b5ff
> select #5.2
817 atoms, 834 bonds, 107 residues, 1 model selected
> transparency sel 70
> transparency sel 50
> select clear
> save "G:/破伤风/结构解析/C-T048-T133/fitinmap-W-R口袋 .cxs"
> color #5.2 #ff5577ff
> color #5.2 #f57c6eff
> select #5.2
817 atoms, 834 bonds, 107 residues, 1 model selected
> transparency sel 50
> select clear
> save "G:/破伤风/结构解析/C-T048-T133/fitinmap-W-R口袋 .cxs"
——— End of log from Tue Apr 15 21:43:05 2025 ———
opened ChimeraX session
> open G:/破伤风/结构解析/C-T048-T133/TeNT-C_T048_T133_final.pdb
Chain information for TeNT-C_T048_T133_final.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
H | No description available
L | No description available
> close #5
> hide #2#!1.1-5 atoms
> show #2#!1.1-5 cartoons
> hide #2 models
> show #2 models
> mmaker #2 to #1
Specify a single 'to' model only
> mmaker #2 #1
> matchmaker #2 #1
Missing required "to" argument
> mmaker #2 to #1.3
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 TeNT-C_T048_T133_final.pdb C, chain C (#1.3) with TeNT-
C_T048_T133_final.pdb, chain C (#2), sequence alignment score = 1950.5
RMSD between 205 pruned atom pairs is 0.000 angstroms; (across all 205 pairs:
0.000)
> hide #!1 models
> show #!1 models
> split #2
Split TeNT-C_T048_T133_final.pdb (#2) into 5 models
Chain information for TeNT-C_T048_T133_final.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for TeNT-C_T048_T133_final.pdb B #2.2
---
Chain | Description
B | No description available
Chain information for TeNT-C_T048_T133_final.pdb C #2.3
---
Chain | Description
C | No description available
Chain information for TeNT-C_T048_T133_final.pdb H #2.4
---
Chain | Description
H | No description available
Chain information for TeNT-C_T048_T133_final.pdb L #2.5
---
Chain | Description
L | No description available
> hide #2.1 models
> hide #2.2 models
> hide #2.4 models
> hide #2.5 models
> select #1.3
1860 atoms, 1748 bonds, 364 residues, 1 model selected
> color sel slate gray target c
> color sel #b2b2b2 target s
> transparency sel 40
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide sel surfaces
> hide #!1.3 models
> select #2.3:1110–1315
Expected an objects specifier or a keyword
> select #2.3:1110-1315
1707 atoms, 1754 bonds, 206 residues, 1 model selected
> color sel slate blue target c
> color sel slate gray target c
> show sel surfaces
> color sel #b2b2b2 target s
> transparency sel 40
> select #2.3:865-1110
1927 atoms, 1962 bonds, 242 residues, 1 model selected
> color sel sienna target c
> color sel rosybrown target s
> show sel surfaces
> transparency sel 40
> select clear
> save G:/破伤风/结构解析/20250416出图/T048_133/T048_133_surface.cxs
> save G:/破伤风/结构解析/20250416出图/T048_133/T048_133_surface.png width 4000 height
> 3000 supersample 3 transparentBackground true
[Repeated 1 time(s)]
> color #!1.1-2,4-5#!2.3 bynucleotide
> select #1.4/H:19@OG
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
56 atoms, 55 bonds, 8 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> color sel bynucleotide
Alignment identifier is 1.4/H
> select #1.5/L:40@CG
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
41 atoms, 42 bonds, 6 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
Alignment identifier is 1.5/L
> select #1.1/A:12@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
63 atoms, 63 bonds, 10 residues, 2 models selected
> select up
945 atoms, 970 bonds, 121 residues, 2 models selected
Alignment identifier is 1.1/A
> select #1.2/B:183@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
42 atoms, 44 bonds, 6 residues, 2 models selected
> select up
801 atoms, 817 bonds, 111 residues, 2 models selected
Alignment identifier is 1.2/B
> select clear
> save G:/破伤风/结构解析/20250416出图/T048_133/T048_133_surface.cxs
——— End of log from Wed Apr 16 22:54:01 2025 ———
opened ChimeraX session
> dssp
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1.3 models
> select #1.3:865–1110
Expected an objects specifier or a keyword
> select #1.3:865-1110
Nothing selected
> show #1.3:865-1110
> show #1.3:865-1110 cartoons
[Repeated 1 time(s)]
> show #1.3:865-1110 surfaces
> show #!2 models
> hide #!1.3 models
> show #!4 models
> hide #!4 models
> open G:/破伤风/pdb/1fv2_GT1b_Hc.pdb
1fv2_GT1b_Hc.pdb title:
The HC fragment of tetanus toxin complexed with an analogue of its ganglioside
receptor GT1B [more info...]
