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Opened 2 days ago
Last modified 16 hours ago
#20857 closed defect
AlphaFold PAE: 'ra' is None — at Version 1
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
> open /Users/aranzaquintana/Documents/D6PK/D6PK_models.cxs
Log from Wed Aug 19 12:14:44 2026UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
> open /Users/aranzaquintana/Documents/D6PK/D6PK_models.cxs
Log from Tue Aug 18 17:27:56 2026UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/aranzaquintana/Documents/D6PK/AF-Q9FG74-F1-model_v6.pdb format
> pdb
AF-Q9FG74-F1-model_v6.pdb title:
Alphafold monomer V2.0 prediction for serine/threonine-protein kinase D6PK
(Q9FG74) [more info...]
Chain information for AF-Q9FG74-F1-model_v6.pdb #1
---
Chain | Description | UniProt
A | serine/threonine-protein kinase D6PK | D6PK_ARATH 1-498
Computing secondary structure
> ui tool show "AlphaFold Error Plot"
Fetching PAE using AlphaFold database version 6
> alphafold pae #1 uniprotId Q9FG74 version 6
> color /A:145-498 lime
> color bfactor #1 palette alphafold
3849 atoms, 498 residues, atom bfactor range 25.2 to 98.8
> alphafold pae #1 colorDomains true
> color bfactor #1 palette alphafold
3849 atoms, 498 residues, atom bfactor range 25.2 to 98.8
> style sphere
Changed 3849 atom styles
> hide cartoons
> style stick
Changed 3849 atom styles
> show cartoons
> hide cartoons
> show cartoons
> rainbow
[Repeated 1 time(s)]
> color bfactor #1 palette alphafold
3849 atoms, 498 residues, atom bfactor range 25.2 to 98.8
> alphafold pae #1 palette paegreen
> color /A:306 lime
> color /A:59 magenta
> color /A:304 lime
> color /A:68 magenta
> color /A:263-371 lime
> color /A:41-57 magenta
> color /A:334 lime
> color /A:77 magenta
> color bfactor #1 palette alphafold
3849 atoms, 498 residues, atom bfactor range 25.2 to 98.8
> color /A:326-337 lime
> color /A:62-74 magenta
> sequence chain #1/A
Alignment identifier is 1/A
> select /A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:236-375
1061 atoms, 1086 bonds, 140 residues, 1 model selected
> select /A:63-64
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:60-64
37 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:60-61
18 atoms, 18 bonds, 2 residues, 1 model selected
> select /A:60-64
37 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:60-61
18 atoms, 18 bonds, 2 residues, 1 model selected
> select /A:60-64
37 atoms, 37 bonds, 5 residues, 1 model selected
> undo
[Repeated 8 time(s)]
> select /A:60-64
37 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:60
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:60-67
59 atoms, 59 bonds, 8 residues, 1 model selected
> select /A:66-67
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:23-67
317 atoms, 319 bonds, 45 residues, 1 model selected
> select /A:67
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:67
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:62
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:62-63
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:62
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select /A:62
6 atoms, 5 bonds, 1 residue, 1 model selected
> color /A:325-332 lime
> color /A:65-69 magenta
> color /A:333 lime
> color /A:61 magenta
> color /A:328-477 lime
> color /A:57-60 magenta
> color /A:352 lime
> color /A:62 magenta
> color /A:49-488 lime
> color /A:344 lime
> color /A:70 magenta
> color /A:325-339 lime
> color /A:60-69 magenta
> color /A:355 lime
> color /A:44 magenta
> color /A:315 lime
> color /A:348 magenta
> color bfactor #1 palette alphafold
3849 atoms, 498 residues, atom bfactor range 25.2 to 98.8
> select /A:81
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:81-94
118 atoms, 121 bonds, 14 residues, 1 model selected
> select /A:62
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:62
6 atoms, 5 bonds, 1 residue, 1 model selected
> color /A:414 lime
> color /A:175 magenta
> select /A:81
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:81
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:81-94
118 atoms, 121 bonds, 14 residues, 1 model selected
> color bfactor #1 palette alphafold
3849 atoms, 498 residues, atom bfactor range 25.2 to 98.8
> color /A:314-363 lime
> color /A:56-70 magenta
> color /A:363 lime
> color /A:68 magenta
> alphafold pae #1 palette paegreen
> open
> /Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_p_auto/fold_2026_08_18_d6pk_p_auto_model_0.cif
Chain information for fold_2026_08_18_d6pk_p_auto_model_0.cif #2
---
Chain | Description
A | .
