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Opened 9 months ago
Closed 4 months ago
#16654 closed defect (fixed)
Session restore: ItemTable's selectionModel() is None (Parsing BlastProtein results failed)
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | 1.10 |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.10.dev202501180816 (2025-01-18 08:16:12 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.dev202501180816 (2025-01-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "E:\KRAS paper-data -20250118\chimerax-kras.cxs" format session
Log from Sat Jan 18 19:27:50 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open C:\Users\User\Desktop\结果\KRAS作图\kras.cxs format session
Log from Sat Jan 18 16:53:59 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/User/Desktop/结果/H43 inter with ASK1/H43 against ASK1-2.cxs"
Log from Sat Oct 12 17:08:30 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/User/Desktop/结果/H43 inter with ASK1/H43 against ASK1.cxs"
Log from Fri Oct 11 16:59:44 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "Z:/hASK1/ASK1-HDX-MS结果/HDX-MS dimer results/ASK.cxs"
Log from Sun Apr 28 22:16:47 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "Z:\hASK1\ASK1-HDX-MS结果\HDX-MS dimer results\ASK1 DIMER-YH-DEMO.cxs"
> format session
Log from Sun Mar 31 23:27:16 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/User/Documents/temp/ASK1-demo.pdb
ASK1-demo.pdb title:
ranked_0 - prepared [more info...]
Chain information for ASK1-demo.pdb #1
---
Chain | Description
B C | No description available
> set bgColor white
> color #1 #55aaffff
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> lighting soft
> graphics silhouettes true
> select /B:1-571
9180 atoms, 9280 bonds, 571 residues, 1 model selected
> show sel surfaces
> transparency (#!1 & sel) 70
> color (#!1 & sel) orange
> transparency (#!1 & sel) 80
> ui tool show "Color Actions"
> color sel salmon
> select /C:1-571
9180 atoms, 9280 bonds, 571 residues, 1 model selected
> show sel surfaces
> transparency (#!1 & sel) 80
> select /B:1-571
9180 atoms, 9280 bonds, 571 residues, 1 model selected
> transparency (#!1 & sel) 80
> select clear
> transparency 0
> transparency 70
Alignment identifier is 1
> select /B:1-571
9180 atoms, 9280 bonds, 571 residues, 1 model selected
> select /B-C:1
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /B-C:1-3
120 atoms, 118 bonds, 6 residues, 1 model selected
> select /B-C:1
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /B-C:1-159
4938 atoms, 4984 bonds, 318 residues, 1 model selected
> select /B-C:1
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /B-C:1-31
956 atoms, 956 bonds, 62 residues, 1 model selected
> select /B-C:1
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /B-C:1-200
6300 atoms, 6360 bonds, 400 residues, 1 model selected
> select /B-C:1
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /B-C:1-180
5606 atoms, 5660 bonds, 360 residues, 1 model selected
> select clear
> save "Z:/ASK1 publication/ASK1-Without Surface/ASK1 Dimer.bmp" width 1977
> height 1209 supersample 3
> hide surfaces
> select /B-C:164
38 atoms, 36 bonds, 2 residues, 1 model selected
> select /B-C:164-166
104 atoms, 104 bonds, 6 residues, 1 model selected
> select /B-C:165
28 atoms, 28 bonds, 2 residues, 1 model selected
> select /B-C:165-167
98 atoms, 98 bonds, 6 residues, 1 model selected
> select
> /B-C:16-36,45-50,53-60,72-87,102-112,144-147,155-162,166-199,203-216,224-236,240-250,262-275,280-294,300-316,322-338,342-354,363-378,382-384,388-401,404-416,421-437,449-463,553-568
10470 atoms, 10530 bonds, 632 residues, 1 model selected
> select /B-C:342
38 atoms, 36 bonds, 2 residues, 1 model selected
> select /B-C:342-343
72 atoms, 70 bonds, 4 residues, 1 model selected
> select /B-C:363
40 atoms, 40 bonds, 2 residues, 1 model selected
> select /B-C:363-375
442 atoms, 442 bonds, 26 residues, 1 model selected
> select /B-C:363
40 atoms, 40 bonds, 2 residues, 1 model selected
> select /B-C:363-410
1554 atoms, 1566 bonds, 96 residues, 1 model selected
> color (#!1 & sel) orange
> select /B-C:571
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /B-C:542-571
972 atoms, 982 bonds, 60 residues, 1 model selected
> select /B-C:542
28 atoms, 26 bonds, 2 residues, 1 model selected
> select /B-C:542-544
74 atoms, 72 bonds, 6 residues, 1 model selected
> select /B-C:553
30 atoms, 28 bonds, 2 residues, 1 model selected
> select /B-C:553-571
630 atoms, 634 bonds, 38 residues, 1 model selected
> color (#!1 & sel) cyan
> select /B-C:514
30 atoms, 28 bonds, 2 residues, 1 model selected
> select /B-C:514-530
524 atoms, 530 bonds, 34 residues, 1 model selected
> color (#!1 & sel) medium blue
> color #1.1 #55aaff4c
> select add #1
18360 atoms, 18560 bonds, 1142 residues, 3 models selected
> color (#!1 & sel) cornflower blue
> select clear
> select /B-C:394
40 atoms, 40 bonds, 2 residues, 1 model selected
> select /B-C:394-395
78 atoms, 78 bonds, 4 residues, 1 model selected
> select
> /B-C:16-36,45-50,53-60,72-87,102-112,144-147,155-162,166-199,203-216,224-236,240-250,262-275,280-294,300-316,322-338,342-354,363-378,382-384,388-401,404-416,421-437,449-463,553-568
10470 atoms, 10530 bonds, 632 residues, 1 model selected
> select /B-C:394
40 atoms, 40 bonds, 2 residues, 1 model selected
> select /B-C:394-414
652 atoms, 654 bonds, 42 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select
> /B-C:16-36,45-50,53-60,72-87,102-112,144-147,155-162,166-199,203-216,224-236,240-250,262-275,280-294,300-316,322-338,342-354,363-378,382-384,388-401,404-416,421-437,449-463,553-568
10470 atoms, 10530 bonds, 632 residues, 1 model selected
> select /B-C:426
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /B-C:426-427
60 atoms, 58 bonds, 4 residues, 1 model selected
> select /B-C:415
40 atoms, 40 bonds, 2 residues, 1 model selected
> select /B-C:415-426
436 atoms, 444 bonds, 24 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark salmon
> color sel salmon
> color sel coral
> color sel saddle brown
> color sel brown
> color sel tomato
> select /B-C:518-519
42 atoms, 40 bonds, 4 residues, 1 model selected
> select /B-C:518-527
272 atoms, 270 bonds, 20 residues, 1 model selected
> select /B-C:518
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /B-C:518-532
438 atoms, 438 bonds, 30 residues, 1 model selected
> ui tool show "Color Actions"
> color sel fire brick
[Repeated 1 time(s)]
> select clear
> select /B-C:518
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /B-C:518-532
438 atoms, 438 bonds, 30 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> color sel lavender
> color sel misty rose
> color sel light coral
[Repeated 1 time(s)]
> select clear
> select /B-C:561
30 atoms, 28 bonds, 2 residues, 1 model selected
> select /B-C:561-571
338 atoms, 336 bonds, 22 residues, 1 model selected
> ui tool show "Color Actions"
> color sel thistle
> select clear
[Repeated 1 time(s)]
> save "Z:/hASK1/ASK1-HDX-MS结果/HDX-MS dimer results/frontier.bmp" width 1981
> height 1220 supersample 4
> open Z:/hASK1/ASK1pymol/ASK1-H43.pdb
Chain information for ASK1-H43.pdb #2
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!1 to #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 ASK1-H43.pdb, chain A (#2) with ASK1-demo.pdb, chain B (#1),
sequence alignment score = 1960.2
RMSD between 374 pruned atom pairs is 0.497 angstroms; (across all 384 pairs:
0.703)
> hide #2 models
> show #2 models
> hide #2 models
> select #2/A:272-655
3131 atoms, 3202 bonds, 384 residues, 1 model selected
> show #2 models
> select add #2
3159 atoms, 3233 bonds, 385 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
3159 atoms, 3233 bonds, 385 residues, 1 model selected
> select subtract #2
Nothing selected
Alignment identifier is 2
Alignment identifier is 2/A
> select
> #2/A:273-286,290-305,311-324,327-338,349-362,367-379,387-403,409-425,429-441,452-466,475-488,491-503,508-524,536-550,640-654
1807 atoms, 1830 bonds, 219 residues, 1 model selected
> select add #2
3159 atoms, 3233 bonds, 385 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #2 models
> select add #2
3159 atoms, 3233 bonds, 385 residues, 1 model selected
> select subtract #2
Nothing selected
> select ligand
28 atoms, 31 bonds, 1 residue, 1 model selected
> show #2 models
> select add #2
3159 atoms, 3233 bonds, 385 residues, 1 model selected
> select subtract #2
Nothing selected
> select #2/A
3131 atoms, 3202 bonds, 384 residues, 1 model selected
> color sel cornflower blue
> select ligand
28 atoms, 31 bonds, 1 residue, 1 model selected
> view #2 clip false
[Repeated 2 time(s)]
> show sel surfaces
> style sel sphere
Changed 28 atom styles
> undo
> select add #2
3159 atoms, 3233 bonds, 385 residues, 2 models selected
> select subtract #2
1 model selected
> hide #!2 models
> select add #2.1
28 atoms, 1 residue, 1 model selected
> hide #2.1 models
> select add #2
3159 atoms, 3233 bonds, 385 residues, 2 models selected
> select subtract #2
1 model selected
> show #2.1 models
> select #2/A
3131 atoms, 3202 bonds, 384 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> open Z:/hASK1/ASK1pymol/ASK1-H43.pdb
Chain information for ASK1-H43.pdb #3
---
Chain | Description
A | No description available
> select add #2
3159 atoms, 3233 bonds, 385 residues, 1 model selected
> select subtract #2
1 model selected
> rename #3 ASK1-H43-2.pdb
> select add #3
3159 atoms, 3233 bonds, 385 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!1 to #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 ASK1-H43-2.pdb, chain A (#3) with ASK1-demo.pdb, chain B (#1),
sequence alignment score = 1960.2
RMSD between 374 pruned atom pairs is 0.497 angstroms; (across all 384 pairs:
0.703)
> ui tool show Matchmaker
> matchmaker #3 to #1/C pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain C (#1) with ASK1-H43-2.pdb, chain A (#3),
sequence alignment score = 1960.2
RMSD between 375 pruned atom pairs is 0.518 angstroms; (across all 384 pairs:
0.711)
> select ligand
56 atoms, 62 bonds, 2 residues, 2 models selected
> show sel surfaces
> ui tool show "Color Actions"
> color sel misty rose
> color sel violet
> color sel light cyan
> color sel light coral
> color sel lavender blush
> color sel misty rose
> color sel khaki
> color sel blanched almond
[Repeated 1 time(s)]
> select add #3
3187 atoms, 3264 bonds, 386 residues, 4 models selected
> select subtract #3
28 atoms, 31 bonds, 1 residue, 3 models selected
> select add #2
3159 atoms, 3233 bonds, 385 residues, 2 models selected
> select subtract #2
1 model selected
> select add #3
3159 atoms, 3233 bonds, 385 residues, 1 model selected
> select #3/A
3131 atoms, 3202 bonds, 384 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #1/B
9180 atoms, 9280 bonds, 571 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light pink
> select clear
> select #1/B-C:34
30 atoms, 28 bonds, 2 residues, 1 model selected
> select #1/B-C:34-97
2006 atoms, 2028 bonds, 128 residues, 1 model selected
> select
> #1/B-C:16-36,45-50,53-60,72-87,102-112,144-147,155-162,166-199,203-216,224-236,240-250,262-275,280-294,300-316,322-338,342-354,363-378,382-384,388-401,404-416,421-437,449-463,553-568
10470 atoms, 10530 bonds, 632 residues, 1 model selected
> select clear
> select #1/B-C:394
40 atoms, 40 bonds, 2 residues, 1 model selected
> select #1/B-C:394-413
614 atoms, 616 bonds, 40 residues, 1 model selected
> select #1/B-C:394
40 atoms, 40 bonds, 2 residues, 1 model selected
> select #1/B-C:394-415
692 atoms, 696 bonds, 44 residues, 1 model selected
> select #1/B-C:394
40 atoms, 40 bonds, 2 residues, 1 model selected
> select #1/B-C:394-414
652 atoms, 654 bonds, 42 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select
> #1/B-C:16-36,45-50,53-60,72-87,102-112,144-147,155-162,166-199,203-216,224-236,240-250,262-275,280-294,300-316,322-338,342-354,363-378,382-384,388-401,404-416,421-437,449-463,553-568
10470 atoms, 10530 bonds, 632 residues, 1 model selected
> select clear
> select #1/B-C:415
40 atoms, 40 bonds, 2 residues, 1 model selected
> select #1/B-C:415-426
436 atoms, 444 bonds, 24 residues, 1 model selected
> ui tool show "Color Actions"
> color sel tomato
[Repeated 1 time(s)]
> select
> #1/B-C:5-10,39-44,64-68,93-97,124-130,136-139,163-165,471-477,483-491,498-503,514-518,522-527,534-539,546-550
2676 atoms, 2698 bonds, 160 residues, 1 model selected
> select clear
> select #1/B-C:518
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B-C:518-527
272 atoms, 270 bonds, 20 residues, 1 model selected
> select #1/B-C:532
30 atoms, 28 bonds, 2 residues, 1 model selected
> select #1/B-C:522-532
352 atoms, 352 bonds, 22 residues, 1 model selected
> select #1/B-C:521
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B-C:521-522
54 atoms, 52 bonds, 4 residues, 1 model selected
> select #1/B-C:521
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B-C:521-522
54 atoms, 52 bonds, 4 residues, 1 model selected
> select #1/B-C:518
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B-C:518-532
438 atoms, 438 bonds, 30 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light pink
> color sel light coral
> select
> #1/B-C:16-36,45-50,53-60,72-87,102-112,144-147,155-162,166-199,203-216,224-236,240-250,262-275,280-294,300-316,322-338,342-354,363-378,382-384,388-401,404-416,421-437,449-463,553-568
10470 atoms, 10530 bonds, 632 residues, 1 model selected
> select clear
> select #1/B-C:561
30 atoms, 28 bonds, 2 residues, 1 model selected
> select #1/B-C:561-571
338 atoms, 336 bonds, 22 residues, 1 model selected
> ui tool show "Color Actions"
> color sel thistle
> color sel light steel blue
> color sel light sky blue
> color sel old lace
> color sel misty rose
[Repeated 2 time(s)]
> color sel lavender blush
> color sel violet
> color sel plum
[Repeated 1 time(s)]
> color sel pink
> color sel plum
> color sel light steel blue
> select clear
> select
> #1/B-C:5-10,39-44,64-68,93-97,124-130,136-139,163-165,471-477,483-491,498-503,514-518,522-527,534-539,546-550
2676 atoms, 2698 bonds, 160 residues, 1 model selected
> select clear
> select #1/B-C:518
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B-C:518-532
438 atoms, 438 bonds, 30 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium violet red
> color sel crimson
> color sel light salmon
> color sel orange red
> select clear
> save "Z:/hASK1/ASK1-HDX-MS结果/HDX-MS dimer results/front-2.bmp" width 1981
> height 1220 supersample 3
> save "Z:/hASK1/ASK1-HDX-MS结果/HDX-MS dimer results/back-2.bmp" width 1981
> height 1220 supersample 3
> save "Z:/hASK1/ASK1-HDX-MS结果/HDX-MS dimer results/front-3.bmp" width 1981
> height 1220 supersample 3
> save "Z:/hASK1/ASK1-HDX-MS结果/HDX-MS dimer results/ASK1 DIMER-YH-DEMO.cxs"
——— End of log from Sun Mar 31 23:27:16 2024 ———
opened ChimeraX session
> select #1/B-C:531
30 atoms, 28 bonds, 2 residues, 1 model selected
> select #1/B-C:529-531
114 atoms, 114 bonds, 6 residues, 1 model selected
> show sel atoms
> ui mousemode right minimize
> ui mousemode right select
> select add #1
18360 atoms, 18560 bonds, 1142 residues, 3 models selected
> ui mousemode right minimize
> ui mousemode right tug
> ui mousemode right minimize
> hide sel atoms
> undo
> ui mousemode right swapaa
> style (#!1 & sel) stick
Changed 18360 atom styles
> style (#!1 & sel) ringFill off
Changed 1142 residue ring styles
> select clear
> select #1/B-C:531-532
60 atoms, 58 bonds, 4 residues, 1 model selected
> select #1/B-C:530-532
100 atoms, 100 bonds, 6 residues, 1 model selected
> select #1/B-C:529
44 atoms, 42 bonds, 2 residues, 1 model selected
> select #1/B-C:529-531
114 atoms, 114 bonds, 6 residues, 1 model selected
> hide (#!1 & sel) target a
> show (#!1 & sel-residues & sidechain) target ab
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> undo
[Repeated 1 time(s)]
> show sel atoms
> hide #* target a
> show (#!1 & sel) target ab
> show (#!1 & sel-residues & sidechain) target ab
> style (#!1 & sel) ball
Changed 114 atom styles
> style (#!1 & sel) sphere
Changed 114 atom styles
> style (#!1 & sel) stick
Changed 114 atom styles
> select H
9168 atoms, 1142 residues, 1 model selected
> delete hydrogen
Missing or invalid "atoms" argument: invalid atoms specifier
> hide sel atoms
> select clear
> select #1/B-C:529
44 atoms, 42 bonds, 2 residues, 1 model selected
> select #1/B-C:529-531
114 atoms, 114 bonds, 6 residues, 1 model selected
> color (#!1 & sel) byhetero
> swapaa mousemode #1/B:529 GLU
> undo
Undo failed, probably because structures have been modified.