Chain information for 1fv2_GT1b_Hc.pdb #5
---
Chain | Description | UniProt
A | tetanus toxin heavy chain | TETX_CLOTE 865-1315
Non-standard residues in 1fv2_GT1b_Hc.pdb #5
---
BGC — β-D-glucopyranose (β-D-glucose; D-glucose; glucose)
CEQ — ethyl-trimethyl-silane
GAL — β-D-galactopyranose (β-D-galactose; D-galactose; galactose)
NGA — 2-acetamido-2-deoxy-β-D-galactopyranose (N-acetyl-β-D-galactosamine;
2-acetamido-2-deoxy-β-D-galactose; 2-acetamido-2-deoxy-D-galactose;
2-acetamido-2-deoxy-galactose; N-acetyl-D-galactosamine)
PO4 — phosphate ion
SIA — N-acetyl-α-neuraminic acid (N-acetylneuraminic acid; sialic acid;
α-sialicacid; O-sialic acid)
SLB — N-acetyl-β-neuraminic acid (N-acetylneuraminic acid; sialic acid;
O-sialic acid; 5-N-acetyl-β-D-neuraminic acid; β-sialic acid)
> close #3
> close #4
> mmaker #5 to #2.2
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 TeNT-C_T048_T133_final.pdb B, chain B (#2.2) with 1fv2_GT1b_Hc.pdb,
chain A (#5), sequence alignment score = 68
RMSD between 6 pruned atom pairs is 1.342 angstroms; (across all 110 pairs:
19.425)
> mmaker #5 to #1.3
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 TeNT-C_T048_T133_final.pdb C, chain C (#1.3) with 1fv2_GT1b_Hc.pdb,
chain A (#5), sequence alignment score = 1877.7
RMSD between 202 pruned atom pairs is 0.645 angstroms; (across all 205 pairs:
0.756)
> hide #!1.2 models
> hide #!1.1 models
> split #5
Split 1fv2_GT1b_Hc.pdb (#5) into 2 models
Chain information for 1fv2_GT1b_Hc.pdb A #5.1
---
Chain | Description
A | No description available
> select #1.4/H:30@OG
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
58 atoms, 58 bonds, 9 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> hide sel cartoons
> select #1.5/L:57@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
92 atoms, 93 bonds, 13 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> hide sel cartoons
> select clear
> hide #5.2 models
> show #5.2 models
> hide #5.1 models
> select #1.4/H:33@CE1
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
58 atoms, 58 bonds, 9 residues, 2 models selected
> select clear
> select #5.2
108 atoms, 114 bonds, 7 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> select clear
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
[Repeated 2 time(s)]
> lighting soft
> graphics silhouettes false
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> select #2.3/C:1156@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
33 atoms, 33 bonds, 4 residues, 2 models selected
> select up
3628 atoms, 3711 bonds, 447 residues, 2 models selected
> hide sel surfaces
> show sel surfaces
> hide sel cartoons
> select clear
> select #5.2
108 atoms, 114 bonds, 7 residues, 1 model selected
> hide sel surfaces
> color #5.2 blue
> color #5.2 yellow
> color #5.2 #00007fff
> color #5.2 blue
> color #5.2 red
> undo
[Repeated 4 time(s)]
> select clear
> select #2.3/C:1141@NE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
41 atoms, 40 bonds, 5 residues, 2 models selected
> select up
3628 atoms, 3711 bonds, 447 residues, 2 models selected
> transparency sel 0
> select clear
> select #2.3/C:1056@CA
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
38 atoms, 37 bonds, 6 residues, 2 models selected
> select up
3628 atoms, 3711 bonds, 447 residues, 2 models selected
> select clear
> hide #!2 models
> show #!2 models
> show #2.2 models
> hide #2.2 models
> hide #!1 models
> show #!1 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.3 models
> show #2.2 models
> hide #2.2 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.1 models
> show #2.2 models
> hide #2.2 models
> hide #2.1 models
> hide #!2.3 models
> show #!2.3 models
> select #2.3:865-1110
1927 atoms, 1962 bonds, 242 residues, 1 model selected
> hide sel
> hide sel surfaces
> select #1.5/L:45@CB
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
35 atoms, 34 bonds, 4 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> transparency sel 60
> transparency sel 40
> select clear
> select #1.4/H:74@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
28 atoms, 28 bonds, 4 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> transparency sel 40
> select clear