Computing secondary structure
> color sel blue
> undo
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #1/A:93-94
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> #1/A:20-31,83-85,89-101,106-108,142-147,151-163,194-200,202-204,208-227,237-239,355-359,365-381,391-400,413-422,427-429,436-441,444-446,451-456,469-471
1189 atoms, 1201 bonds, 146 residues, 1 model selected
> select #1/A:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:2-303
2304 atoms, 2342 bonds, 302 residues, 1 model selected
> select #1/A:303
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:36-303
2063 atoms, 2099 bonds, 268 residues, 1 model selected
> select #1/A:36
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:36
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:44-45
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/A:44-57
101 atoms, 100 bonds, 14 residues, 1 model selected
> select clear
> color red
> color #1 #00f900ff
> color #1 #0433ffff
> color bfactor #1 palette alphafold
3849 atoms, 498 residues, atom bfactor range 25.2 to 98.8
> alphafold pae #2 palette paegreen
No predicted aligned error (PAE) data opened for structure #2
> alphafold pae #2 palette paegreen
No predicted aligned error (PAE) data opened for structure #2
> ui tool show Match→Align
> msa3d #1/A#2/A
Match→Align cutoff: 5.0, in column if within cutoff of: any
50 residue pairs aligned
50 fully populated columns
Pairwise RMSDs across all fully populated columns
---
Model | 1 | 2
1 | 0.000 | 3.201
2 | 3.201 | 0.000
Overall RMSD: 3.201
Sequence lengths: 498 498
SDM (cutoff 5.0): 183.207
Q-score: 0.005
Alignment identifier is MA-1
Showing conservation header ("seq_conservation" residue attribute) for
alignment MA-1
Chains used in RMSD evaluation for alignment MA-1: AF-Q9FG74-F1-model_v6.pdb
#1/A, fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1
> alphafold pae #2 file
> /Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_p_auto/fold_2026_08_18_d6pk_p_auto_full_data_0.json
> color bfactor #2 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.75 to 98.9
> alphafold pae #2 palette paegreen
> color bfactor #2 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.75 to 98.9
> open
> /Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_non_p_auto/fold_2026_08_18_d6pk_non_p_auto_model_0.cif
Chain information for fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3
---
Chain | Description
A | .
Computing secondary structure
> alphafold pae #2 file
> /Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_non_p_auto/fold_2026_08_18_d6pk_non_p_auto_full_data_0.json
Structure fold_2026_08_18_d6pk_p_auto_model_0.cif #2 does not match PAE matrix
size 498.The structure has 497 polymer residues and 10 non-polymer atoms
This can happen if chains or atoms were deleted from the AlphaFold model or if
the PAE data was applied to a structure that was not the one predicted by
AlphaFold. Use the full-length AlphaFold model to show predicted aligned
error.
> alphafold pae #2 file
> /Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_p_auto/fold_2026_08_18_d6pk_p_auto_summary_confidences_0.json
JSON file
"/Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_p_auto/fold_2026_08_18_d6pk_p_auto_summary_confidences_0.json"
is not AlphaFold predicted aligned error data, expected a top level list
> help help:user/tools/alphafold.html#pae
> alphafold pae #2 file
> /Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_p_auto/fold_2026_08_18_d6pk_p_auto_full_data_0.json
> color bfactor #2 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.75 to 98.9
> alphafold pae #3 palette paegreen
No predicted aligned error (PAE) data opened for structure #3
> color bfactor #2 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.75 to 98.9
> color bfactor #2 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.75 to 98.9
> color bfactor #2 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.75 to 98.9
> color bfactor #2 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.75 to 98.9
> alphafold pae #2 palette paegreen
> color #1/A:187 lime
> color #1/A:444 magenta
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file
> /Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_non_p_auto/fold_2026_08_18_d6pk_non_p_auto_full_data_0.json
Structure fold_2026_08_18_d6pk_p_auto_model_0.cif #2 does not match PAE matrix
size 498.The structure has 497 polymer residues and 10 non-polymer atoms
This can happen if chains or atoms were deleted from the AlphaFold model or if
the PAE data was applied to a structure that was not the one predicted by
AlphaFold. Use the full-length AlphaFold model to show predicted aligned
error.