> select add #1
18353 atoms, 18553 bonds, 1142 residues, 3 models selected
> select H
9161 atoms, 1142 residues, 1 model selected
> hide sel atoms
> swapaa mousemode #1/B:57 TRP
> hide sel atoms
> select H
9167 atoms, 1142 residues, 1 model selected
> hide sel atoms
> open 75SH
Fetching url http://files.rcsb.org/download/75sh.cif failed:
HTTP Error 404: Not Found
> select clear
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660d5d3c5e975745/test_7b510_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
test_7b510_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #4
---
Chain | Description
A | No description available
B | No description available
> hide #!1 models
> hide #!2 models
> hide #!3 models
> swapaa mousemode #4/B:416 LEU
> color #4 bychain
> view clip false
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660d5d865e9875e4/test_7b510_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
test_7b510_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb #5
---
Chain | Description
A | No description available
B | No description available
> hide #4 models
> color #5 bychain
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660d5df85e9a340f/test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb #6
---
Chain | Description
A | No description available
B | No description available
> hide #5 models
> color #6 bychain
> show #!1 models
> ui tool show Matchmaker
> matchmaker #6 to #1/C pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain C (#1) with
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#6), sequence alignment score = 2831.9
RMSD between 486 pruned atom pairs is 1.117 angstroms; (across all 571 pairs:
1.769)
> view #1 clip false
> hide #6 models
> show #6 models
> hide #!1 models
> hide #6 models
> show #6 models
> hide #6 models
> show #!1 models
> hide #!1 models
> show #6 models
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660d5f165e9e90d2/test_7b510_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
test_7b510_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb #7
---
Chain | Description
A | No description available
B | No description available
> hide #6 models
> view #6 clip false
No displayed objects specified.
> view #7 clip false
> color #7 bychain
> show #7 surfaces
> show #!1 models
> hide #!7 models
> show #!1 surfaces
> show target m
> hide #!2 models
> hide #!3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #!7 models
> view #4 clip false
> view #1 clip false
> hide #!1 models
> show #!7 models
> view #7 clip false
> swapaa mousemode #7/A:523 ASP
> swapaa mousemode #7/A:594 ILE
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660d5fb25ea0f31c/test_7b510_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_000.pdb
Chain information for
test_7b510_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_000.pdb #8
---
Chain | Description
A | No description available
B | No description available
> hide #!7 models
> color #8 bychain
> hide #8 models
> show #!7 models
> show #!1 models
> hide #!1 models
> transparency #7 70
> hide #!7 models
> show #!1 models
> view #1 clip false
> hide #!1 models
> show #!7 models
> view #7 clip false
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660e9bd36373d1f1/test_85b81_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
test_85b81_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #9
---
Chain | Description
A | No description available
B | No description available
> hide #!7 models
> color #9 bychain
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660e9bf263744dc8/test_85b81_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
test_85b81_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb #10
---
Chain | Description
A | No description available
B | No description available
> hide #9 models
> color #10 bychain
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660e9c1f6374fdce/test_85b81_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
test_85b81_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb #11
---
Chain | Description
A | No description available
B | No description available
> hide #10 models
> color #11 bychain
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660e9c6463760c21/test_85b81_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb
Chain information for
test_85b81_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb #12
---
Chain | Description
A | No description available
B | No description available
> hide #11 models
> color #12 bychain
> hide #12 models
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660e9c926376bca5/test_85b81_unrelaxed_rank_005_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
test_85b81_unrelaxed_rank_005_alphafold2_multimer_v3_model_4_seed_000.pdb #13
---
Chain | Description
A | No description available
B | No description available
> color #13 bychain
> hide #13 models
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660ea193638a4b7b/hASK1vsTrx_c99da_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
hASK1vsTrx_c99da_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#14
---
Chain | Description
A | No description available
B | No description available
> color #14 bychain
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660ea1c8638b18ae/hASK1vsTrx_c99da_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
hASK1vsTrx_c99da_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb
#15
---
Chain | Description
A | No description available
B | No description available
> hide #14 models
> color #15 bychain
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660ea1e4638b87d3/hASK1vsTrx_c99da_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb
Chain information for
hASK1vsTrx_c99da_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb
#16
---
Chain | Description
A | No description available
B | No description available
> hide #15 models
> color #16 bychain
> hide #16 models
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660ea1ff638beff4/hASK1vsTrx_c99da_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
hASK1vsTrx_c99da_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb
#17
---
Chain | Description
A | No description available
B | No description available
> color #17 bychain
> show #17 surfaces
> hide #!17 surfaces
> open
> C:/Users/User/AppData/Local/Temp/BNZ.660ea227638c8a40/hASK1vsTrx_c99da_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
hASK1vsTrx_c99da_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb
#18
---
Chain | Description
A | No description available
B | No description available
> hide #!17 models
> show #18 surfaces
> color #!18 bychain
> show #!17 models
> hide #!18 models
> color #!17 bychain
> show #!17 surfaces
> hide #!17 models
> show #16 models
> show #16 surfaces
> hide #!16 models
> show #15 models
> show #15 surfaces
> hide #!15 surfaces
> hide #!15 models
> show #14 models
> show #14 surfaces
> hide #!14 surfaces
> hide #!14 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 surfaces
> select add #17
2557 atoms, 2610 bonds, 337 residues, 1 model selected
Alignment identifier is 17/A
Alignment identifier is 17/B
> select #17/B:69
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #17/B:67-69
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #17/B:37-38
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #17/B:37-38
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #17/B:33
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #17/B:33-38
45 atoms, 44 bonds, 6 residues, 1 model selected
> select #17/B:68
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #17/B:3-68
527 atoms, 537 bonds, 66 residues, 1 model selected
> select #17/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #17/B
550 atoms, 560 bonds, 69 residues, 1 model selected
> select #17/B:69
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #17/B
550 atoms, 560 bonds, 69 residues, 1 model selected
> hide #!17 models
> show #6 models
> swapaa mousemode #6/B:116 ASN
[Repeated 1 time(s)]
> swapaa mousemode #6/B:113 CYS
> swapaa mousemode #6/B:114 GLN
[Repeated 1 time(s)]
> swapaa mousemode #6/B:106 GLN
> view #17 clip false
No displayed objects specified.
> view #6 clip false
> show #6 surfaces
> hide #!6 surfaces
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> view #7 clip false
> transparency #7 0
> show #!6 models
> show #!6-7 surfaces
> hide #!7 models
> view #6 clip false
> open
> C:/Users/User/AppData/Local/Temp/BNZ.661007cd69019bd8/test_4f524_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
test_4f524_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #19
---
Chain | Description
A | No description available
B | No description available
> hide #!6 models
> view #19 clip false
> color #19 bychain
> open
> C:/Users/User/AppData/Local/Temp/BNZ.661007e66901fe3c/test_4f524_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
test_4f524_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb #20
---
Chain | Description
A | No description available
B | No description available
> hide #19 models
> color #20 bychain
> hide #20 models
> open
> C:/Users/User/AppData/Local/Temp/BNZ.661007ff69025e9c/test_4f524_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb
Chain information for
test_4f524_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb #21
---
Chain | Description
A | No description available
B | No description available
> color #21 bychain
> select add #17
2557 atoms, 2610 bonds, 337 residues, 2 models selected
> select subtract #17
2 models selected
> open
> C:/Users/User/AppData/Local/Temp/BNZ.6610081b6902cb40/test_4f524_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
test_4f524_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb #22
---
Chain | Description
A | No description available
B | No description available
> hide #21 models
> color #22 bypolymer
> color #22 bychain
> color #22 bypolymer
> color #22 bychain
> hide #22 models
> open
> C:/Users/User/AppData/Local/Temp/BNZ.661008326903273b/test_4f524_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
test_4f524_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb #23
---
Chain | Description
A | No description available
B | No description available
> hide #23 models
> show #!6 models
> view #6 clip false
> swapaa mousemode #6/A:523 LEU
> hide #!6 models
> show #!7 models
> view #7 clip false
> hide #!7 models
> open
> C:/Users/User/AppData/Local/Temp/BNZ.661292d572f0aef2/test_ccf3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
test_ccf3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #24
---
Chain | Description
A | No description available
B | No description available
> color #24 bychain
> show #24 surfaces
> hide #!24 surfaces
> select add #24
2827 atoms, 2885 bonds, 373 residues, 1 model selected
Alignment identifier is 24/A
Alignment identifier is 24/B
> select #24/B:32
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #24/B:32-35
23 atoms, 23 bonds, 4 residues, 1 model selected
> open
> C:/Users/User/AppData/Local/Temp/BNZ.6612931d72f1c91c/test_ccf3d_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
test_ccf3d_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb #25
---
Chain | Description
A | No description available
B | No description available
> hide #!24 models
> color #25 bychain
> show #25 surfaces
> hide #!25 surfaces
> select #24/B:32
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #24/B:32-35
23 atoms, 23 bonds, 4 residues, 1 model selected
> select #24/B:35-36
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #24/B:32-36
32 atoms, 32 bonds, 5 residues, 1 model selected
> show #!24 models
> hide #!25 models
> hide #!24 models
> open
> C:/Users/User/AppData/Local/Temp/BNZ.6612935672f2a582/test_ccf3d_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
test_ccf3d_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb #26
---
Chain | Description
A | No description available
B | No description available
> color #26 bychain
> open
> C:/Users/User/AppData/Local/Temp/BNZ.6612936972f2ef3d/test_ccf3d_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
test_ccf3d_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb #27
---
Chain | Description
A | No description available
B | No description available
> hide #26 models
> color #27 bychain
> show #27 surfaces
> hide #!27 surfaces
> hide #!27 models
> show #!27 models
> open
> C:/Users/User/AppData/Local/Temp/BNZ.6612939a72f3b0b8/test_ccf3d_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_000.pdb
Chain information for
test_ccf3d_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_000.pdb #28
---
Chain | Description
A | No description available
B | No description available
> select add #24
2827 atoms, 2885 bonds, 373 residues, 2 models selected
> select subtract #24
2 models selected
> hide #!27 models
> view #28 clip false
> color #28 bychain
> show #28 surfaces
> hide #!28 surfaces
> hide #!28 models
> show #!27 models
> show #!27 surfaces
> hide #!27 surfaces
> show #!28 models
> hide #!28 models
> hide #!27 models
> show #26 models
> hide #26 models
> show #!25 models
> select #24/B:32
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #24/B:32-35
23 atoms, 23 bonds, 4 residues, 1 model selected
Destroying pre-existing alignment with identifier 24/B
Alignment identifier is 24/B
> select #24/B:8-18,33-48,63-68,94-104
342 atoms, 344 bonds, 44 residues, 1 model selected
> select #24/B:32
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #24/B:32-36
32 atoms, 32 bonds, 5 residues, 1 model selected
> select #17/B:35
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #17/B:35-39
37 atoms, 37 bonds, 5 residues, 1 model selected
> show #!25 surfaces
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 surfaces
> select #17/A:85
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #17/A:85-90
40 atoms, 39 bonds, 6 residues, 1 model selected
> hide #!25 models
> show #!24 models
> show #!24 surfaces
> hide #!24 surfaces
> hide #!24 models
> show #!25 models
> show #!25 surfaces
> hide #!25 surfaces
> select #17/A:85
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #17/A:85-90
40 atoms, 39 bonds, 6 residues, 1 model selected
Alignment identifier is 17/A
> select #17/A:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> undo
> select #17/A:6-8
21 atoms, 20 bonds, 3 residues, 1 model selected
> select #17/A:3-8
42 atoms, 41 bonds, 6 residues, 1 model selected
> select add #25
2869 atoms, 2926 bonds, 379 residues, 3 models selected
Alignment identifier is 1
Alignment identifier is 25/B
> select #25/B:32
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/B:32-35
23 atoms, 23 bonds, 4 residues, 1 model selected
> show sel atoms
> show #!1 models
> hide sel surfaces
> select add #1
18388 atoms, 18590 bonds, 1146 residues, 3 models selected
> hide sel surfaces
> ui tool show Matchmaker
> matchmaker #!25 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with
test_ccf3d_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#25), sequence alignment score = 859.1
RMSD between 172 pruned atom pairs is 0.649 angstroms; (across all 181 pairs:
1.809)
> view #25 clip false
> select clear
> select add #1
18365 atoms, 18567 bonds, 1142 residues, 1 model selected
> show sel surfaces
> select subtract #1
2 models selected
> select add #1
18365 atoms, 18567 bonds, 1142 residues, 1 model selected
> select subtract #1
2 models selected
> select add #1
18365 atoms, 18567 bonds, 1142 residues, 1 model selected
> hide sel surfaces
> select #17/A:83 #25/A:83
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #17/A:83-90 #25/A:83-90
106 atoms, 104 bonds, 16 residues, 2 models selected
1 [ID: 1] region 2 chains [83-90] RMSD: 107.517
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!6 models
> hide #!6 models
> hide #!1 models
> show #5 models
> hide #5 models
> show #5 models
> view #5 clip false
> show #4 models
> hide #5 models
> hide #4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide sel & #!25 surfaces
[Repeated 1 time(s)]
> select add #7
9592 atoms, 9798 bonds, 1206 residues, 5 models selected
> hide sel & #!7,25 surfaces
> hide #!7 models
> select subtract #7
106 atoms, 104 bonds, 16 residues, 6 models selected
> close #4-5#6
> show #!7 models
> hide #!7 models
> show #8 models
> close #8
> show #!7 models
> log metadata #7
No models had metadata
> log chains #7
Chain information for
test_7b510_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb #7
---
Chain | Description
A | No description available
B | No description available
> select add #7
9592 atoms, 9798 bonds, 1206 residues, 5 models selected
> log metadata #7
No models had metadata
> log chains #7
Chain information for
test_7b510_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb #7