> color #5.2 #550000ff
> color #5.2 #00007fff
> undo
[Repeated 1 time(s)]
> select #5.2
108 atoms, 114 bonds, 7 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> cartoon style width 2.0 thickness 0.8
> cartoon style width 2.0 thickness 2
> size stickRadius 0.3
Changed 16448 bond radii
> select clear
> color #5.2 #00007fff
> color #5.2 blue
> color #5.2 red
> color #5.2 #ff5500ff
> undo
[Repeated 3 time(s)]
> color #5.2 #00007fff
> select #2.3/C:1299@CA
1 atom, 1 residue, 1 model selected
> select #5.3
Nothing selected
> select #5.2
108 atoms, 114 bonds, 7 residues, 1 model selected
> color byhetero
> color sel byhetero
> select clear
> select #5.2
108 atoms, 114 bonds, 7 residues, 1 model selected
> color sel magenta
> select clear
> color #5.2 #ccee44ff
> color #5.2 #ce4459ff
> select #5.2
108 atoms, 114 bonds, 7 residues, 1 model selected
> color sel byhetero
> select clear
> select #1.4/H:28@CA
1 atom, 1 residue, 1 model selected
> select #1.4/H:28@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
58 atoms, 58 bonds, 9 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> transparency sel 60
> select clear
> color #5.2 #dd4459ff
> color #5.2 #dd3959ff
> color #5.2 #dd397eff
> select #5.2
108 atoms, 114 bonds, 7 residues, 1 model selected
> color sel byhetero
> select clear
> turn y 90
[Repeated 8 time(s)]
> turn y -90
[Repeated 4 time(s)]
> ui tool show "Side View"
> hide #!2.3 models
> show #!1.3 models
> select #1.3
1860 atoms, 1748 bonds, 364 residues, 1 model selected
> show sel surfaces
> hide sel cartoons
> transparency sel 0
> select clear
> turn y -90
> turn y 90
> turn y -90
> turn y 90
> turn y -90
> turn y 90
> turn y -90
> turn y 90
> turn y -90
> turn y 90
> save G:/破伤风/结构解析/20250416出图/T048_133/48_GT1b_clash.png width 4000 height
> 3000 supersample 3 transparentBackground true
> turn y -90
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> save G:/破伤风/结构解析/20250416出图/T048_133/48_GT1b_clash.png width 3934 height
> 3000 supersample 3 transparentBackground true
> select #1.4/H:77@NE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
57 atoms, 57 bonds, 7 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> select #1.5/L:57@O
1 atom, 1 residue, 1 model selected
> select clear
> select #1.5/L:57@O
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
92 atoms, 93 bonds, 13 residues, 2 models selected
> select up
836 atoms, 855 bonds, 109 residues, 2 models selected
> transparency sel 60
> transparency sel 30
> select clear
> select #1.4/H:76@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
28 atoms, 28 bonds, 4 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> transparency sel 30
> select clear
> turn y -90
> turn y 90
> save G:/破伤风/结构解析/20250416出图/T048_133/48_GT1b_clash.png width 4000 height
> 3050 supersample 3 transparentBackground true
> select #1.4/H:24@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
56 atoms, 55 bonds, 8 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> transparency sel 40
> select clear
> save G:/破伤风/结构解析/20250416出图/T048_133/48_GT1b_clash.png width 4000 height
> 3050 supersample 3 transparentBackground true
> turn y -90
> save G:/破伤风/结构解析/20250416出图/T048_133/48_GT1b_clash_2.png width 4000 height
> 3050 supersample 3 transparentBackground true
> select #1.4/H:75@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
28 atoms, 28 bonds, 4 residues, 2 models selected
> select up
902 atoms, 925 bonds, 117 residues, 2 models selected
> transparency sel 40
> transparency sel 50
> select clear
> save G:/破伤风/结构解析/20250416出图/T048_133/48_GT1b_clash_2.png width 4000 height
> 3050 supersample 3 transparentBackground true
> save G:/破伤风/结构解析/20250416出图/T048_133/T048_133_GT1b.cxs
——— End of log from Fri Apr 18 17:18:18 2025 ———
opened ChimeraX session
> view name 1
> select #1.3:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> color sel #87ceeb
> select clear
> select #1.3:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> color sel #E1cbe2
> select clear
> select #1.3:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> color sel #C0a3ed
> select clear
> view 1
> turn y 90
> save G:/破伤风/结构解析/20250416出图/T048_133/48_GT1b_clash_3.png width 699 height