> ui tool show "AlphaFold Error Plot"
> alphafold pae #3 file
> /Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_non_p_auto/fold_2026_08_18_d6pk_non_p_auto_full_data_0.json
> color bfactor #3 palette alphafold
3849 atoms, 498 residues, atom bfactor range 6.18 to 98.8
> alphafold pae #3 palette paegreen
> color bfactor #3 palette alphafold
3849 atoms, 498 residues, atom bfactor range 6.18 to 98.8
> color bfactor #2 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.75 to 98.9
> color bfactor #1 palette alphafold
3849 atoms, 498 residues, atom bfactor range 25.2 to 98.8
> 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 fold_2026_08_18_d6pk_p_auto_model_0.cif, chain A (#2) with
AF-Q9FG74-F1-model_v6.pdb, chain A (#1), sequence alignment score = 2484.4
RMSD between 333 pruned atom pairs is 0.384 angstroms; (across all 498 pairs:
24.621)
> matchmaker #3 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 fold_2026_08_18_d6pk_p_auto_model_0.cif, chain A (#2) with
fold_2026_08_18_d6pk_non_p_auto_model_0.cif, chain A (#3), sequence alignment
score = 2489.2
RMSD between 346 pruned atom pairs is 0.539 angstroms; (across all 498 pairs:
11.041)
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> cd /Users/aranzaquintana/Documents/D6PK
Current working directory is: /Users/aranzaquintana/Documents/D6PK
> save /Users/aranzaquintana/Documents/D6PK/D6PK_models.cxs
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> save /Users/aranzaquintana/Documents/D6PK/D6PK_models.cxs
> color #2/A:286 lime
> color #2/A:117 magenta
> color #2/A:177 lime
> color #2/A:322 magenta
> color #1/A:238-239 lime
> color #1/A:272 magenta
> color bfactor #2 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.75 to 98.9
> hide #1 models
> show #1 models
> color bfactor #1 palette alphafold
3849 atoms, 498 residues, atom bfactor range 25.2 to 98.8
> 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 #3 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
> show #3 models
> color #1/A:305 lime
> color #1/A:40 magenta
> color bfactor #1 palette alphafold
3849 atoms, 498 residues, atom bfactor range 25.2 to 98.8
> select clear
[Repeated 2 time(s)]
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:2-3
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:2-8
51 atoms, 51 bonds, 7 residues, 1 model selected
> select #1/A:8
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:1-8
59 atoms, 59 bonds, 8 residues, 1 model selected
> select add #1
3849 atoms, 3937 bonds, 498 residues, 1 model selected
> select subtract #1
Nothing selected
> select clear
> hide #1 models
> hide #2 models
> hide #3 models
> show #2 models
> select #1/A:81-82
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:81-89
71 atoms, 72 bonds, 9 residues, 1 model selected
> select add #1
3849 atoms, 3937 bonds, 498 residues, 1 model selected
> select subtract #1
Nothing selected
> select #1/A:81-82
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:81-94
118 atoms, 121 bonds, 14 residues, 1 model selected
> select #1/A:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:80-86
56 atoms, 57 bonds, 7 residues, 1 model selected
> select add #2
3909 atoms, 3998 bonds, 505 residues, 2 models selected
> select subtract #2
56 atoms, 57 bonds, 7 residues, 1 model selected
> select add #1
3849 atoms, 3937 bonds, 498 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
3853 atoms, 3941 bonds, 498 residues, 1 model selected
> select subtract #2
Nothing selected
> select #1/A:80-81
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A:80-90
90 atoms, 91 bonds, 11 residues, 1 model selected
> show #1 models
> hide #1 models
> select add #1
3849 atoms, 3937 bonds, 498 residues, 1 model selected
> select subtract #1
Nothing selected
> show #2 target m
>
Unknown command: sequence #2
>
Unknown command: sequence #2
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:81
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:81-94
118 atoms, 121 bonds, 14 residues, 1 model selected
> select #2/A:52
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:52-54
19 atoms, 18 bonds, 3 residues, 1 model selected
> select #2/A:52
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:52-56
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #2/A:81-82
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:81-89
71 atoms, 72 bonds, 9 residues, 1 model selected
> select #2/A:53
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:53-66
99 atoms, 99 bonds, 14 residues, 1 model selected
> select #2/A:81-82
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:81-94
118 atoms, 121 bonds, 14 residues, 1 model selected
> select #2/A:53
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:53-60
55 atoms, 54 bonds, 8 residues, 1 model selected
> select clear
> select #2/A:53-60
55 atoms, 54 bonds, 8 residues, 1 model selected
> select #2/A:81
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:81-94
118 atoms, 121 bonds, 14 residues, 1 model selected
> select #2/A:52-56
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #2/A:54
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:53-54
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #2/A:52-56
34 atoms, 33 bonds, 5 residues, 1 model selected
> select
> #2/A:57-60,109-114,122-128,133-141,172-177,181-187,240-242,248-250,264-266,333-335,346-349
446 atoms, 444 bonds, 55 residues, 1 model selected
> select #2/A:49
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:45-49
40 atoms, 39 bonds, 5 residues, 1 model selected
> select #2/A:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:78-80
20 atoms, 19 bonds, 3 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #2/A:52-56
34 atoms, 33 bonds, 5 residues, 1 model selected
> select clear
> select #2/A:52-56
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #2/A:270
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:268-270
19 atoms, 18 bonds, 3 residues, 1 model selected
> select clear
> select #2/A:52-56
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #2/A:52-56
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #2/A:22-62
293 atoms, 295 bonds, 41 residues, 1 model selected
> select #2/A:22-69
342 atoms, 344 bonds, 48 residues, 1 model selected
> select clear
> select #2/A:22-69
342 atoms, 344 bonds, 48 residues, 1 model selected
> select clear
> select #2/A:22-69
342 atoms, 344 bonds, 48 residues, 1 model selected
> select #2/A:56-57
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #2/A:57
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:57
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:57
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:57-61
37 atoms, 37 bonds, 5 residues, 1 model selected
> select #2/A:57-61
37 atoms, 37 bonds, 5 residues, 1 model selected
> select #2/A:57-61
37 atoms, 37 bonds, 5 residues, 1 model selected
> select #2/A:56
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:56-70
111 atoms, 111 bonds, 15 residues, 1 model selected
> select #2/A:71-72
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:71-78
54 atoms, 54 bonds, 8 residues, 1 model selected
> select #2/A:57
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:57-78
159 atoms, 160 bonds, 22 residues, 1 model selected
> select #2/A:53
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:53
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:53-78
184 atoms, 185 bonds, 26 residues, 1 model selected
> select clear
> select #2/A:81
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:81-94
118 atoms, 121 bonds, 14 residues, 1 model selected
> select #2/A:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:73-80
55 atoms, 55 bonds, 8 residues, 1 model selected
> select #2/A:53
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:53-94
316 atoms, 321 bonds, 42 residues, 1 model selected
> select clear
> show #1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #1 models
> show #2 models
> hide #1 models
> hide #2 models
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> show #3 models
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> show #1 models
> show #2 models
> hide #1 models
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> hide #3 models
> show #3 models
> show #2 models
> show #1 models
> hide #2 models
> hide #3 models
> save /Users/aranzaquintana/Documents/D6PK/D6PK_models.cxs
> show #2 models
> show #3 models
> save modelos-d6pk_alineados.pdb models #1-3
> hide #1 models
> hide #2 models
> show #2 models
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> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> open
> /Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_p_5s/fold_2026_08_18_d6pk_p_5s_model_0.cif
Chain information for fold_2026_08_18_d6pk_p_5s_model_0.cif #4
---
Chain | Description
A | .