---
Chain | Description
A | No description available
B | No description available
> select clear
> ui tool show Matchmaker
> matchmaker #!25 to #7/A pairing bs
Parameters
---
Chain pairing | bs
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
test_7b510_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#7) with
test_ccf3d_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#25), sequence alignment score = 1241.7
RMSD between 16 pruned atom pairs is 1.295 angstroms; (across all 264 pairs:
18.161)
> matchmaker #!25 to #7/B pairing bs
Parameters
---
Chain pairing | bs
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
test_7b510_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain B (#7) with
test_ccf3d_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#25), sequence alignment score = 941.7
RMSD between 179 pruned atom pairs is 0.584 angstroms; (across all 181 pairs:
0.622)
> show #9 models
> hide #9 models
> hide #!7 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #!7 models
> open
> C:/Users/User/AppData/Local/Temp/BNZ.661299df730c2de3/test_7b510_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
test_7b510_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #4
---
Chain | Description
A | No description available
B | No description available
> hide #!25 models
> hide #!7 models
> hide #4 models
> show #!28 models
> hide #!28 models
> show #4 models
> color #4 bychain
> select add #4
9490 atoms, 9699 bonds, 1190 residues, 1 model selected
> close #4
> open
> C:/Users/User/AppData/Local/Temp/BNZ.66129a11730cf133/test_7b510_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
test_7b510_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb #4
---
Chain | Description
A | No description available
B | No description available
> color #4 bychain
> select add #4
9490 atoms, 9699 bonds, 1190 residues, 1 model selected
> select subtract #4
Nothing selected
> hide #4 models
> open
> C:/Users/User/AppData/Local/Temp/BNZ.66129a45730dbcc0/test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb #5
---
Chain | Description
A | No description available
B | No description available
> color #5 bychain
> show #26 models
> hide #26 models
> show #!27 models
> hide #!27 models
> show #!25 models
> hide #5 models
> show #!7 models
> select #25/B:32
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/B:32-35
23 atoms, 23 bonds, 4 residues, 1 model selected
> show #!1 models
> hide #!25 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> view #1 clip false
> hide #!1 models
> show #4 models
> view #4 clip false
> hide #4 models
> show #5 models
> show #5 surfaces
> hide #!5 surfaces
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!5 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5), sequence alignment score = 2822.1
RMSD between 488 pruned atom pairs is 1.116 angstroms; (across all 571 pairs:
1.758)
> matchmaker #!5 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5), sequence alignment score = 2822.1
RMSD between 488 pruned atom pairs is 1.116 angstroms; (across all 571 pairs:
1.758)
> view clip false
> show #!25 models
> select #25/B:31
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #25/B:31-35
37 atoms, 39 bonds, 5 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!25 to #1/C pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain C (#1) with
test_ccf3d_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#25), sequence alignment score = 866.1
RMSD between 172 pruned atom pairs is 0.643 angstroms; (across all 181 pairs:
1.808)
> matchmaker #!25 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with
test_ccf3d_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#25), sequence alignment score = 859.1
RMSD between 172 pruned atom pairs is 0.649 angstroms; (across all 181 pairs:
1.809)
> matchmaker #!25 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with
test_ccf3d_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#25), sequence alignment score = 859.1
RMSD between 172 pruned atom pairs is 0.649 angstroms; (across all 181 pairs:
1.809)
> select add #25
2827 atoms, 2885 bonds, 373 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select #25/A
2007 atoms, 2050 bonds, 268 residues, 1 model selected
> hide #!25 models
> select add #25
2827 atoms, 2885 bonds, 373 residues, 2 models selected
> close #19-23#24
> hide #!5 models
> show #!18 models
> hide #!18 models
> close #14-17
> select subtract #25
2 models selected
> show #!25 models
> hide #!25 models
> show #!25 models
> ui tool show Matchmaker
> select #25/B
820 atoms, 835 bonds, 105 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select clear
> select #25/B:31
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #25/B:31-35
37 atoms, 39 bonds, 5 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select add #25
2827 atoms, 2885 bonds, 373 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select clear
> select #25/A:83
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:83-91
60 atoms, 59 bonds, 9 residues, 1 model selected
> view #25 clip false
> swapaa mousemode #25/A:90 VAL
> undo
> hide #!1 models
> show sel surfaces
> undo
> select add #25
2823 atoms, 2881 bonds, 373 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select clear
> select #25/A:250
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:249-250
14 atoms, 13 bonds, 2 residues, 1 model selected
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> select add #25
2823 atoms, 2881 bonds, 373 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select clear
> select #25/B:8-18,33-48,63-68,94-104
342 atoms, 344 bonds, 44 residues, 1 model selected
> select #25/B:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/B:35-36
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #25/B:35-36
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #25/B:35-40
47 atoms, 47 bonds, 6 residues, 1 model selected
> select #25/B:31
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #25/B:27-31
43 atoms, 45 bonds, 5 residues, 1 model selected
> show sel atoms
> select #25/B:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/B:32-35
23 atoms, 23 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> select #25/A:247-248
11 atoms, 11 bonds, 2 residues, 1 model selected
> select #25/A:247-252
40 atoms, 41 bonds, 6 residues, 1 model selected
> show sel cartoons
> show sel atoms
> color (#!25 & sel) byhetero
> select #25/A:214-215
19 atoms, 20 bonds, 2 residues, 1 model selected
> select #25/A:214-219
49 atoms, 51 bonds, 6 residues, 1 model selected
> select #25/A:221
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #25/A:221-223
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #25/A:221
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #25/A:221
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #25/A:222
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:222-224
28 atoms, 28 bonds, 3 residues, 1 model selected
> select #25/A:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #25/A:227-268
325 atoms, 330 bonds, 42 residues, 1 model selected
> select #25/A:228
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:227-228
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #25/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:128-130
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #25/B:71
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #25/B:71-72
16 atoms, 15 bonds, 2 residues, 1 model selected
> hide #!25 models
> select add #25
2823 atoms, 2881 bonds, 373 residues, 2 models selected
> show #!18 models
> view clip false
> hide #!18 surfaces
> hide #!18 models
> select subtract #25
2 models selected
> show #13 models
> hide #13 models
> show #!25 models
> view #13 clip false
No displayed objects specified.
> view #25 clip false
> show #26 models
> hide #26 models
> show #26 models
> hide #!25 models
> view #26 clip false
> hide #26 models
> show #!27 models
> show #!28 models
> hide #!27 models
> hide #!28 models
> show #!25 models
> view #25 clip false
> show #!25 surfaces
> hide #!25 surfaces
> select #25/A:250
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:251
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #25/A:251
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #25
2823 atoms, 2881 bonds, 373 residues, 2 models selected
> show sel surfaces
> show #!1 models
> show sel surfaces
> select add #1
21188 atoms, 21448 bonds, 1515 residues, 4 models selected
> show sel surfaces
> hide #18.2 models
> hide #18.1 models
> hide #!25 models
> select subtract #25
18365 atoms, 18567 bonds, 1142 residues, 5 models selected
> hide #25.1 models
> hide #25.2 models
> select add #25.1
20368 atoms, 18567 bonds, 1410 residues, 4 models selected
> select subtract #25.1
18365 atoms, 18567 bonds, 1142 residues, 4 models selected
> select add #25.2
19185 atoms, 18567 bonds, 1247 residues, 4 models selected
> show #!25 models
> hide #!25 models
> show #25.2 models
> view #25.2 clip false
> ui tool show AlphaFold
> alphafold predict #1/B
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> alphafold predict #1/B
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> alphafold predict #1/B
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> alphafold predict #1/B
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> alphafold predict #1/B
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> alphafold predict #1/B
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> hide #!1 models
> select clear
> hide #25.2 models
> show #25.2 models
> hide #25.2 models
> select add #25.2
820 atoms, 105 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
test_ccf3d_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb_B
SES surface #25.2: minimum, -18.46, mean -2.55, maximum 6.85
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select #25/A:86
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #25/A:86
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #25/A:83
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:83-91
56 atoms, 55 bonds, 9 residues, 1 model selected
> select
> #25/A:104-123,132-137,140-148,159-161,163-175,189-205,228-237,240-244,253-267
787 atoms, 792 bonds, 98 residues, 1 model selected
> select #25/A:174
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:174
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/B:47
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/B:9-47
298 atoms, 306 bonds, 39 residues, 1 model selected
> select clear
> select #25/A:83
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:83-91
56 atoms, 55 bonds, 9 residues, 1 model selected
> show sel atoms
> select add #25.2
876 atoms, 55 bonds, 114 residues, 2 models selected
> select subtract #25.2
56 atoms, 55 bonds, 9 residues, 3 models selected
> select add #25.2
876 atoms, 55 bonds, 114 residues, 2 models selected
> select subtract #25.2
56 atoms, 55 bonds, 9 residues, 3 models selected
> select add #25.2
876 atoms, 55 bonds, 114 residues, 2 models selected
> select subtract #25.2
56 atoms, 55 bonds, 9 residues, 3 models selected
> select subtract #25.1
1 model selected
> select add #25.1
2003 atoms, 268 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
test_ccf3d_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb_A
SES surface #25.1: minimum, -16.49, mean -2.56, maximum 11.28
To also show corresponding color key, enter the above coulombic command and
add key true
> swapaa mousemode #25/B:53 GLN
> undo
> swapaa mousemode #25/A:170 CYS
> hide sel surfaces
> select #25/A:141
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #25/A:140-141
14 atoms, 13 bonds, 2 residues, 1 model selected
> show #!1 models
> hide sel surfaces
> select add #1
18379 atoms, 18580 bonds, 1144 residues, 3 models selected
> hide sel surfaces
> select clear
> open
> C:/Users/User/AppData/Local/Temp/BNZ.66153a2d7d4e5c8f/3MutsDimer_35860_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
3MutsDimer_35860_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #6
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #6 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with
3MutsDimer_35860_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain
A (#6), sequence alignment score = 2817.1
RMSD between 359 pruned atom pairs is 0.756 angstroms; (across all 570 pairs:
28.047)
> open
> C:/Users/User/AppData/Local/Temp/BNZ.66153a8d7d4fd5d1/3MutsDimer_35860_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
3MutsDimer_35860_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb #8
---
Chain | Description
A | No description available
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #8 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with
3MutsDimer_35860_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb, chain
A (#8), sequence alignment score = 2824.9
RMSD between 362 pruned atom pairs is 0.696 angstroms; (across all 570 pairs:
27.736)
> matchmaker #8 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with
3MutsDimer_35860_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb, chain
A (#8), sequence alignment score = 2824.9
RMSD between 362 pruned atom pairs is 0.696 angstroms; (across all 570 pairs:
27.736)
> view clip false
> open
> C:/Users/User/AppData/Local/Temp/BNZ.66153b007d51945a/3MutsDimer_35860_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
3MutsDimer_35860_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb #14
---
Chain | Description
A | No description available
> color #14 #ffaaffff
> ui tool show Matchmaker
> matchmaker #14 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with
3MutsDimer_35860_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb, chain
A (#14), sequence alignment score = 2809.9
RMSD between 370 pruned atom pairs is 0.967 angstroms; (across all 570 pairs:
5.062)
> open
> C:/Users/User/AppData/Local/Temp/BNZ.66153b697d532fab/3MutsDimer_35860_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb
Chain information for
3MutsDimer_35860_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb #15
---
Chain | Description
A | No description available
> open
> C:/Users/User/AppData/Local/Temp/BNZ.66153b6e7d5342d5/3MutsDimer_35860_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
3MutsDimer_35860_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb #16
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #15-16 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with
3MutsDimer_35860_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb, chain
A (#15), sequence alignment score = 2811.1
RMSD between 360 pruned atom pairs is 0.741 angstroms; (across all 570 pairs:
28.073)
Matchmaker ASK1-demo.pdb, chain B (#1) with
3MutsDimer_35860_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb, chain
A (#16), sequence alignment score = 2806.3
RMSD between 389 pruned atom pairs is 0.665 angstroms; (across all 570 pairs:
3.643)
> matchmaker #15-16 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with
3MutsDimer_35860_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb, chain
A (#15), sequence alignment score = 2811.1
RMSD between 360 pruned atom pairs is 0.741 angstroms; (across all 570 pairs:
28.073)
Matchmaker ASK1-demo.pdb, chain B (#1) with
3MutsDimer_35860_unrelaxed_rank_005_alphafold2_ptm_model_2_seed_000.pdb, chain
A (#16), sequence alignment score = 2806.3
RMSD between 389 pruned atom pairs is 0.665 angstroms; (across all 570 pairs:
3.643)
> color #15 #0055ffff
> color #15 cyan
> color #15 #aaaaffff
> color #15 cyan
> select add #15
4577 atoms, 4673 bonds, 570 residues, 1 model selected
> select subtract #15
Nothing selected
> select add #16
4577 atoms, 4673 bonds, 570 residues, 1 model selected
> select subtract #16
Nothing selected
> select add #16
4577 atoms, 4673 bonds, 570 residues, 1 model selected
> select subtract #16
Nothing selected
> select add #6
4577 atoms, 4673 bonds, 570 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
4577 atoms, 4673 bonds, 570 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
4577 atoms, 4673 bonds, 570 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #1
18365 atoms, 18567 bonds, 1142 residues, 1 model selected
> select subtract #1
2 models selected
> select add #1
18365 atoms, 18567 bonds, 1142 residues, 1 model selected
> select subtract #1
2 models selected
> select add #16
4577 atoms, 4673 bonds, 570 residues, 1 model selected
> select add #14
9154 atoms, 9346 bonds, 1140 residues, 2 models selected
> hide #!25 models
> hide #!1 models
> show #!1 models
> open "C:/Users/User/Downloads/AF-Q99683-F1-model_v4 (2).pdb"
AF-Q99683-F1-model_v4 (2).pdb title:
Alphafold monomer V2.0 prediction for mitogen-activated protein kinase kinase
kinase 5 (Q99683) [more info...]