> 533 supersample 3
> save G:/破伤风/结构解析/20250416出图/T048_133/48_GT1b_clash_3.png width 4000 height
> 3050 supersample 3 transparentBackground true
> select #1.3:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> color sel #f3d9a6
> select clear
> select #1.3:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> color sel #cee2f5
> select clear
> select #1.3:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> color sel #bccbe8
> color sel #1d73b6
> color sel #bccbe8
> select clear
> select #1.3:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> color sel #87ceeb
> color sel #E1cbe2
> select clear
> select #1.3:1226,1216,1214,1147,1229
47 atoms, 43 bonds, 5 residues, 1 model selected
> color sel ##C0a3ed
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel #C0a3ed
> select clear
> save G:/破伤风/结构解析/20250416出图/T048_133/T048_133_GT1b.cxs
——— End of log from Fri Apr 18 20:12:23 2025 ———
opened ChimeraX session
> show #!1.1 models
> show #!1.2 models
> hide #!1.2 models
> hide #!1.1 models
> open "C:/Users/fanka/Desktop/20250407
> C_T045/0414Final_deleteH2O_250407_C_T045_fit-
> coot-1_real_space_refined_005.pdb"
Chain information for 0414Final_deleteH2O_250407_C_T045_fit-
coot-1_real_space_refined_005.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> mmaker #3/C to #1.3/C
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 TeNT-C_T048_T133_final.pdb C, chain C (#1.3) with
0414Final_deleteH2O_250407_C_T045_fit-coot-1_real_space_refined_005.pdb, chain
C (#3), sequence alignment score = 1925.9
RMSD between 204 pruned atom pairs is 0.612 angstroms; (across all 205 pairs:
0.684)
> view 1
> view 2
Expected an objects specifier or a view name or a keyword
> view 1
> show #!1.1 models
> show #!1.2 models
> hide #!1.2 models
> hide #!1.1 models
> split #3
Split 0414Final_deleteH2O_250407_C_T045_fit-coot-1_real_space_refined_005.pdb
(#3) into 3 models
Chain information for 0414Final_deleteH2O_250407_C_T045_fit-
coot-1_real_space_refined_005.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for 0414Final_deleteH2O_250407_C_T045_fit-
coot-1_real_space_refined_005.pdb B #3.2
---
Chain | Description
B | No description available
Chain information for 0414Final_deleteH2O_250407_C_T045_fit-
coot-1_real_space_refined_005.pdb C #3.3
---
Chain | Description
C | No description available
> hide #3.1 models
> show #3.1 models
> hide #3.3 models
> select #3.1/A:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
32 atoms, 31 bonds, 4 residues, 1 model selected
> select up
948 atoms, 970 bonds, 123 residues, 1 model selected
> select #3.2/B:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
33 atoms, 32 bonds, 4 residues, 1 model selected
> select up
809 atoms, 828 bonds, 107 residues, 1 model selected
> show sel surfaces
> hide sel cartoons
> select #3.1/A:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
32 atoms, 31 bonds, 4 residues, 1 model selected
> select up
948 atoms, 970 bonds, 123 residues, 1 model selected
> show sel surfaces
> hide sel cartoons
> select clear
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 45_48_133_GT1b.cxs"
> open 3hmy
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 319,
in execute
cmd.run(cmd_text)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
154, in provider_open
models, status = collated_open(session, database_name, ident,
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open
return remember_data_format()
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 97,
in fetch
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\manager.py",
line 198, in open_data
return provider_open(self.session, [path], _return_status=True,
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
465, in collated_open
return remember_data_format()
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 43,
in open
return mmcif.open_mmcif(session, data, file_name, **kw)
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
MemoryError: not enough memory
MemoryError: not enough memory
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
> open G:/破伤风/pdb/3hmy_GT2_Rpocket.pdb
3hmy_GT2_Rpocket.pdb title:
Crystal structure of HCR/T complexed with GT2 [more info...]