Computing secondary structure
> matchmaker #4 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 fold_2026_08_18_d6pk_p_auto_model_0.cif, chain A (#2) with
fold_2026_08_18_d6pk_p_5s_model_0.cif, chain A (#4), sequence alignment score
= 2527.6
RMSD between 368 pruned atom pairs is 0.469 angstroms; (across all 498 pairs:
5.732)
> ui tool show "AlphaFold Error Plot"
> alphafold pae #4 file
> /Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_p_5s/fold_2026_08_18_d6pk_p_5s_full_data_0.json
> color bfactor #4 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.45 to 98.9
> alphafold pae #4 palette paegreen
> color #4/A:330-336 lime
> color #4/A:54-61 #4/A:62@N magenta
> color #4/A:352 lime
> color #4/A:73-74 magenta
> color #4/A:333 lime
> color #4/A:60 magenta
> color bfactor #3 palette alphafold
3849 atoms, 498 residues, atom bfactor range 6.18 to 98.8
> color bfactor #3 palette alphafold
3849 atoms, 498 residues, atom bfactor range 6.18 to 98.8
> color bfactor #4 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.45 to 98.9
> hide #4 models
> show #4 models
> open
> /Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_p_2s/fold_2026_08_18_d6pk_p_2s_model_0.cif
Chain information for fold_2026_08_18_d6pk_p_2s_model_0.cif #5
---
Chain | Description
A | .
Computing secondary structure
> matchmaker #5 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 fold_2026_08_18_d6pk_p_auto_model_0.cif, chain A (#2) with
fold_2026_08_18_d6pk_p_2s_model_0.cif, chain A (#5), sequence alignment score
= 2512.6
RMSD between 360 pruned atom pairs is 0.461 angstroms; (across all 498 pairs:
5.758)
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #1 models
> hide #1 models
> show #2 models
> hide #2 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #5 models
> ui tool show AlphaFold
> ui tool show "AlphaFold Error Plot"
> alphafold pae #5 file
> /Users/aranzaquintana/Documents/D6PK/fold_2026_08_18_d6pk_p_2s/fold_2026_08_18_d6pk_p_2s_full_data_0.json
> color bfactor #5 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.58 to 98.9
> alphafold pae #5 palette paegreen
> color #5/A:229 lime
> color #5/A:351 magenta
> color #2/A:349 lime
> color #2/A:62@N magenta
> color bfactor #5 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.58 to 98.9
> color bfactor #2 palette alphafold
3853 atoms, 498 residues, atom bfactor range 8.75 to 98.9
> show #4 models
> hide #4 models
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> show #2 models
> hide #2 models
> show #2 models
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> show #2 models
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> show #2 models
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> show #2 models
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> show #4 models
> hide #4 models
> show #4 models
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> show #4 models
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> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #4 models
> show #3 models
> hide #4 models
> hide #5 models
> show #4 models
> hide #4 models
> show #4 models
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> show #4 models
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> show #4 models
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> show #4 models
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> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
[deleted to fit within ticket limits]
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O AF-Q9FG74-F1-model_v6.pdb #1/A ASN 13 C 9.817
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CA AF-Q9FG74-F1-model_v6.pdb #1/A THR 12 OG1 9.817
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 32 N 9.817
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 32 N 9.818
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 CB fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 38 N 9.818
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 CA fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ASP 39 CA 9.818
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A PRO 36 N 9.819
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CA fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 28 O 9.819
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 28 O 9.819
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CB fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A PHE 33 CE2 9.820
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ARG 148 CD 9.820
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A THR 58 CG2 9.821
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CB fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ASP 35 OD1 9.822
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 C fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 38 CA 9.823
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 30 CB 9.823
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CB fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 38 CA 9.824
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A PHE 33 CE2 9.824
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A LEU 31 N 9.824
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A LEU 31 CB 9.827
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CB fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A PHE 33 C 9.828
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 CB fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 32 CA 9.828
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 56 CB 9.828
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CB fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A LEU 31 CD2 9.828
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A LEU 31 CG 9.828
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 O fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 32 O 9.829
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CA fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A LEU 31 O 9.829
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 C AF-Q9FG74-F1-model_v6.pdb #1/A SER 14 OG 9.831
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 C fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 28 O 9.831
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 O fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 28 CA 9.832
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 32 C 9.834
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A LEU 31 CD1 9.834
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O AF-Q9FG74-F1-model_v6.pdb #1/A SER 15 OG 9.836
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CA fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A PHE 33 CD2 9.837
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A PHE 33 CE1 9.837
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 C fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A VAL 27 O 9.840
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 32 C 9.840
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CA fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ASP 35 CA 9.840
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ASP 119 CG 9.842
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 C fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A LEU 31 CD1 9.843
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 N fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ASP 35 CB 9.844
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 N fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A PRO 36 N 9.844
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 N fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A LEU 31 CD2 9.846
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CB fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 28 O 9.847