Chain information for AF-Q99683-F1-model_v4 (2).pdb #17
---
Chain | Description | UniProt
A | mitogen-activated protein kinase kinase kinase 5 | M3K5_HUMAN 1-1374
> ui tool show Matchmaker
> matchmaker #17 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with AF-Q99683-F1-model_v4 (2).pdb,
chain A (#17), sequence alignment score = 2832.3
RMSD between 389 pruned atom pairs is 0.461 angstroms; (across all 571 pairs:
5.780)
> matchmaker #17 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with AF-Q99683-F1-model_v4 (2).pdb,
chain A (#17), sequence alignment score = 2832.3
RMSD between 389 pruned atom pairs is 0.461 angstroms; (across all 571 pairs:
5.780)
> view clip false
> color #1 #aaaa00ff
> color #1 #aaaaffff
> select clear
> view #1 clip false
[Repeated 1 time(s)]
> hide #17 models
> select add #15
4577 atoms, 4673 bonds, 570 residues, 1 model selected
> color #6 #aa0000ff
> select clear
> show #!25 models
> select add #25
2826 atoms, 2884 bonds, 373 residues, 1 model selected
> hide sel surfaces
> select clear
> swapaa mousemode #16/A:37 HIS
> swapaa mousemode #14/A:172 HIS
> swapaa mousemode #14/A:32 CYS
> ui mousemode right "move picked models"
> ui mousemode right translate
> hide #6 models
> hide #8 models
> hide #14 models
> hide #15 models
> hide #16 models
> select #25/B:33
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #25/B:33
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #25/B:31
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #25/B:31-35
37 atoms, 39 bonds, 5 residues, 1 model selected
> show sel atoms
> select #25/A:250
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:250
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:226
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:225-226
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> select #25/A:250
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:250
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #25/A:104-105
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #25/A:104-120
127 atoms, 126 bonds, 17 residues, 1 model selected
> select #25/A:92
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #25/A:92-99
63 atoms, 63 bonds, 8 residues, 1 model selected
> select #25/A:163-164
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #25/A:163-164
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #25/A:185
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:185
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:206
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:206
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:207
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #25/A:207-210
31 atoms, 31 bonds, 4 residues, 1 model selected
> select #25/A:206
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:200-206
53 atoms, 52 bonds, 7 residues, 1 model selected
> show sel atoms
> color (#!25 & sel) byhetero
> show #15 models
> hide #15 models
> show #6 models
> select add #6
4630 atoms, 4725 bonds, 577 residues, 3 models selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
[Repeated 1 time(s)]
> transparency (#!6,25 & sel) 60
> hide sel surfaces
> select #25/A:78
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #25/A:78-91
92 atoms, 91 bonds, 14 residues, 1 model selected
> show sel atoms
> color (#!25 & sel) byhetero
> hide #!25 models
> hide #25.1 models
> hide #25.2 models
> hide #!6 models
> hide #!1 models
> show #!6 models
> color #!6 bychain
> coulombic #!6
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
3MutsDimer_35860_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb_A SES
surface #6.1: minimum, -18.47, mean -2.35, maximum 17.12
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!25 target m
> view #6 clip false
> hide #!6 models
> select subtract #25.1
1 model selected
> hide #!25 models
> show #!25 models
> open
> C:/Users/User/AppData/Local/Temp/BNZ.6617e10b87aa2fde/test_a73c1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
test_a73c1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #19
---
Chain | Description
A | No description available
> hide #!25 models
> color #19 bychain
> view clip false
> open "D:/ASK1
> alphafold/88-658/W476S/test_a73c1/test_a73c1_unrelaxed_rank_002_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
test_a73c1_unrelaxed_rank_002_alphafold2_ptm_model_3_seed_000.pdb #20
---
Chain | Description
A | No description available
> open "D:/ASK1
> alphafold/88-658/W476S/test_a73c1/test_a73c1_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
test_a73c1_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb #21
---
Chain | Description
A | No description available
> open "D:/ASK1
> alphafold/88-658/W476S/test_a73c1/test_a73c1_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
test_a73c1_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb #22
---
Chain | Description
A | No description available
> open "D:/ASK1
> alphafold/88-658/W476S/test_a73c1/test_a73c1_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb"
Chain information for
test_a73c1_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb #23
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #20-23 to #19/A pairing bs
Parameters
---
Chain pairing | bs
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 test_a73c1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#19) with
test_a73c1_unrelaxed_rank_002_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#20), sequence alignment score = 2957.8
RMSD between 561 pruned atom pairs is 0.722 angstroms; (across all 571 pairs:
0.824)
Matchmaker test_a73c1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#19) with
test_a73c1_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#21), sequence alignment score = 2913.4
RMSD between 338 pruned atom pairs is 0.840 angstroms; (across all 571 pairs:
29.477)
Matchmaker test_a73c1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#19) with
test_a73c1_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#22), sequence alignment score = 2913.4
RMSD between 369 pruned atom pairs is 0.547 angstroms; (across all 571 pairs:
28.612)
Matchmaker test_a73c1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#19) with
test_a73c1_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#23), sequence alignment score = 2956.6
RMSD between 520 pruned atom pairs is 0.872 angstroms; (across all 571 pairs:
1.186)
> hide #23 models
> show #23 models
> hide #22 models
> show #22 models
> hide #22 models
> hide #21 models
> show #4 models
> hide #4 models
> show #!5 models
> ui tool show Matchmaker
> matchmaker #4 to #19/A pairing bs
Parameters
---
Chain pairing | bs
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 test_a73c1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#19) with
test_7b510_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#4), sequence alignment score = 2915.1
RMSD between 341 pruned atom pairs is 0.525 angstroms; (across all 571 pairs:
25.842)
> matchmaker #!5 to #19/A pairing bs
Parameters
---
Chain pairing | bs
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 test_a73c1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#19) with
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5), sequence alignment score = 2916.9
RMSD between 364 pruned atom pairs is 0.696 angstroms; (across all 571 pairs:
26.597)
> show #21 models
> show #22 models
> hide #22 models
> show #22 models
> open "D:/ASK1 alphafold/88-658/WT/test_2c303/WT-1-88-658.pdb"
Chain information for WT-1-88-658.pdb #24
---
Chain | Description
A | No description available
> open "D:/ASK1 alphafold/88-658/WT/test_2c303/WT-2-88-658.pdb"
Chain information for WT-2-88-658.pdb #29
---
Chain | Description
A | No description available
> open "D:/ASK1 alphafold/88-658/WT/test_2c303/WT-4-88-658.pdb"
Chain information for WT-4-88-658.pdb #30
---
Chain | Description
A | No description available
> open "D:/ASK1 alphafold/88-658/WT/test_2c303/WT-5-88-658.pdb"
Chain information for WT-5-88-658.pdb #31
---
Chain | Description
A | No description available
> open "D:/ASK1 alphafold/88-658/WT/test_2c303/WT-3-88-658.pdb"
Chain information for WT-3-88-658.pdb #32
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #24,29-32 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain B (#1) with WT-1-88-658.pdb, chain A (#24),
sequence alignment score = 2828.1
RMSD between 361 pruned atom pairs is 0.715 angstroms; (across all 571 pairs:
27.778)
Matchmaker ASK1-demo.pdb, chain B (#1) with WT-2-88-658.pdb, chain A (#29),
sequence alignment score = 2823.9
RMSD between 364 pruned atom pairs is 0.675 angstroms; (across all 571 pairs:
27.545)
Matchmaker ASK1-demo.pdb, chain B (#1) with WT-4-88-658.pdb, chain A (#30),
sequence alignment score = 2835.9
RMSD between 387 pruned atom pairs is 0.681 angstroms; (across all 571 pairs:
4.004)
Matchmaker ASK1-demo.pdb, chain B (#1) with WT-5-88-658.pdb, chain A (#31),
sequence alignment score = 2829.3
RMSD between 378 pruned atom pairs is 0.692 angstroms; (across all 571 pairs:
4.864)
Matchmaker ASK1-demo.pdb, chain B (#1) with WT-3-88-658.pdb, chain A (#32),
sequence alignment score = 2829.9
RMSD between 293 pruned atom pairs is 0.844 angstroms; (across all 571 pairs:
6.204)
> matchmaker #24,29-32 to #1/C pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-demo.pdb, chain C (#1) with WT-1-88-658.pdb, chain A (#24),
sequence alignment score = 2837.9
RMSD between 361 pruned atom pairs is 0.714 angstroms; (across all 571 pairs:
27.791)
Matchmaker ASK1-demo.pdb, chain C (#1) with WT-2-88-658.pdb, chain A (#29),
sequence alignment score = 2833.7
RMSD between 363 pruned atom pairs is 0.668 angstroms; (across all 571 pairs:
27.560)
Matchmaker ASK1-demo.pdb, chain C (#1) with WT-4-88-658.pdb, chain A (#30),
sequence alignment score = 2845.7
RMSD between 388 pruned atom pairs is 0.687 angstroms; (across all 571 pairs:
3.988)
Matchmaker ASK1-demo.pdb, chain C (#1) with WT-5-88-658.pdb, chain A (#31),
sequence alignment score = 2839.1
RMSD between 378 pruned atom pairs is 0.694 angstroms; (across all 571 pairs:
4.841)
Matchmaker ASK1-demo.pdb, chain C (#1) with WT-3-88-658.pdb, chain A (#32),
sequence alignment score = 2839.7
RMSD between 295 pruned atom pairs is 0.847 angstroms; (across all 571 pairs:
6.202)
> matchmaker #24,29-32 to #5/A pairing bs
Parameters
---
Chain pairing | bs
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
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#5) with WT-1-88-658.pdb, chain A (#24), sequence alignment score =
2507.7
RMSD between 273 pruned atom pairs is 0.912 angstroms; (across all 529 pairs:
29.425)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#5) with WT-2-88-658.pdb, chain A (#29), sequence alignment score =
2470.5
RMSD between 278 pruned atom pairs is 0.931 angstroms; (across all 529 pairs:
28.771)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#5) with WT-4-88-658.pdb, chain A (#30), sequence alignment score =
2478.9
RMSD between 295 pruned atom pairs is 0.882 angstroms; (across all 529 pairs:
4.329)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#5) with WT-5-88-658.pdb, chain A (#31), sequence alignment score =
2493.3
RMSD between 281 pruned atom pairs is 0.908 angstroms; (across all 529 pairs:
5.657)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#5) with WT-3-88-658.pdb, chain A (#32), sequence alignment score =
2486.1
RMSD between 264 pruned atom pairs is 0.955 angstroms; (across all 529 pairs:
6.176)
> matchmaker #24,29-32 to #5/A pairing bs
Parameters
---
Chain pairing | bs
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
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#5) with WT-1-88-658.pdb, chain A (#24), sequence alignment score =
2507.7
RMSD between 273 pruned atom pairs is 0.912 angstroms; (across all 529 pairs:
29.425)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#5) with WT-2-88-658.pdb, chain A (#29), sequence alignment score =
2470.5
RMSD between 278 pruned atom pairs is 0.931 angstroms; (across all 529 pairs:
28.771)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#5) with WT-4-88-658.pdb, chain A (#30), sequence alignment score =
2478.9
RMSD between 295 pruned atom pairs is 0.882 angstroms; (across all 529 pairs:
4.329)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#5) with WT-5-88-658.pdb, chain A (#31), sequence alignment score =
2493.3
RMSD between 281 pruned atom pairs is 0.908 angstroms; (across all 529 pairs:
5.657)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#5) with WT-3-88-658.pdb, chain A (#32), sequence alignment score =
2486.1
RMSD between 264 pruned atom pairs is 0.955 angstroms; (across all 529 pairs:
6.176)
> color #29 #00aaffff
> ui tool show Matchmaker
> matchmaker #29-32 to #5/B pairing bs
Parameters
---
Chain pairing | bs
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
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with WT-2-88-658.pdb, chain A (#29), sequence alignment score =
2901.5
RMSD between 363 pruned atom pairs is 0.622 angstroms; (across all 571 pairs:
26.415)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with WT-4-88-658.pdb, chain A (#30), sequence alignment score =
2906.9
RMSD between 386 pruned atom pairs is 0.637 angstroms; (across all 571 pairs:
4.621)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with WT-5-88-658.pdb, chain A (#31), sequence alignment score =
2906.9
RMSD between 369 pruned atom pairs is 0.653 angstroms; (across all 571 pairs:
5.086)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with WT-3-88-658.pdb, chain A (#32), sequence alignment score =
2914.1
RMSD between 312 pruned atom pairs is 0.711 angstroms; (across all 571 pairs:
7.402)
> matchmaker #29-32 to #5/B pairing bs
Parameters
---
Chain pairing | bs
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
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with WT-2-88-658.pdb, chain A (#29), sequence alignment score =
2901.5
RMSD between 363 pruned atom pairs is 0.622 angstroms; (across all 571 pairs:
26.415)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with WT-4-88-658.pdb, chain A (#30), sequence alignment score =
2906.9
RMSD between 386 pruned atom pairs is 0.637 angstroms; (across all 571 pairs:
4.621)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with WT-5-88-658.pdb, chain A (#31), sequence alignment score =
2906.9
RMSD between 369 pruned atom pairs is 0.653 angstroms; (across all 571 pairs:
5.086)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with WT-3-88-658.pdb, chain A (#32), sequence alignment score =
2914.1
RMSD between 312 pruned atom pairs is 0.711 angstroms; (across all 571 pairs:
7.402)
> color #30 #aaaaffff
> color #31 cyan
> color #32 #aaffffff
> color #29 #aa55ffff
> color #29 #00aaffff
> color #24 #5555ffff
> select add #29