Chain information for 3hmy_GT2_Rpocket.pdb #4
---
Chain | Description | UniProt
A | tentoxylysin | TETX_CLOTE 866-1315
Non-standard residues in 3hmy_GT2_Rpocket.pdb #4
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SIA — N-acetyl-α-neuraminic acid (N-acetylneuraminic acid; sialic acid;
α-sialicacid; O-sialic acid)
SO4 — sulfate ion
> mmaker #4/A to #1.3/C
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 TeNT-C_T048_T133_final.pdb C, chain C (#1.3) with
3hmy_GT2_Rpocket.pdb, chain A (#4), sequence alignment score = 1887.9
RMSD between 199 pruned atom pairs is 0.474 angstroms; (across all 205 pairs:
0.857)
> select #3.2/B:60@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
90 atoms, 91 bonds, 13 residues, 2 models selected
> select up
809 atoms, 828 bonds, 107 residues, 2 models selected
> transparency #3.2/B #3.1A 50
Missing or invalid "percent" argument: Expected a number
> transparency #3.2/B #3.1A 50 s
Missing or invalid "percent" argument: Expected a number
> transparency #3.2/B #3.1A 50 target s
Missing or invalid "percent" argument: Expected a number
> transparency #3.2/B 50 target s
> transparency #3.1/A 50 target s
> split #4
Split 3hmy_GT2_Rpocket.pdb (#4) into 2 models
Chain information for 3hmy_GT2_Rpocket.pdb A #4.1
---
Chain | Description
A | No description available
> hide #4.2 models
> show #4.2 models
> hide #!4.1 models
> color #4.2 #00007fff
> select clear
> select #4.2
60 atoms, 62 bonds, 3 residues, 1 model selected
> color sel byhetero
> select clear
> select #4.2
60 atoms, 62 bonds, 3 residues, 1 model selected
> size stickRadius 0.3
Changed 25696 bond radii
> select clear
> color #3.1/A #a2a9eb target s
> select clear
> color #3.1/A #a2a9eb target c
> color #3.1 #a2a9ebff
[Repeated 1 time(s)]
> color #3.2/B #f57c6e target c
> color #3.2/B #f57c6e target s
> color #3.2 #f57c6eff
> color #3.2 whitesmoke
> color #3.2 #f57c6eff
> transparency #3.1/A 50 target s
> transparency #3.2/B 50 target s
> hide #4.2 models
> hide #!1.3 models
> show #!1.3 models
> hide #!3.1 models
> hide #!3.2 models
> select #1.3/C:1155@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
12 atoms, 12 bonds, 2 residues, 2 models selected
> select up
1701 atoms, 1748 bonds, 205 residues, 2 models selected
> color sel #999895
> select clear
> show #4.2 models
> show #!3.1 models
> show #!3.2 models
> view name 2
> turn y 90
> turn y -90
> turn y 90
> turn y -90
[Repeated 1 time(s)]
> view name 3
> turn y 90
> turn y -90
> view 1
> view 2
> view 3
> view 1
> view 2
[Repeated 1 time(s)]
> turn y 90
> view 2
> turn y 90
> view 4
Expected an objects specifier or a view name or a keyword
> view name 4
> view 2
> hide #4.2 models
> hide #!3.1 models
> hide #!3.2 models
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 48-GT1b v1.png" width 701
> height 534 supersample 4 transparentBackground true
> ui tool show "Side View"
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 48-GT1b v1.png" width 3000
> height 2285 supersample 3 transparentBackground true
> view 3
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 48-GT1b v2.png" width 3000
> height 2285 supersample 2 transparentBackground true
> show #4.2 models
> show #!3.1 models
> show #!3.2 models
> view 2
> hide #!5.2 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 45-GT2 v1.png" width 3000
> height 2285 supersample 3 transparentBackground true
> view 4
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 45-GT2 v2.png" width 3000
> height 2285 supersample 3 transparentBackground true
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 45_48_133_GT1b.cxs"
——— End of log from Thu Aug 7 13:25:40 2025 ———
opened ChimeraX session
> hide #!1.3 models