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 O fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A PHE 33 CA 9.847
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 28 N 9.847
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CB fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 32 OG 9.848
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 O fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A PHE 33 CE1 9.849
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 CB fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A LEU 31 O 9.850
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 N fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A PRO 36 CA 9.850
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CB fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A PHE 33 CA 9.850
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A LEU 31 CD1 9.851
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 C AF-Q9FG74-F1-model_v6.pdb #1/A ASN 13 OD1 9.851
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CB fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A LEU 31 CA 9.852
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A LEU 31 CG 9.852
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 C fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 37 C 9.853
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A LYS 150 NZ 9.853
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A VAL 27 O 9.853
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A LEU 31 C 9.853
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 C fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 38 OG 9.854
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 N fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ASP 35 CG 9.855
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 N fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ASP 35 CB 9.856
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 56 OG 9.856
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ASP 35 OD2 9.856
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CA fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 37 C 9.857
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 32 O 9.857
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CA fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A LEU 31 CD2 9.857
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 O fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 32 C 9.858
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 O fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A PHE 33 CA 9.859
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 30 C 9.859
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N AF-Q9FG74-F1-model_v6.pdb #1/A LYS 150 CE 9.859
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 C AF-Q9FG74-F1-model_v6.pdb #1/A SER 15 OG 9.860
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 30 OG 9.862
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 C fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 37 CB 9.862
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 C fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 32 O 9.862
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 C fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A PRO 36 CB 9.862
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A PHE 33 CE1 9.863
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A LEU 31 N 9.865
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 N fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A PHE 33 CE2 9.865
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 O fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A PRO 36 CD 9.865
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CB fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 29 C 9.865
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 CA fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A PHE 33 CA 9.865
AF-Q9FG74-F1-model_v6.pdb #1/A ALA 34 C AF-Q9FG74-F1-model_v6.pdb #1/A SER 37 O 9.866
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA AF-Q9FG74-F1-model_v6.pdb #1/A LYS 150 NZ 9.867
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 CB fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 37 OG 9.869
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 30 CB 9.870
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 37 OG 9.870
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A VAL 27 O 9.871
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ASP 35 OD2 9.872
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A GLN 26 CA 9.872
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CB fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A LEU 31 CA 9.873
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CB fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A PRO 36 N 9.873
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 N fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 30 O 9.873
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 O fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 38 CB 9.874
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CB fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 28 CB 9.874
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 N fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A LEU 31 CD1 9.876
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A PHE 33 N 9.877
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 37 O 9.877
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A VAL 27 C 9.878
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 N fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 28 O 9.878
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 C fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 30 N 9.878
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CA fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 30 CA 9.880
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CA fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 30 CB 9.880
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB AF-Q9FG74-F1-model_v6.pdb #1/A ASP 119 OD1 9.881
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CB fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A LEU 31 CG 9.882
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C AF-Q9FG74-F1-model_v6.pdb #1/A LEU 11 CB 9.885
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A PRO 36 CA 9.886
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 N fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 28 CB 9.887
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CB fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A PHE 33 CD2 9.888
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB AF-Q9FG74-F1-model_v6.pdb #1/A ARG 148 NE 9.891
AF-Q9FG74-F1-model_v6.pdb #1/A ALA 34 C AF-Q9FG74-F1-model_v6.pdb #1/A SER 32 OG 9.891
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 57 C 9.891
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ASP 35 CA 9.892
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N AF-Q9FG74-F1-model_v6.pdb #1/A ASN 391 ND2 9.893
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 C fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A LEU 31 CD1 9.893
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 C fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A LEU 31 CA 9.893
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CB fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 28 CA 9.894
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA AF-Q9FG74-F1-model_v6.pdb #1/A THR 12 CA 9.894
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 38 N 9.895