4596 atoms, 4694 bonds, 571 residues, 1 model selected
> select add #30
9192 atoms, 9388 bonds, 1142 residues, 2 models selected
> select add #31
13788 atoms, 14082 bonds, 1713 residues, 3 models selected
> select add #32
18384 atoms, 18776 bonds, 2284 residues, 4 models selected
> select add #5.2
22980 atoms, 18776 bonds, 2855 residues, 5 models selected
> select clear
> hide #5.1 models
> select add #5.1
4894 atoms, 619 residues, 1 model selected
> select subtract #5.1
1 model selected
> select add #5.1
4894 atoms, 619 residues, 1 model selected
> hide sel cartoons
> select subtract #5.1
1 model selected
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> ui tool show Matchmaker
> matchmaker #24 to #5/B pairing bs
Parameters
---
Chain pairing | bs
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
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with WT-1-88-658.pdb, chain A (#24), sequence alignment score =
2932.1
RMSD between 362 pruned atom pairs is 0.687 angstroms; (across all 571 pairs:
26.638)
> matchmaker #24 to #5/B pairing bs
Parameters
---
Chain pairing | bs
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
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with WT-1-88-658.pdb, chain A (#24), sequence alignment score =
2932.1
RMSD between 362 pruned atom pairs is 0.687 angstroms; (across all 571 pairs:
26.638)
> select add #24
4596 atoms, 4694 bonds, 571 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for WT-1-88-658.pdb_A SES surface #24.1: minimum, -24.95,
mean -2.33, maximum 18.92
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select add #29
9192 atoms, 9388 bonds, 1142 residues, 3 models selected
> select subtract #29
4596 atoms, 4694 bonds, 571 residues, 2 models selected
> select subtract #24
1 model selected
> select add #30
4596 atoms, 4694 bonds, 571 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for WT-4-88-658.pdb_A SES surface #30.1: minimum, -20.00,
mean -2.14, maximum 11.14
To also show corresponding color key, enter the above coulombic command and
add key true
> open Z:/hASK1/ASK1pymol/ASK1-H43-01.pdb
Chain information for ASK1-H43-01.pdb #33
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #33 to #5/B pairing bs
Parameters
---
Chain pairing | bs
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
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with ASK1-H43-01.pdb, chain A (#33), sequence alignment score =
1933.8
RMSD between 349 pruned atom pairs is 0.974 angstroms; (across all 384 pairs:
1.396)
> matchmaker #33 to #5/B pairing bs
Parameters
---
Chain pairing | bs
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
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with ASK1-H43-01.pdb, chain A (#33), sequence alignment score =
1933.8
RMSD between 349 pruned atom pairs is 0.974 angstroms; (across all 384 pairs:
1.396)
> select clear
> hide #!24 models
> show #!24 models
> select add #30
4596 atoms, 4694 bonds, 571 residues, 1 model selected
> select subtract #30
1 model selected
> select add #29
4596 atoms, 4694 bonds, 571 residues, 1 model selected
> select subtract #29
Nothing selected
> select add #32
4596 atoms, 4694 bonds, 571 residues, 1 model selected
> select subtract #32
Nothing selected
> select add #33
3159 atoms, 3233 bonds, 385 residues, 1 model selected
> select subtract #33
Nothing selected
> select add #24
4596 atoms, 4694 bonds, 571 residues, 1 model selected
> select subtract #24
1 model selected
> select add #24
4596 atoms, 4694 bonds, 571 residues, 1 model selected
> select subtract #24
1 model selected
> select add #23
4588 atoms, 4684 bonds, 571 residues, 1 model selected
> select subtract #23
Nothing selected
> select add #22
4588 atoms, 4684 bonds, 571 residues, 1 model selected
> select subtract #22
Nothing selected
> select add #19
4588 atoms, 4684 bonds, 571 residues, 1 model selected
> select subtract #19
Nothing selected
> select add #20
4588 atoms, 4684 bonds, 571 residues, 1 model selected
> select subtract #20
Nothing selected
> select add #5.2
4596 atoms, 571 residues, 1 model selected
> select subtract #5.2
1 model selected
> select add #5.2
4596 atoms, 571 residues, 1 model selected
> select subtract #5.2
1 model selected
> select add #5
9490 atoms, 9699 bonds, 1190 residues, 1 model selected
> select subtract #5
2 models selected
> hide #19-23,29,31-33#!5,24,30 surfaces
> hide #!30 models
> hide #31 models
> hide #32 models
> hide #33 models
> show #33 models
> hide #!24 models
> hide #23 models
> hide #22 models
> hide #21 models
> hide #20 models
> hide #19 models
> select ligand
84 atoms, 93 bonds, 3 residues, 3 models selected
> select sel @<3
697 atoms, 531 bonds, 203 residues, 32 models selected
> show sel & #29,33#!5 atoms
> color (#29,33#!5 & sel) byhetero
> color (#29,33#!5 & sel) byelement
> select clear
> show #32 models
> hide #29 models
> show #31 models
> show #!30 models
> show #29 models
> show #!24 models
> hide #!24 models
> select add #29
4596 atoms, 4694 bonds, 571 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for WT-2-88-658.pdb_A SES surface #29.1: minimum, -27.05,
mean -2.40, maximum 18.23
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> mlp sel
Map values for surface "WT-2-88-658.pdb_A SES surface": minimum -29.59, mean
-4.281, maximum 24.11
To also show corresponding color key, enter the above mlp command and add key
true
> select subtract #29
1 model selected
> select add #29
4596 atoms, 4694 bonds, 571 residues, 1 model selected
Alignment identifier is 29/A
> ui tool show "Renumber Residues"
> renumber #29/A seqStart 88
571 residues renumbered
> renumber #29/A seqStart 88
0 residues renumbered
> hide sel surfaces
> coulombic sel
Coulombic values for WT-2-88-658.pdb_A SES surface #29.1: minimum, -27.05,
mean -2.40, maximum 18.23
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #29
1 model selected
> select add #29
4596 atoms, 4694 bonds, 571 residues, 1 model selected
> hide sel surfaces
> coulombic sel
Coulombic values for WT-2-88-658.pdb_A SES surface #29.1: minimum, -27.05,
mean -2.40, maximum 18.23
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #29
1 model selected
> select add #29
4596 atoms, 4694 bonds, 571 residues, 1 model selected
> hide sel surfaces
> open
> C:/Users/User/AppData/Local/Temp/BNZ.66180a8a884c476a/test_15821_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
test_15821_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #34
---
Chain | Description
A | No description available
> open
> C:/Users/User/AppData/Local/Temp/BNZ.66180aaf884cd93a/test_15821_unrelaxed_rank_002_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
test_15821_unrelaxed_rank_002_alphafold2_ptm_model_3_seed_000.pdb #35
---
Chain | Description
A | No description available
> open
> C:/Users/User/AppData/Local/Temp/BNZ.66180ab3884ceb3b/test_15821_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
test_15821_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb #36
---
Chain | Description
A | No description available
> open
> C:/Users/User/AppData/Local/Temp/BNZ.66180ab7884cfa8d/test_15821_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb
Chain information for
test_15821_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb #37
---
Chain | Description
A | No description available
> open
> C:/Users/User/AppData/Local/Temp/BNZ.66180aba884d0470/test_15821_unrelaxed_rank_005_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
test_15821_unrelaxed_rank_005_alphafold2_ptm_model_4_seed_000.pdb #38
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #34-38 to #5/B pairing bs
Parameters
---
Chain pairing | bs
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
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with
test_15821_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#34), sequence alignment score = 2908.1
RMSD between 356 pruned atom pairs is 0.875 angstroms; (across all 571 pairs:
5.247)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with
test_15821_unrelaxed_rank_002_alphafold2_ptm_model_3_seed_000.pdb, chain A
(#35), sequence alignment score = 2933.9
RMSD between 363 pruned atom pairs is 0.580 angstroms; (across all 571 pairs:
5.116)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with
test_15821_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#36), sequence alignment score = 2908.1
RMSD between 382 pruned atom pairs is 0.620 angstroms; (across all 571 pairs:
5.190)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with
test_15821_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#37), sequence alignment score = 2919.5
RMSD between 381 pruned atom pairs is 0.708 angstroms; (across all 571 pairs:
4.536)
Matchmaker
test_7b510_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#5) with
test_15821_unrelaxed_rank_005_alphafold2_ptm_model_4_seed_000.pdb, chain A
(#38), sequence alignment score = 2939.9
RMSD between 366 pruned atom pairs is 0.568 angstroms; (across all 571 pairs:
6.599)
> hide #!29 models
> select add #34
9783 atoms, 9997 bonds, 1229 residues, 3 models selected
Destroying pre-existing alignment with identifier 29/A
Alignment identifier is 29/A
Alignment identifier is 34/A
> select clear
> select #34/A:47
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:47-55
70 atoms, 77 bonds, 9 residues, 1 model selected
> select #34/A:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:56-58
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #34/A:49-50
14 atoms, 15 bonds, 2 residues, 1 model selected
> select #34/A:49-58
80 atoms, 85 bonds, 10 residues, 1 model selected
> select #34/A:82
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #34/A:82-84
19 atoms, 18 bonds, 3 residues, 1 model selected
> select #34/A:78
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #34/A:78-80
26 atoms, 25 bonds, 3 residues, 1 model selected
> select #34/A:16
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #34/A:16-29
97 atoms, 100 bonds, 14 residues, 1 model selected
> select clear
> select #34/A:10
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #34/A:1-10
71 atoms, 70 bonds, 10 residues, 1 model selected
> select clear
> select #34/A:10
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #34/A:10-19
74 atoms, 78 bonds, 10 residues, 1 model selected
> select #34/A:54
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #34/A:54-58
49 atoms, 51 bonds, 5 residues, 1 model selected
> select #34/A:60
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #34/A:52-60
70 atoms, 72 bonds, 9 residues, 1 model selected
> hbonds sel reveal true
128 hydrogen bonds found
> hbonds sel reveal true
128 hydrogen bonds found
> show sel atoms
> select sel @<4
3194 atoms, 2773 bonds, 128 pseudobonds, 696 residues, 29 models selected
> select sel @<3
39605 atoms, 6814 bonds, 128 pseudobonds, 5275 residues, 30 models selected
> select clear
> select #34/A:52
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #34/A:52-60
70 atoms, 72 bonds, 2 pseudobonds, 9 residues, 2 models selected
> select sel @<3
1925 atoms, 1614 bonds, 98 pseudobonds, 487 residues, 29 models selected
> select clear
> show #!1 models
> hide #!1 models
> show #5.1 models
> select add #5.1
4894 atoms, 619 residues, 1 model selected
> show sel cartoons
> show sel surfaces
> hide #39 models
> hide #38 models
> hide #37 models
> hide #36 models
> hide #35 models
> hide #31 models
> hide #32 models
> hide #33 models
> hide #!30 models
> select clear
> select #34/A:30
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #34/A:22-30
59 atoms, 59 bonds, 9 residues, 1 model selected
> hide #5.1 models
> show #5.1 models
> select add #5.1
4953 atoms, 59 bonds, 628 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> show sel atoms
> show sel cartoons
> hide sel atoms
> select clear
> hide #!5 models
> show #!5 models
> select add #5.1
4894 atoms, 619 residues, 1 model selected
> hide sel cartoons
> hide #!5 models
> select subtract #5.1
1 model selected
> select add #5
9490 atoms, 9699 bonds, 1190 residues, 1 model selected
> select subtract #5
2 models selected
> select add #5.2
4596 atoms, 571 residues, 1 model selected
> select subtract #5.2
1 model selected
> show #!5 models
> select #34/A:7-8
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #34/A:7-12
45 atoms, 45 bonds, 6 residues, 1 model selected
> select add #5.2
4641 atoms, 45 bonds, 577 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select clear
> select add #5.2
4596 atoms, 571 residues, 1 model selected
> show sel surfaces
> select add #5
9490 atoms, 9699 bonds, 1190 residues, 2 models selected
> select subtract #5
2 models selected
> select add #5.2
4596 atoms, 571 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> select clear
> select #34/A:6
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:6-15
74 atoms, 76 bonds, 10 residues, 1 model selected
> select sel @<3
5801 atoms, 580 bonds, 820 residues, 27 models selected
> select clear
[Repeated 1 time(s)]
> select #34/A:6
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:6-14
67 atoms, 68 bonds, 9 residues, 1 model selected
> select sel @<3
5770 atoms, 548 bonds, 813 residues, 27 models selected
> select clear
> select #34/A:6
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:6-12
53 atoms, 53 bonds, 7 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> show #35 models
> show #36 models
> show #37 models
> show #38 models
> show #39 models
> hide #39 models
> hide sel surfaces
[Repeated 1 time(s)]
> select add #5
9543 atoms, 9752 bonds, 1197 residues, 3 models selected
> select subtract #5
53 atoms, 53 bonds, 7 residues, 4 models selected
> select add #5
9543 atoms, 9752 bonds, 1197 residues, 3 models selected
> hide sel surfaces
> select clear
> select #34/A:4
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:4-7
31 atoms, 30 bonds, 4 residues, 1 model selected
> select #34/A:8
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #34/A:8-19
86 atoms, 90 bonds, 12 residues, 1 model selected
> show sel atoms
> select add #5
9576 atoms, 9789 bonds, 1202 residues, 3 models selected
> select subtract #5
86 atoms, 90 bonds, 12 residues, 4 models selected
> show #10 models
> hide #10 models
> show #11 models
> hide #11 models
> show #12 models
> hide #12 models
> show #!24 models
> hide #!24 models
> select add #5
9576 atoms, 9789 bonds, 1202 residues, 3 models selected
> show sel cartoons
> select subtract #5
86 atoms, 90 bonds, 12 residues, 4 models selected
> select add #5.1
4980 atoms, 90 bonds, 631 residues, 3 models selected
Alignment identifier is 5/A
Destroying pre-existing alignment with identifier 34/A
Alignment identifier is 34/A
> select clear
> select #5/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:1-40
280 atoms, 286 bonds, 40 residues, 1 model selected