> show #!1.3 models
> select #1.3
1860 atoms, 1748 bonds, 364 residues, 1 model selected
> color sel #b2b2b2
> select clear
> view 3
> view 2
> view 4
> view 2
> view 3
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 45-GT2 v2.png" width 2000
> height 1524 supersample 3 transparentBackground true
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 45_48_133_GT1b.cxs"
——— End of log from Thu Aug 7 13:44:26 2025 ———
opened ChimeraX session
> show #!1.1 models
> show #!1.2 models
> hide #4.2 models
> hide #!3.1 models
> hide #!3.2 models
> view 2
> select #1.1 #1.2
1746 atoms, 1787 bonds, 232 residues, 2 models selected
> hide sel target c
> select clear
> open G:/破伤风/pdb/SV2A_C_9fyr.pdb
SV2A_C_9fyr.pdb title:
Cryo-em structure of native SV2A In complex with tent-HC, pro- macrobody 5 and
levetiracetam [more info...]
Chain information for SV2A_C_9fyr.pdb #6
---
Chain | Description | UniProt
A | synaptic vesicle glycoprotein 2A |
C | tetanus toxin chain H | TETX_CLOTE 875-1315
D | pro-macrobody 5,maltose/maltodextrin-binding periplasmic
protein,maltose/maltodextrin-binding periplasmic protein | MALE_ECOLI 128-487
Non-standard residues in SV2A_C_9fyr.pdb #6
---
6UZ — ω-undecylenyl-β-D-maltopyranoside
((2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-4,5-bis(oxidanyl
)-6-undec-10-enoxy-oxan-3-yl]oxy-oxane-3,4,5-triol)
FUC — α-L-fucopyranose (α-L-fucose; 6-deoxy-α-L-galactopyranose; L-fucose;
fucose)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
UKX — (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide (levetiracetam)
> ui tool show "Side View"
> mmaker #6/C to #1.3/C
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 TeNT-C_T048_T133_final.pdb C, chain C (#1.3) with SV2A_C_9fyr.pdb,
chain C (#6), sequence alignment score = 1842.2
RMSD between 198 pruned atom pairs is 0.686 angstroms; (across all 199 pairs:
0.748)
> show #!4.1 models
> hide #!4.1 models
> split #6
Split SV2A_C_9fyr.pdb (#6) into 5 models
Chain information for SV2A_C_9fyr.pdb A #6.1
---
Chain | Description
A | No description available
Chain information for SV2A_C_9fyr.pdb C #6.2
---
Chain | Description
C | No description available
Chain information for SV2A_C_9fyr.pdb D #6.3
---
Chain | Description
D | No description available
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.2 models
> hide #6.4 models
> hide #6.5 models
> hide #6.3 models
> show #6.3 models
> hide #6.3 models
> show #6.3 models
> hide #6.3 models
> show #6.3 models
> hide #6.3 models
> show #6.5 models
> hide #6.5 models
> show #6.4 models
> hide #6.4 models
> show #6.3 models
> show #!6.2 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.2 models
> show #!6.2 models
> hide #6.3 models
> show #6.3 models
> hide #6.3 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.2 models
> view 2
> select #6.1/A:210
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
768 atoms, 774 bonds, 50 residues, 1 model selected
> select up
5156 atoms, 5238 bonds, 346 residues, 1 model selected
> select up
5474 atoms, 5559 bonds, 365 residues, 1 model selected
> select up
8544 atoms, 8664 bonds, 565 residues, 1 model selected
> show sel surfaces
> view 2
> ui tool show "Side View"
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color sel peachpuff
> color sel dark orange
> select clear
> view 2
> show #!3.1 models
> show #!3.2 models
> hide #!3.1 models
> hide #!3.2 models
> select #6.1/A:263@CD2
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> select up
432 atoms, 438 bonds, 29 residues, 2 models selected
> select up
5156 atoms, 5238 bonds, 346 residues, 2 models selected
> select up
5474 atoms, 5559 bonds, 365 residues, 2 models selected
> select up