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 N AF-Q9FG74-F1-model_v6.pdb #1/A SER 10 C 9.895
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CA fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 29 CA 9.895
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ARG 148 NH1 9.895
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 N fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A PRO 36 CD 9.895
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 N fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A PHE 33 CZ 9.895
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 56 OG 9.896
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A PHE 33 C 9.897
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A VAL 27 CA 9.897
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 CB fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ASP 39 C 9.898
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CB fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 37 CA 9.898
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CA fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 37 C 9.898
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 N fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A PHE 33 CD2 9.899
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 N fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 37 C 9.899
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A LEU 31 CD2 9.899
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ARG 148 CD 9.900
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ASP 25 O 9.901
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ASP 119 CG 9.901
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A PHE 33 CE2 9.901
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ARG 148 CZ 9.902
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 C fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ASP 39 CA 9.903
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 O fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ASP 35 C 9.905
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 C fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 32 O 9.905
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 28 O 9.906
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 30 CA 9.907
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 30 O 9.907
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 28 CA 9.908
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 CB fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A GLY 40 N 9.908
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 O fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 32 CA 9.908
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 37 C 9.909
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 N fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A PHE 33 CD2 9.910
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A PRO 36 CB 9.910
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CA fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A VAL 27 CG1 9.911
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CB fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A LEU 31 CG 9.912
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 N fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 37 CB 9.912
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 N fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A VAL 27 CG1 9.912
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 37 C 9.912
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 37 C 9.913
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 C fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A LEU 31 CB 9.913
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A PRO 36 CB 9.914
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 37 CB 9.914
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A PRO 36 CB 9.915
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 56 CA 9.915
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 O fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A PRO 36 CB 9.915
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CA fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 32 N 9.916
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 C fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ASP 35 CG 9.917
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A LEU 31 CB 9.918
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 C fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A PHE 33 CD2 9.918
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 CB fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 38 O 9.918
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CB AF-Q9FG74-F1-model_v6.pdb #1/A ASN 13 CA 9.918
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ASN 391 ND2 9.919
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CB fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A PRO 36 O 9.920
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 32 O 9.920
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 C AF-Q9FG74-F1-model_v6.pdb #1/A SER 10 CA 9.920
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CA fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 28 C 9.920
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 37 C 9.921
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB AF-Q9FG74-F1-model_v6.pdb #1/A LEU 11 C 9.922
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 O fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 32 OG 9.922
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A PHE 33 CE2 9.923
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 O fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 38 N 9.923
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CB AF-Q9FG74-F1-model_v6.pdb #1/A THR 12 CB 9.924
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 C fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 32 CB 9.925
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 O fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 37 C 9.925
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CA fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A PRO 36 CB 9.925
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ASP 35 OD1 9.926
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A PRO 36 CD 9.926
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A THR 58 CG2 9.926
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 N fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ASP 35 O 9.927
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 C fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 30 CA 9.927
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 CA fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 37 C 9.928
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 C fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 29 N 9.928
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O AF-Q9FG74-F1-model_v6.pdb #1/A LEU 11 CD2 9.929
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A VAL 27 O 9.930
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ARG 148 CD 9.930
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 30 OG 9.930
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ASP 35 C 9.931
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A PRO 36 O 9.932
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 29 O 9.932
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CA AF-Q9FG74-F1-model_v6.pdb #1/A SER 15 OG 9.933
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 N fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 29 CB 9.936
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 29 O 9.936