> select #5/A:41
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/A:41-56
121 atoms, 129 bonds, 16 residues, 1 model selected
> select #5/A:57
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:57-69
77 atoms, 77 bonds, 13 residues, 1 model selected
> select #5/A:70
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:70-90
139 atoms, 139 bonds, 21 residues, 1 model selected
> select clear
> select #5/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:1-91
624 atoms, 641 bonds, 91 residues, 1 model selected
> select #34/A:55
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #34/A:23-55
237 atoms, 246 bonds, 3 pseudobonds, 33 residues, 2 models selected
> select clear
> select #5/A:92
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:92-258
1307 atoms, 1332 bonds, 167 residues, 1 model selected
> open
> C:/Users/User/AppData/Local/Temp/BNZ.661f4cf5a4a7ba5c/ASK1ASK2_94e95_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
ASK1ASK2_94e95_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#40
---
Chain | Description
A | No description available
B | No description available
> open
> C:/Users/User/AppData/Local/Temp/BNZ.661f4cf5a4a7ba5c/ASK1ASK2_94e95_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
ASK1ASK2_94e95_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb
#41
---
Chain | Description
A | No description available
B | No description available
> open
> C:/Users/User/AppData/Local/Temp/BNZ.661f4cf5a4a7ba5c/ASK1ASK2_94e95_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
ASK1ASK2_94e95_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb
#42
---
Chain | Description
A | No description available
B | No description available
> open
> C:/Users/User/AppData/Local/Temp/BNZ.661f4cf5a4a7ba5c/ASK1ASK2_94e95_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
ASK1ASK2_94e95_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb
#43
---
Chain | Description
A | No description available
B | No description available
> open
> C:/Users/User/AppData/Local/Temp/BNZ.661f4cf5a4a7ba5c/ASK1ASK2_94e95_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_000.pdb
Chain information for
ASK1ASK2_94e95_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_000.pdb
#44
---
Chain | Description
A | No description available
B | No description available
> hide #40 models
> hide #41 models
> hide #42 models
> hide #43 models
> hide #44 models
> hide #38 models
> hide #37 models
> hide #36 models
> hide #35 models
> hide #!34 models
> hide #!5 models
> select add #5
9490 atoms, 9699 bonds, 1190 residues, 2 models selected
> select subtract #5
2 models selected
> show #40 models
> color #40 bychain
> show #41 models
> show #42 models
> show #43 models
> show #44 models
> hide #40 models
> hide #41 models
> show #41 models
> hide #42 models
> hide #44 models
> hide #43 models
> color #41 bychain
> show #42 models
> hide #41 models
> color #42 bychain
> show #43 models
> hide #43 models
> hide #42 models
> show #43 models
> hide #43 models
> show #44 models
> color #44 bychain
> hide #44 models
> show #40 models
> show #41 models
> hide #40 models
> select add #41
10048 atoms, 10281 bonds, 1282 residues, 1 model selected
> select subtract #41
Nothing selected
Alignment identifier is 1/B
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 7/A
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 18/B
Alignment identifier is 25/A
Alignment identifier is 25/B
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 14/A
Alignment identifier is 16/A
Alignment identifier is 17/A
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
QWindowsWindow::setGeometry: Unable to set geometry 2560x1425+0+23 (frame:
2576x1464-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 2560x1417+0+23 (frame: 2576x1456-8-8) margins: 8, 31, 8, 8
minimum size: 468x1425 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=484, y=1464)))
> select add #41
10048 atoms, 10281 bonds, 1282 residues, 1 model selected
Alignment identifier is 41/A
Alignment identifier is 41/B
> select clear
> select #41/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/B:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #41/B:2-56
396 atoms, 411 bonds, 55 residues, 1 model selected
> select #41/B:57
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #41/B:57-60
27 atoms, 26 bonds, 4 residues, 1 model selected
> select #41/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/A:1-21
150 atoms, 154 bonds, 21 residues, 1 model selected
> select #41/A:21-22
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #41/A:21-33
92 atoms, 91 bonds, 13 residues, 1 model selected
> select #41/A:13
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #41/A:13-28
113 atoms, 115 bonds, 16 residues, 1 model selected
> select #41/A:29
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #41/A:29-40
82 atoms, 83 bonds, 12 residues, 1 model selected
> select #41/A:45
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/A:41-45
43 atoms, 43 bonds, 5 residues, 1 model selected
> select #41/A:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #41/A:47-68
173 atoms, 176 bonds, 22 residues, 1 model selected
> select #41/A:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/A:70-80
84 atoms, 84 bonds, 11 residues, 1 model selected
> select #41/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/B:1-36
252 atoms, 258 bonds, 36 residues, 1 model selected
> select #41/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/A:1-95
713 atoms, 732 bonds, 95 residues, 1 model selected
> select #41/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/A:1-44
313 atoms, 320 bonds, 44 residues, 1 model selected
> select #41/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/A:1-43
306 atoms, 312 bonds, 43 residues, 1 model selected
> select sel @<3
6941 atoms, 6159 bonds, 1447 residues, 36 models selected
> show sel & #41 atoms
> hide sel & #41 atoms
> show sel & #41 atoms
> hide sel & #41 atoms
> select clear
> select #41/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/A:1-13
88 atoms, 89 bonds, 13 residues, 1 model selected
> select clear
> select #41/B:4
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/B:4-13
74 atoms, 74 bonds, 10 residues, 1 model selected
> hide #41 models
> select add #41
10048 atoms, 10281 bonds, 1282 residues, 1 model selected
> hide #5.2 models
> hide #5.1 models
> show #40 models
> select #41/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/B:1-66
464 atoms, 480 bonds, 66 residues, 1 model selected
> hide #40 models
> show #41 models
> show #!5 models
> hide #!5 models
> show #9 models
> hide #9 models
> show #19 models
> hide #19 models
> show #35 models
> hide #41 models
> color #35 #aaaaffff
> hide #35 models
> show #40 models
> show #41 models
> hide #40 models
> select clear
> hide #41 models
> show #35 models
> select #41/B:66
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #41/B:64-66
16 atoms, 15 bonds, 3 residues, 1 model selected
> select #41/B:54
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #41/B:54-64
81 atoms, 84 bonds, 11 residues, 1 model selected
> select ~sel & ##selected
9967 atoms, 10197 bonds, 1271 residues, 1 model selected
> select add #35
15154 atoms, 15500 bonds, 1929 residues, 2 models selected
Alignment identifier is 1
Destroying pre-existing alignment with identifier 41/A
Alignment identifier is 41/A
> select clear
> select #41/A:232-233
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #41/A:232-256
218 atoms, 221 bonds, 25 residues, 1 model selected
> select clear
> select #41/B:226
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #41/B:226-250
191 atoms, 194 bonds, 25 residues, 1 model selected
> show #41 models
> hide #35 models
> show sel atoms
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> hide #2.1 models
> select add #2
3350 atoms, 3427 bonds, 410 residues, 2 models selected
> show #!2 models
> show #41 target m
> show sel cartoons
> show sel atoms
> hide sel atoms
> ui tool show Matchmaker
> matchmaker #!2 to #41/A pairing bs
Parameters
---
Chain pairing | bs
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
ASK1ASK2_94e95_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#41) with ASK1-H43.pdb, chain A (#2), sequence alignment score =
1185.8
RMSD between 282 pruned atom pairs is 1.052 angstroms; (across all 383 pairs:
2.278)
> matchmaker #!2 to #41/B pairing bs
Parameters
---
Chain pairing | bs
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
ASK1ASK2_94e95_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#41) with ASK1-H43.pdb, chain A (#2), sequence alignment score =
1933.8
RMSD between 339 pruned atom pairs is 0.923 angstroms; (across all 384 pairs:
1.398)
> show #16 models
> hide #16 models
> show #5.1 models
> hide #5.1 models
> hide #!5 models
> show #4 models
> hide #4 models
> show #18.2 models
> hide #18.2 models
> hide #!18 models
> select clear
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #33 models
> hide #33 models
> show #!34 models
> hide #!2 models
> hide #41 models
> color #34 #ff557fff
> show #41 models
> hide #41 models
> show #40 models
> hide #40 models
> ui tool show Matchmaker
> matchmaker #!34 to #2/A pairing bs
Parameters
---
Chain pairing | bs
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 ASK1-H43.pdb, chain A (#2) with
test_15821_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#34), sequence alignment score = 1936.8
RMSD between 300 pruned atom pairs is 0.929 angstroms; (across all 384 pairs:
1.667)
> show #41 models
> hide #41 models
> show #41 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #41 models
> show #41 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> show #!2 models
Alignment identifier is 1/B
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 7/A
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 18/B
Alignment identifier is 25/A
Alignment identifier is 25/B
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 14/A
Alignment identifier is 16/A
Alignment identifier is 17/A
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
QWindowsWindow::setGeometry: Unable to set geometry 2560x1490+0+23 (frame:
2576x1529-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 2560x1417+0+23 (frame: 2576x1456-8-8) margins: 8, 31, 8, 8
minimum size: 468x1490 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=484, y=1529)))
QWindowsWindow::setGeometry: Unable to set geometry 2560x1555+0+23 (frame:
2576x1594-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 2560x1417+0+23 (frame: 2576x1456-8-8) margins: 8, 31, 8, 8
minimum size: 468x1555 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=484, y=1594)))
QWindowsWindow::setGeometry: Unable to set geometry 2560x1620+0+23 (frame:
2576x1659-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 2560x1417+0+23 (frame: 2576x1456-8-8) margins: 8, 31, 8, 8
minimum size: 468x1620 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=484, y=1659)))
> select add #34
5187 atoms, 5303 bonds, 8 pseudobonds, 658 residues, 2 models selected
Alignment identifier is 34/A
> select #34/A:49
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:49-59
86 atoms, 91 bonds, 3 pseudobonds, 11 residues, 2 models selected
> select sel @<3
7226 atoms, 1862 bonds, 6 pseudobonds, 1116 residues, 28 models selected
> select clear
[Repeated 1 time(s)]
> select #34/A:49
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:49-59
86 atoms, 91 bonds, 3 pseudobonds, 11 residues, 2 models selected
> select sel @<3
7226 atoms, 1862 bonds, 6 pseudobonds, 1116 residues, 28 models selected
> select clear
> select #34/A:49
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:49-59
86 atoms, 91 bonds, 3 pseudobonds, 11 residues, 2 models selected
> select sel @<4
8261 atoms, 2869 bonds, 14 pseudobonds, 1302 residues, 29 models selected
> select clear
> select add #41
10048 atoms, 10281 bonds, 1282 residues, 1 model selected
Alignment identifier is 41/A
Alignment identifier is 41/B
> select clear
> select #41/B:52
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #41/B:52-65
99 atoms, 102 bonds, 14 residues, 1 model selected
> show sel atoms
> select add #41
10048 atoms, 10281 bonds, 1282 residues, 1 model selected
> select subtract #41
Nothing selected
> select #41/B:52
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #41/B:52-63
87 atoms, 90 bonds, 12 residues, 1 model selected
> select sel @<4
3189 atoms, 2836 bonds, 20 pseudobonds, 677 residues, 33 models selected
> select clear
> hide #41 models
> select #41/B:22
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #41/B:22-30
59 atoms, 59 bonds, 9 residues, 1 model selected
> select #34/A:48-49
14 atoms, 15 bonds, 2 residues, 1 model selected
> select #34/A:48-58
87 atoms, 93 bonds, 3 pseudobonds, 11 residues, 2 models selected
> select sel @<4
8360 atoms, 2971 bonds, 14 pseudobonds, 1333 residues, 30 models selected
> select clear
[Repeated 1 time(s)]
> select #34/A:48
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:48-58
87 atoms, 93 bonds, 3 pseudobonds, 11 residues, 2 models selected
> select sel @<3
7281 atoms, 1923 bonds, 5 pseudobonds, 1127 residues, 29 models selected
> select clear
Drag select of 4 residues
> select clear
> select #34/A:48
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:48-58
87 atoms, 93 bonds, 3 pseudobonds, 11 residues, 2 models selected
> hide #!2 models
> show #!2 models
> select sel @<3
7281 atoms, 1923 bonds, 5 pseudobonds, 1127 residues, 29 models selected
> select sel @<4
86907 atoms, 70270 bonds, 86 pseudobonds, 12713 residues, 41 models selected
> select clear
> select #34/A:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:49-58
80 atoms, 85 bonds, 3 pseudobonds, 10 residues, 2 models selected
> select sel @<4
8169 atoms, 2783 bonds, 14 pseudobonds, 1293 residues, 29 models selected
> select clear
> select #34/A:58-59
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #34/A:48-59
93 atoms, 99 bonds, 3 pseudobonds, 12 residues, 2 models selected
> select sel @< 3
7370 atoms, 2000 bonds, 6 pseudobonds, 1143 residues, 29 models selected
> select clear
> show #35 models
> show #36 models
> show #37 models
> show #38 models
> hide #!34 models
> hide #!2 models
> show #!34 models
> hide #!34 models
> select #34/A:48
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:48-58
87 atoms, 93 bonds, 3 pseudobonds, 11 residues, 2 models selected
> select add #38
5274 atoms, 5396 bonds, 3 pseudobonds, 669 residues, 4 models selected
Alignment identifier is 1
> select #34/A:52 #38/A:52
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #34/A:52-60 #38/A:52-60
140 atoms, 144 bonds, 5 pseudobonds, 18 residues, 3 models selected
1 [ID: 1] region 2 chains [52-60] RMSD: 14.092
> select #34/A:30 #38/A:30