8544 atoms, 8664 bonds, 565 residues, 2 models selected
> hide sel surfaces
> select clear
> view 2
> hide #!6 models
> show #!6 models
> hide #!6.1 models
> show #!6.1 models
> view 2
[Repeated 1 time(s)]
> turn y -90
> turn y 90
[Repeated 1 time(s)]
> turn y -90
> turn y 45
> view name 5
> view 2
> select #6.1/A:699
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
401 atoms, 403 bonds, 26 residues, 2 models selected
> select up
2238 atoms, 2257 bonds, 148 residues, 2 models selected
> select up
2391 atoms, 2411 bonds, 159 residues, 2 models selected
> select up
7394 atoms, 7495 bonds, 494 residues, 2 models selected
> select up
7691 atoms, 7795 bonds, 512 residues, 2 models selected
> select up
8544 atoms, 8664 bonds, 565 residues, 2 models selected
> select up
8646 atoms, 8767 bonds, 567 residues, 2 models selected
> select up
8646 atoms, 8767 bonds, 3 pseudobonds, 567 residues, 3 models selected
> select up
8646 atoms, 8767 bonds, 3 pseudobonds, 567 residues, 3 models selected
> color sel darkorange
> cartoon style width 2.0 thickness 0.8
> select clear
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 133-SV2A v1.png" width 2000
> height 1524 supersample 3 transparentBackground true
> view 5
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 133-SV2A v2.png" width 2000
> height 1524 supersample 3 transparentBackground true
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 45_48_133_GT1b.cxs"
——— End of log from Thu Aug 7 14:31:42 2025 ———
opened ChimeraX session
> select #1.1/A #1.2/B
1746 atoms, 1787 bonds, 232 residues, 2 models selected
> transparency sel 40 target s
> transparency sel 45 target s
> transparency sel 50 target s
> select clear
> view 5
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 133-SV2A v2.png" width 2000
> height 1524 supersample 3 transparentBackground true
> view 2
> ui tool show "Side View"
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 133-SV2A v1.png" width 2000
> height 1524 supersample 3 transparentBackground true
> save "G:/破伤风/结构解析/20250416出图/T048_133/25-08-07 45_48_133_GT1b.cxs"
——— End of log from Thu Aug 7 14:39:36 2025 ———
opened ChimeraX session
> open 7OH0
Summary of feedback from opening 7OH0 fetched from pdb
---
note | Fetching compressed mmCIF 7oh0 from
http://files.rcsb.org/download/7oh0.cif
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 319,
in execute
cmd.run(cmd_text)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
154, in provider_open
models, status = collated_open(session, database_name, ident,
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open
return remember_data_format()
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 97,
in fetch
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\manager.py",
line 198, in open_data
return provider_open(self.session, [path], _return_status=True,
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
465, in collated_open
return remember_data_format()
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 43,
in open
return mmcif.open_mmcif(session, data, file_name, **kw)
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
MemoryError: not enough memory
MemoryError: not enough memory
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 442.62
OpenGL renderer: GeForce MX350/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: LENOVO
Model: 82DN
OS: Microsoft Windows 11 专业版 (Build 26100)
Memory: 17,001,664,512
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Change History (2)
comment:1 by , 3 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError opening mmCIF files |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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