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ARG 148 CD 9.936
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CB fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 30 CB 9.938
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 28 C 9.938
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 O fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A LEU 31 CB 9.938
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CA fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A PRO 36 CG 9.939
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 C AF-Q9FG74-F1-model_v6.pdb #1/A SER 14 CB 9.940
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C AF-Q9FG74-F1-model_v6.pdb #1/A SER 15 C 9.941
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A LEU 31 O 9.941
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 37 CB 9.941
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CB fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 29 CB 9.942
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A LYS 150 NZ 9.943
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 O fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 37 CA 9.946
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 C fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A PRO 36 CA 9.946
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A LEU 31 CD2 9.948
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 O fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 37 CB 9.954
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N AF-Q9FG74-F1-model_v6.pdb #1/A ARG 148 CG 9.954
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 O fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A PHE 33 CE1 9.954
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 29 C 9.955
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 28 OG 9.955
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 C fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A LEU 31 CB 9.956
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 32 OG 9.957
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 N fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 38 C 9.957
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CB fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ASP 35 O 9.957
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 37 O 9.958
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 C fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 30 OG 9.959
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CB fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A SER 37 O 9.960
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A LEU 31 CD2 9.961
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 C fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A PHE 33 CE1 9.961
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 N fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A SER 30 C 9.961
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 28 O 9.962
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ASP 119 OD1 9.963
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 O AF-Q9FG74-F1-model_v6.pdb #1/A SER 10 C 9.963
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A LYS 150 NZ 9.964
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 C fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A PRO 36 CA 9.965
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CA AF-Q9FG74-F1-model_v6.pdb #1/A ASN 13 O 9.965
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 28 C 9.966
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CB fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 37 O 9.968
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 O fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A PHE 33 CD2 9.970
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 37 O 9.970
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A SER 56 OG 9.970
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 C fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 37 O 9.970
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 37 OG 9.971
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 N AF-Q9FG74-F1-model_v6.pdb #1/A SER 15 OG 9.971
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 N fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A PHE 33 CD1 9.972
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CB fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A LEU 31 CA 9.972
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A LEU 31 CD1 9.973
AF-Q9FG74-F1-model_v6.pdb #1/A ALA 34 N AF-Q9FG74-F1-model_v6.pdb #1/A SER 37 N 9.973
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ARG 148 CZ 9.974
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CA fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 38 CA 9.974
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 N fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 37 CA 9.974
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 O fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ARG 148 NH1 9.975
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ASP 119 OD1 9.976
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A VAL 27 CG1 9.977
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A THR 58 CA 9.977
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 C fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A LEU 31 CB 9.979
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ARG 148 NH1 9.979
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A LYS 150 NZ 9.981
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CB fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A PHE 33 CZ 9.981
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A LYS 150 NZ 9.982
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ARG 148 CZ 9.982
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CB fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ASP 35 CA 9.982
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A GLN 26 C 9.983
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 O fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 38 N 9.985
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 CB fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A PRO 36 C 9.986
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 37 C 9.986
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 56 CA 9.987
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 O fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A GLN 26 O 9.988
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 C fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A VAL 27 O 9.988
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O AF-Q9FG74-F1-model_v6.pdb #1/A LEU 11 CA 9.988
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A SER 29 OG 9.989
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ASN 391 ND2 9.989
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 O fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ARG 148 NH1 9.990
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O AF-Q9FG74-F1-model_v6.pdb #1/A ASN 391 ND2 9.990
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 O fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A PRO 36 CB 9.991
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ASP 35 C 9.991
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 CB fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 32 OG 9.992
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 C fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 38 N 9.992
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CA fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ASP 119 OD1 9.992