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #34/A:23-30 #38/A:23-30
106 atoms, 106 bonds, 16 residues, 2 models selected
1 [ID: 1] region 2 chains [23-30] RMSD: 55.949
> select #34/A:22 #38/A:22
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #34/A:22 #38/A:22
12 atoms, 10 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [22] RMSD: 67.603
> select #34/A:30 #38/A:30
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #34/A:22-30 #38/A:22-30
118 atoms, 118 bonds, 18 residues, 2 models selected
1 [ID: 1] region 2 chains [22-30] RMSD: 57.361
> select #34/A:2 #38/A:2
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #34/A:2-21 #38/A:2-21
290 atoms, 300 bonds, 40 residues, 2 models selected
1 [ID: 1] region 2 chains [2-21] RMSD: 65.998
> select #34/A:12 #38/A:12
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #34/A:12-16 #38/A:12-16
76 atoms, 80 bonds, 10 residues, 2 models selected
1 [ID: 1] region 2 chains [12-16] RMSD: 61.442
> select #34/A:18 #38/A:18
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #34/A:18-25 #38/A:18-25
112 atoms, 116 bonds, 16 residues, 2 models selected
1 [ID: 1] region 2 chains [18-25] RMSD: 65.606
> select #34/A:4 #38/A:4
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #34/A:4-7 #38/A:4-7
62 atoms, 60 bonds, 8 residues, 2 models selected
1 [ID: 1] region 2 chains [4-7] RMSD: 69.485
> select #34/A:8 #38/A:8
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #34/A:8-11 #38/A:8-11
60 atoms, 60 bonds, 8 residues, 2 models selected
1 [ID: 1] region 2 chains [8-11] RMSD: 58.166
> select #34/A:7 #38/A:7
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #34/A:7-11 #38/A:7-11
78 atoms, 78 bonds, 10 residues, 2 models selected
1 [ID: 1] region 2 chains [7-11] RMSD: 59.733
> select sel @< 3
6924 atoms, 1413 bonds, 1128 residues, 34 models selected
> show sel & #35-38 atoms
> hide sel & #35-38 atoms
> select clear
> select add #38
5187 atoms, 5303 bonds, 658 residues, 1 model selected
Alignment identifier is 38/A
> select clear
> select #38/A:6
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #38/A:6-11
47 atoms, 47 bonds, 6 residues, 1 model selected
> select #38/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:7-11
39 atoms, 39 bonds, 5 residues, 1 model selected
> show sel atoms
> select sel @< 3
817 atoms, 627 bonds, 245 residues, 34 models selected
> show sel & #35-38 atoms
[Repeated 2 time(s)]
> hide sel & #35-38 atoms
> select clear
> show #!34 models
> ui tool show Matchmaker
> matchmaker #!34 to #38/A pairing bs
Parameters
---
Chain pairing | bs
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 test_15821_unrelaxed_rank_005_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#38) with
test_15821_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#34), sequence alignment score = 3394.2
RMSD between 401 pruned atom pairs is 0.980 angstroms; (across all 658 pairs:
10.827)
> select add #34
5187 atoms, 5303 bonds, 8 pseudobonds, 658 residues, 2 models selected
Alignment identifier is 34/A
> select clear
> select #38/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:233
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #34/A:233
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #34/A:6
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:6-10
36 atoms, 35 bonds, 5 residues, 1 model selected
> select #34/A:11
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #34/A:11-16
49 atoms, 52 bonds, 6 residues, 1 model selected
> select clear
> select #34/A:103
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #34/A:103-657
4474 atoms, 4571 bonds, 555 residues, 1 model selected
> select clear
> select #34/A:195
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:195-658
3763 atoms, 3848 bonds, 464 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select clear
> select add #36
5187 atoms, 5303 bonds, 658 residues, 1 model selected
Alignment identifier is 36/A
> select #36/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:1-87
591 atoms, 608 bonds, 87 residues, 1 model selected
> blastprotein 36/A:1 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp1
Webservices job id: W9QWU9WEXKBO4XW5
> open pdb:8QGY
Summary of feedback from opening 8QGY fetched from pdb
---
note | Fetching compressed mmCIF 8qgy from http://files.rcsb.org/download/8qgy.cif
8qgy title:
Cryo-EM structure of C-terminally truncated Apoptosis signal-regulating kinase
1 (ASK1) [more info...]
Chain information for 8qgy #45
---
Chain | Description | UniProt
A B | Mitogen-activated protein kinase kinase kinase 5 | M3K5_HUMAN 88-976
> matchmaker #45/A to #36/A
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 test_15821_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#36) with 8qgy, chain A (#45), sequence alignment score = 2634.2
RMSD between 281 pruned atom pairs is 1.122 angstroms; (across all 542 pairs:
5.331)
> hide #!34 models
> hide #35 models
> hide #36 models
> hide #38 models
> hide #37 models
> select add #36
5187 atoms, 5303 bonds, 658 residues, 1 model selected
> select subtract #36
Nothing selected
> view #45 clip false
> color #!45 bychain
> ui tool show Matchmaker
> select ~sel & ##selected
Nothing selected
> matchmaker #!45 to #36/A pairing bs
Parameters
---
Chain pairing | bs
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 test_15821_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#36) with 8qgy, chain A (#45), sequence alignment score = 2634.2
RMSD between 281 pruned atom pairs is 1.122 angstroms; (across all 542 pairs:
5.331)
> matchmaker #!45 to #36/A pairing bs
Parameters
---
Chain pairing | bs
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 test_15821_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#36) with 8qgy, chain A (#45), sequence alignment score = 2634.2
RMSD between 281 pruned atom pairs is 1.122 angstroms; (across all 542 pairs:
5.331)
> show #44 models
> hide #44 models
> show #35 models
> matchmaker #!2 to #36/A pairing bs
Parameters
---
Chain pairing | bs
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 test_15821_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#36) with ASK1-H43.pdb, chain A (#2), sequence alignment score =
1937.4
RMSD between 359 pruned atom pairs is 0.758 angstroms; (across all 384 pairs:
1.064)
> select add #2
3159 atoms, 3233 bonds, 385 residues, 1 model selected
> show #!2 models
> matchmaker #!2 to #36/A pairing bs
Parameters
---
Chain pairing | bs
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 test_15821_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#36) with ASK1-H43.pdb, chain A (#2), sequence alignment score =
1937.4
RMSD between 359 pruned atom pairs is 0.758 angstroms; (across all 384 pairs:
1.064)
> select clear
> show #44 models
> hide #44 models
> show #44 models
> hide #44 models
> hide #35 models
> hide #!2 models
> coulombic #!45
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 8qgy_A SES surface #45.2: minimum, -16.03, mean -0.76,
maximum 20.94
Coulombic values for 8qgy_B SES surface #45.3: minimum, -19.19, mean -0.76,
maximum 18.86
To also show corresponding color key, enter the above coulombic command and
add key true
> show #35 models
> hide #35 models
> hide #!45 surfaces
> show #!29 models
> hide #!29 models
> show #!30 models
> coulombic #!30,45
Coulombic values for WT-4-88-658.pdb_A SES surface #30.1: minimum, -20.00,
mean -2.14, maximum 11.14
Coulombic values for 8qgy_A SES surface #45.2: minimum, -16.03, mean -0.76,
maximum 20.94
Coulombic values for 8qgy_B SES surface #45.3: minimum, -19.19, mean -0.76,
maximum 18.86
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!45 models
> show #35 models
> hide #!30 models
> show #!30 models
> show #!34 models
> select add #34
5187 atoms, 5303 bonds, 8 pseudobonds, 658 residues, 2 models selected
> select clear
> select #34/A:5-6
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #34/A:6-12
53 atoms, 53 bonds, 7 residues, 1 model selected
> select #34/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:7-11
39 atoms, 39 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select ~sel & ##selected
Nothing selected
> select #38/A:8
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #38/A:8
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #38/A:8-13
43 atoms, 43 bonds, 6 residues, 1 model selected
> select #34/A:7-8
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #34/A:7-12
45 atoms, 45 bonds, 6 residues, 1 model selected
> select #34/A:9-10
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #34/A:9-12
32 atoms, 32 bonds, 4 residues, 1 model selected
> select #34/A:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #34/A:13-14
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #34/A:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #34/A:10-12
24 atoms, 24 bonds, 3 residues, 1 model selected
> select #34/A:9-12
32 atoms, 32 bonds, 4 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> hide #!30 models
> show #36 models
> show #37 models
> hide #37 models
> show #38 models
> show #37 models
> hide #!34 models
> show #!34 models
> hide #35 models
> hide #!34 models
> hide #36 models
> hide #37 models
> hide #38 models
> show #40 models
> hide #40 models
> show #40 models
> hide #40 models
> show #41 models
> select add #41
10048 atoms, 10281 bonds, 1282 residues, 1 model selected
> hide sel atoms
> select clear
> view #41 clip false
> style
> cartoon
> cartoon style helix width 1.5 thickness 0.15
> ui tool show "Side View"
> view #41 clip false
> graphics silhouettes false
> graphics silhouettes true
> view #41 clip false
> hide #41 models
> show #35 models
> show #36 models
> show #37 models
> show #38 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!30 models
> hide #35-38#!30 surfaces
> show #!24 models
> hide #!24 models
> hide #35 models
> hide #36 models
> hide #37 models
> hide #38 models
> show #31 models
> show #32 models
> hide #32 models
> show #32 models
> hide #31-32#!30 atoms
> open Z:/hASK1/ASK1pymol/H43-002/ask1-002.pdb
Chain information for ask1-002.pdb #46
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #46 to #30/A pairing bs
Parameters
---
Chain pairing | bs
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 WT-4-88-658.pdb, chain A (#30) with ask1-002.pdb, chain A (#46),
sequence alignment score = 1930.2
RMSD between 363 pruned atom pairs is 0.775 angstroms; (across all 384 pairs:
1.044)
> hide #!30 models
> hide #31 models
> show #31 models
> show #!30 models
> show #35 models
> hide #35 models
> show #35 models
> hide #35 models
> show #36 models
> hide #32 models
> hide #!30 models
> hide #31 models
> show #32 models
> hide #32 models
> show #31 models
> hide #31 models
> show #!30 models
> color #46 #ffaaffff
> color #36,46#!30 byhetero
> hide #36 models
> show #35 models
> hide #35 models
> show #!45 models
> hide #46#!30,45 surfaces
> select add #45.2
12499 atoms, 780 residues, 1 model selected
> select subtract #45.2
1 model selected
> select add #45.3
12944 atoms, 809 residues, 1 model selected
> hide #45.3 target m
[Repeated 2 time(s)]
> select #45/A
12499 atoms, 12633 bonds, 4 pseudobonds, 780 residues, 2 models selected
> select clear
> select add #45.3
12944 atoms, 809 residues, 1 model selected
> select subtract #45.3
1 model selected
> select add #45.3
12944 atoms, 809 residues, 1 model selected
> hide sel cartoons
> select subtract #45.3
1 model selected
> select add #45.2
12499 atoms, 780 residues, 1 model selected
Alignment identifier is 45/A
> select clear
[Repeated 1 time(s)]
> select #45/A:670-940
3782 atoms, 3821 bonds, 2 pseudobonds, 238 residues, 2 models selected
> hide sel cartoons
> view #45.3 clip false
No displayed objects specified.
> view #45 clip false
> select clear
> select ligand
116 atoms, 128 bonds, 4 residues, 4 models selected
> ui tool show "Color Actions"
> color sel violet
> color sel dark salmon
> color sel salmon
> color sel byhetero
> select clear
> save "Z:/hASK1/ASK1-HDX-MS结果/HDX-MS dimer results/H_002.bmp" width 1584
> height 1220 supersample 3
> select clear
> save "Z:/hASK1/ASK1-HDX-MS结果/HDX-MS dimer results/H_002_2.bmp" width 1584
> height 1220 supersample 3
> save "Z:/hASK1/ASK1-HDX-MS结果/HDX-MS dimer results/ASK.cxs"
——— End of log from Sun Apr 28 22:16:47 2024 ———
opened ChimeraX session
BLAST job failed
> hide #46 models
> hide #!45 models
> hide #!30 models
> show #!2 models
> show #!3 models
> hide #!3 models
> select ligand
116 atoms, 128 bonds, 4 residues, 4 models selected
> show sel & #!2 atoms
> select w476
Expected an objects specifier or a keyword
> select W476
Expected an objects specifier or a keyword
> select zone ligand 4 protein residues true
Selected 4926 atoms
> hide sel & #!2 atoms
> show sel & #!2 atoms
> undo
[Repeated 2 time(s)]
> select ligand
116 atoms, 128 bonds, 4 residues, 4 models selected
> show sel & #!2 atoms
> select zone ligand 3.5 protein residues true
Selected 3341 atoms
> show sel & #!2 atoms
> color sel & #!2 byhetero
> select clear
> ui mousemode right distance
> distance #2/?:1@N17 #2/A:388@OD1
Distance between ASK1-H43.pdb #2/? UNK 1 N17 and /A ASP 388 OD1: 2.774Å
> distance #2/?:1@O14 #2/A:430@NE2
Distance between ASK1-H43.pdb #2/? UNK 1 O14 and /A GLN 430 NE2: 3.530Å
> select add #2
3159 atoms, 3233 bonds, 2 pseudobonds, 385 residues, 2 models selected
Alignment identifier is 2/A
> select subtract #2
1 model selected
> select #2/A:430
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:430
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:362
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:362
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/A:322
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:322
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> distance #2/?:1@O19 #2/A:322@NH1
Distance between ASK1-H43.pdb #2/? UNK 1 O19 and /A ARG 322 NH1: 4.026Å
> hide #47.1 models
> ui tool show "Side View"
> save "C:/Users/User/Desktop/结果/H43 inter with ASK1/H43 against ASK1.cxs"
——— End of log from Fri Oct 11 16:59:44 2024 ———
opened ChimeraX session
BLAST job failed
> select #2/A:395
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:395
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> color sel byhetero
> select clear
> select #2/A:509
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:509
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> save "C:/Users/User/Desktop/结果/H43 inter with ASK1/H43 against ASK1-2.cxs"
——— End of log from Sat Oct 12 17:08:30 2024 ———
opened ChimeraX session
BLAST job failed
> hide #!47 models
> show #!47 models
> open 7rpz
Summary of feedback from opening 7rpz fetched from pdb
---
note | Fetching compressed mmCIF 7rpz from http://files.rcsb.org/download/7rpz.cif
7rpz title:
KRAS G12D in complex with MRTX-1133 [more info...]
Chain information for 7rpz #48
---
Chain | Description | UniProt
A | Isoform 2B of GTPase KRas | RASK-2_HUMAN 0-169
Non-standard residues in 7rpz #48
---
6IC —
4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)-5-ethynyl-6-fluoronaphthalen-2-ol
(MRTX-1133)
GDP — guanosine-5'-diphosphate
MG — magnesium ion
> hide #!47 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> view #2 clip false
> view #48 clip false
> cartoon
> cartoon style width 1.5 thickness 0.3
> color #48 #b5b5b3ff
> color #!48 byhetero
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting full
> lighting shadows false
> lighting soft
> graphics silhouettes true
> close #4,8-17,19-23,26,31-33,35-44,46#1-3,5-7,18,24-25,27-30,34,45
> cartoon style width 1.5 thickness 0.2
> cartoon style width 1.5 thickness 0.15
> graphics silhouettes false
> lighting full
> lighting shadows false
> cartoon style width 1.5 thickness 0.3
> open "H:/KRAS paper-data -20250118/structures/13D-1133-KRAS-
> deposit-2025_refine_1.pdb"
Chain information for 13D-1133-KRAS-deposit-2025_refine_1.pdb #1
---
Chain | Description
A | No description available
> close #1
> cartoon style width 1.2 thickness 0.3
> cartoon style width 1.2 thickness 0.2
> cartoon style width 1.2 thickness 0.18
> style stick
Changed 1690 atom styles
> style stick
Changed 1690 atom styles
> style stick
Changed 1690 atom styles
> style stick
Changed 1690 atom styles
> stick
Unknown command: stick
> style stick
Changed 1690 atom styles
> style stick 0.2
Expected a keyword
> style stick width 0.2
Expected a keyword
> select add #48
1690 atoms, 1444 bonds, 6 pseudobonds, 446 residues, 2 models selected
> style (#!48 & sel) stick
Changed 1690 atom styles
> style stick width 0.2
Expected a keyword
> select clear
> stickScale bond radius 0.15
Unknown command: stickScale bond radius 0.15
> style
> echo stickScale bond radius 0.15
stickScale bond radius 0.15
> style
> echo stickScale bond radius 0.1
stickScale bond radius 0.1
> bond radius 0.1
Missing or invalid "atoms" argument: invalid atoms specifier
> setattr m stickScale bond radius 0.15
Expected a keyword
> setattr m stickScale 0.2
Assigning stickScale attribute to 3 items
Not creating attribute 'stickScale'; use 'create true' to override
> setattr m stickScale 0.5
Assigning stickScale attribute to 3 items
Not creating attribute 'stickScale'; use 'create true' to override
> setattr m stickScale .5
Assigning stickScale attribute to 3 items
Not creating attribute 'stickScale'; use 'create true' to override
> setattr radius 0.2
Missing or invalid "attrValue" argument: Expected a text string
> select add #48
1690 atoms, 1444 bonds, 6 pseudobonds, 446 residues, 2 models selected
> setattr select radius 0.3
Unknown attribute target: 'select'
> setattr b radius 0.3
Assigning radius attribute to 1444 items
> setattr b radius 0.1
Assigning radius attribute to 1444 items
> setattr b radius 0.15
Assigning radius attribute to 1444 items
> setattr b radius 0.2
Assigning radius attribute to 1444 items
> setattr b radius 0.18
Assigning radius attribute to 1444 items
> setattr b radius 0.15
Assigning radius attribute to 1444 items
> select clear
> select /A:11
5 atoms, 4 bonds, 1 residue, 1 model selected
> linewidth width 2
Unknown command: linewidth width 2
> linewidth width 1
Unknown command: linewidth width 1
> linewidth width 5
Unknown command: linewidth width 5
> linewidth 1
Unknown command: linewidth 1
> linewidth 2
Unknown command: linewidth 2
> linewidth
Unknown command: linewidth
> select clear
Unknown or unsupported skia image format
> cartoon style width 1.2 thickness 0.2
> select clear
> select ligand
72 atoms, 81 bonds, 2 residues, 1 model selected
> color sel bychain
> color sel byhetero
> color #48.1 #fa9c9bff models
> undo
[Repeated 2 time(s)]
> select ~sel & ##selected
1618 atoms, 1363 bonds, 6 pseudobonds, 444 residues, 2 models selected
> select gtp
Expected an objects specifier or a keyword
> select clear
> ui mousemode right translate
> ui mousemode right select
> select clear
> ui mousemode right select
> select /A:202@C23
1 atom, 1 residue, 1 model selected
> select clear
> select ::name="GDP"
28 atoms, 30 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> select ligand
72 atoms, 81 bonds, 2 residues, 1 model selected
> select ::name="GDP"
28 atoms, 30 bonds, 1 residue, 1 model selected
> split #7rpz ligand
Expected a structures specifier or a keyword
> split #1 ligands
> select clear
> split #1 ligands
> split #1 ligands ::name="GDP"
Expected a keyword
> split #1 ligands name="GDP"
Expected a keyword
> split #1 ::name="GDP"
[Repeated 1 time(s)]
> select add #48
1690 atoms, 1444 bonds, 6 pseudobonds, 446 residues, 2 models selected
> select subtract #48
Nothing selected
> split #0 connected"
Expected a keyword
> split #0 connected
> select subtract #47
Nothing selected
> select add #48
1690 atoms, 1444 bonds, 6 pseudobonds, 446 residues, 2 models selected
> split #0 connected
> split #1 connected
> split #1
> select clear
> select ::name="GDP"
28 atoms, 30 bonds, 1 residue, 1 model selected
> split sel
Did not split 7rpz, has only one piece
> split select
Expected a structures specifier or a keyword
> split sel
Did not split 7rpz, has only one piece
> color sel #fa9c9bff
> color sel byhetero
> select ::name="6IC"
44 atoms, 51 bonds, 1 residue, 1 model selected
> color sel #28a2aeff
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> save C:/Users/User/Desktop/结果/KRAS作图/v1.bmp width 1981 height 1220
> supersample 4
> lighting soft
> graphics silhouettes true
> save C:/Users/User/Desktop/结果/KRAS作图/v2.bmp width 1981 height 1220
> supersample 3
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> open "H:/KRAS paper-data -20250118/structures/13D-1133-KRAS-
> deposit-2025_refine_1.pdb"
Chain information for 13D-1133-KRAS-deposit-2025_refine_1.pdb #1
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #1 to #48
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 7rpz, chain A (#48) with 13D-1133-KRAS-deposit-2025_refine_1.pdb,
chain A (#1), sequence alignment score = 841.1
RMSD between 165 pruned atom pairs is 0.350 angstroms; (across all 167 pairs:
0.503)
> hide #48.1 models
> hide #!48 models
> show #48.1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> open "H:/KRAS paper-data -20250118/structures/13D-1133-KRAS-
> deposit-2025_refine_1.pdb"
Chain information for 13D-1133-KRAS-deposit-2025_refine_1.pdb #2
---
Chain | Description
A | No description available
> show #1 models
> cartoon style width 1.2 thickness 0.2
Unknown or unsupported skia image format
> setattr b radius 0.2
Assigning radius attribute to 4346 items
> hide #1 models
> show #1 models
> hide #1 models
> setattr b radius 0.15
Assigning radius attribute to 4346 items
> show #1 models
> save C:/Users/User/Desktop/结果/KRAS作图/v3.bmp width 1981 height 1220
> supersample 4
> hide #!48 models
> hide #48.1 models
> show #!48 models
> save C:/Users/User/Desktop/结果/KRAS作图/kras.cxs
——— End of log from Sat Jan 18 16:53:59 2025 ———
opened ChimeraX session
BLAST job failed
> save "H:/KRAS paper-data -20250118/chimerax-kras.cxs"
——— End of log from Sat Jan 18 19:27:50 2025 ———
> view name session-start
opened ChimeraX session
Error checking the status of job W9QWU9WEXKBO4XW5; if this job was restored
from a session and results are still available, be sure to save them so they
aren't lost!
Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys'
> close #2
> select subtract #47
Nothing selected
> color #48 #cfced2ff
> color #1 #74a4a4ff
> color byhetero
[Repeated 1 time(s)]
> hide cartoons
> show cartoons
> ui tool show "Side View"
> select add #1
1537 atoms, 1451 bonds, 286 residues, 1 model selected
> select add #48
3227 atoms, 2895 bonds, 6 pseudobonds, 732 residues, 3 models selected
Alignment identifier is 48/A
Alignment identifier is 1/A
> select clear
> hide cartoons
> undo
> select #1/A:32
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:32-33
20 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> undo
> select #1/A:30
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:30-36
59 atoms, 60 bonds, 7 residues, 1 model selected
> show sel atoms
> select clear
> select #48/A:30
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #48/A:30-37
61 atoms, 62 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> save C:/Users/zhangxy/Desktop/chimerax-kras-13d-2.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 184, in take_snapshot
"table_session": self.table.session_info(),
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 668, in session_info
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'selectedRows'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001B8D1A03450>,
<chimerax.seq_view.tool.SequenceViewer object at 0x000001B889CC4F90>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001B8D1A5AF10>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001B8D1991710>,
<chimerax.sideview.tool.SideViewUI object at 0x000001B8D1A35D10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x000001B884054F50>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001B899615B90>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001B883E1FFD0>] -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x000001B883E1FFD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 1053, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.log.tool.Log object at
0x000001B8D1A03450>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001B889CC4F90>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001B8D1A5AF10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001B8D1991710>, <chimerax.sideview.tool.SideViewUI object at
0x000001B8D1A35D10>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001B884054F50>, <chimerax.model_panel.tool.ModelPanel object at
0x000001B899615B90>, <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x000001B883E1FFD0>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001B883E1FFD0>: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001B8D1A03450>,
<chimerax.seq_view.tool.SequenceViewer object at 0x000001B889CC4F90>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001B8D1A5AF10>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001B8D1991710>,
<chimerax.sideview.tool.SideViewUI object at 0x000001B8D1A35D10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x000001B884054F50>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001B899615B90>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001B883E1FFD0>] -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x000001B883E1FFD0>
ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , , ] ->
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 184, in take_snapshot
"table_session": self.table.session_info(),
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 668, in session_info
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'selectedRows'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001B8D1A03450>,
<chimerax.seq_view.tool.SequenceViewer object at 0x000001B889CC4F90>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001B8D1A5AF10>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001B8D1991710>,
<chimerax.sideview.tool.SideViewUI object at 0x000001B8D1A35D10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x000001B884054F50>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001B899615B90>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001B883E1FFD0>] -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x000001B883E1FFD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 1053, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.log.tool.Log object at
0x000001B8D1A03450>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001B889CC4F90>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001B8D1A5AF10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001B8D1991710>, <chimerax.sideview.tool.SideViewUI object at
0x000001B8D1A35D10>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001B884054F50>, <chimerax.model_panel.tool.ModelPanel object at
0x000001B899615B90>, <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x000001B883E1FFD0>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001B883E1FFD0>: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001B8D1A03450>,
<chimerax.seq_view.tool.SequenceViewer object at 0x000001B889CC4F90>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001B8D1A5AF10>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001B8D1991710>,
<chimerax.sideview.tool.SideViewUI object at 0x000001B8D1A35D10>,
<chimerax.seq_view.tool.SequenceViewer object at 0x000001B884054F50>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001B899615B90>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001B883E1FFD0>] -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x000001B883E1FFD0>
ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , , ] ->
File "C:\Program Files\ChimeraX 1.10.dev202501180816\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 566.36
OpenGL renderer: NVIDIA GeForce RTX 4070 Ti SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 34,163,953,664
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i5-14600KF
OSLanguage: zh-CN
Installed Packages:
alabaster: 1.0.0
anyio: 4.8.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.2.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.12.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202501180816
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-ProfileGrids: 1.0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.15
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.43
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
coverage: 7.6.10
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.12
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.5
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
pluggy: 1.5.0
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
pytest: 8.3.4
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (5)
comment:1 by , 9 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Session restore: ItemTable's selectionModel() is None |
comment:2 by , 9 months ago
| Cc: | added; removed |
|---|---|
| Milestone: | → 1.10 |
| Owner: | changed from to |
| Status: | accepted → assigned |
| Summary: | Session restore: ItemTable's selectionModel() is None → Session restore: ItemTable's selectionModel() is None (Parsing BlastProtein results failed) |
comment:3 by , 9 months ago
I'm not entirely sure why the results table came up for a failed job. Does it reproduce every time you open that session and try to save another one? I tried running a blast job, saving a session, and closing ChimeraX -- then I deleted the job's results from our server. If I open it it tells me "BLAST job failed" and I can save a session normally. The weirdest thing is that I can close ChimeraX, reopen that session, and somehow the results for some job magically appear. That could be a backend bug.
comment:4 by , 9 months ago
| Status: | assigned → feedback |
|---|
Aha, OK. If you get an error from the server that says 'no such job', it sets the status of the task to FINISHED instead of DELTED like it should. I made the change for tomorrow's build. Can you try opening and saving your session again?
comment:5 by , 4 months ago
| Resolution: | → fixed |
|---|---|
| Status: | feedback → closed |
I am going to assume this was fixed.
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It looks like this can only happen if the table's launch() method is never called, which I suspect is a side effect of the "Parsing BlastProtein results failed" error - so that BlastProteinResults._on_report_hits_signal() is not called -- which is where launch() would get called.