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CB fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A PHE 33 CZ 9.992
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 C fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A LEU 31 CA 9.993
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CA fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 29 N 9.993
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CB fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A VAL 27 O 9.994
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 O fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A SER 37 O 9.994
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 N fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A VAL 27 CA 9.994
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 CB fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A PRO 36 N 9.994
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 O fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ARG 148 NE 9.995
fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A ALA 34 C fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ASP 35 O 9.996
fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A ALA 34 C fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A LEU 31 O 9.997
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 CB fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ARG 148 NE 9.997
fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A ALA 34 N fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A SER 32 OG 9.998
fold_2026_08_18_d6pk_non_p_5s_model_0.cif #6/A ALA 34 N fold_2026_08_18_d6pk_p_5s_model_0.cif #4/A THR 58 CA 9.998
fold_2026_08_18_d6pk_p_auto_model_0.cif #2/A ALA 34 O fold_2026_08_18_d6pk_p_2s_model_0.cif #5/A LEU 31 CG 9.998
fold_2026_08_18_d6pk_non_p_2s_model_0.cif #7/A ALA 34 CA fold_2026_08_18_d6pk_non_p_auto_model_0.cif #3/A PRO 36 CD 9.999
7794 distances
> color bfactor #2 palette alphafold
3592 atoms, 464 residues, 1 surfaces, atom bfactor range 8.75 to 98.9
> color #2/A:22-35 lime
> color #2/A:85-262 magenta
> color #2/A:401 lime
> color magenta
> color #2/A:18-37 lime
> color #2/A:84-261 magenta
> color bfactor #2 palette alphafold
3592 atoms, 464 residues, 1 surfaces, atom bfactor range 8.75 to 98.9
> color #2/A:19-36 lime
> color #2/A:85-257 magenta
> color #2/A:25 lime
> color #2/A:341 magenta
> color bfactor #2 palette alphafold
3592 atoms, 464 residues, 1 surfaces, atom bfactor range 8.75 to 98.9
> color #2/A:19-36 lime
> color #2/A:84-265 magenta
> color #2/A:21-33 lime
> color #2/A:335-464 magenta
> color #2/A:456 lime
> color #2/A:292 magenta
> color #2/A:54-61 #2/A:62@N,CA,CB,OG,C lime
> color #2/A:348-464 magenta
> color #2/A:23-35 lime
> color #2/A:354-464 magenta
> color #2/A:414 lime
> color #2/A:155 magenta
> color #2/A:19-36 lime
> color #2/A:332-464 magenta
> color #2/A:26 lime
> color #2/A:353 magenta
> color #2/A:309 lime
> color #2/A:372 magenta
> color #2/A:460 lime
> color #2/A:276 magenta
> color #2/A:19-35 lime
> color #2/A:330-464 magenta
> color #2/A:438 lime
> color #2/A:306 magenta
> color #2/A:17-37 lime
> color #2/A:328-464 magenta
> color lime
> color #2/A:283 magenta
> color #2/A:51-61 #2/A:62@N,CA,CB,OG,C,O,P,O1P lime
> color #2/A:335-464 magenta
> color #2/A:70-266 lime
> color #2/A:333-464 magenta
> color #2/A:437 lime
> color #2/A:353 magenta
> color #2/A:90-193 lime
> color magenta
> color #2/A:402 lime
> color #2/A:411 magenta
> color lime
> color magenta
> color lime
> color #2/A:337-464 magenta
> select clear
> color lime
> color #2/A:84-260 magenta
> color #2/A:339-464 lime
> color #2/A:15-33 magenta
> color #2/A:355 lime
> color #2/A:24 magenta
> color #2/A:355 lime
> color #2/A:23 magenta
> color #2/A:387-402 lime
> color #2/A:15-30 magenta
> color #2/A:417 lime
> color #2/A:35 magenta
> color #2/A:342-365 lime
> color #2/A:18-36 magenta
> color #2/A:365 lime
> color #2/A:36 magenta
> color #2/A:340-368 lime
> color #2/A:17-33 magenta
> color #2/A:348 lime
> color #2/A:23 magenta
> color #2/A:358-361 lime
> color #2/A:17-35 magenta
> color #2/A:391-399 lime
> color #2/A:19-30 magenta
> color #2/A:422 lime
> color #2/A:34 magenta
> color #2/A:440 lime
> color #2/A:171 magenta
> color #2/A:434 lime
> color magenta
> color bfactor #2 palette alphafold
3592 atoms, 464 residues, 1 surfaces, atom bfactor range 8.75 to 98.9
> color #2/A:406-448 lime
> color #2/A:263-266 magenta
> color #2/A:299-306 lime
> color #2/A:82-260 magenta
> color #2/A:300-303 lime
> color #2/A:339-464 magenta
> color #2/A:54-61 #2/A:62 lime
> color #2/A:20-29 magenta
> color #2/A:84-270 lime
> select clear
[Repeated 3 time(s)]
> color lime
> color #2/A:272 magenta
> color bfactor #2 palette alphafold
3592 atoms, 464 residues, 1 surfaces, atom bfactor range 8.75 to 98.9
> color #2/A:443 lime
> color #2/A:150 magenta
> color #2/A:76-268 lime
> color #2/A:49-60 magenta
> color #2/A:247 lime
> color #2/A:62@O2P magenta
> select clear
> color #2/A:443 lime
> color #2/A:214 magenta
> color bfactor #2 palette alphafold
3592 atoms, 464 residues, 1 surfaces, atom bfactor range 8.75 to 98.9
> clear contacts
Unknown command: clear contacts
> distance delete
> contacts delete
> select #2 :1-55
389 atoms, 391 bonds, 55 residues, 1 model selected
> select down
389 atoms, 391 bonds, 55 residues, 2 models selected
> select down
389 atoms, 391 bonds, 55 residues, 2 models selected
> select down
389 atoms, 391 bonds, 55 residues, 2 models selected
> select down
389 atoms, 391 bonds, 55 residues, 2 models selected
> select #2 :1-55
389 atoms, 391 bonds, 55 residues, 1 model selected
> delete sel
> save D6PK_P_truncated-C-term-465-498_n-term-1-55.pdb #2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 885, in mouseMoveEvent
self._report_residues_and_atoms_callback(int(x),int(y))
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 695, in _report_residues_or_atoms
column_name, row_name = [pae.row_residue_or_atom_name(i) for i in
(column_index, row_index)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 695, in <listcomp>
column_name, row_name = [pae.row_residue_or_atom_name(i) for i in
(column_index, row_index)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1091, in row_residue_or_atom_name
ra = self.row_residues_or_atoms()[row]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1044, in row_residues_or_atoms
self._row_residues_or_atoms = tuple((None if ra.deleted else ra)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1044, in <genexpr>
self._row_residues_or_atoms = tuple((None if ra.deleted else ra)
^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'deleted'
AttributeError: 'NoneType' object has no attribute 'deleted'
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1044, in
self._row_residues_or_atoms = tuple((None if ra.deleted else ra)
^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 885, in mouseMoveEvent
self._report_residues_and_atoms_callback(int(x),int(y))
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 695, in _report_residues_or_atoms
column_name, row_name = [pae.row_residue_or_atom_name(i) for i in
(column_index, row_index)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 695, in <listcomp>
column_name, row_name = [pae.row_residue_or_atom_name(i) for i in
(column_index, row_index)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1091, in row_residue_or_atom_name
ra = self.row_residues_or_atoms()[row]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1044, in row_residues_or_atoms
self._row_residues_or_atoms = tuple((None if ra.deleted else ra)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1044, in <genexpr>
self._row_residues_or_atoms = tuple((None if ra.deleted else ra)
^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'deleted'
AttributeError: 'NoneType' object has no attribute 'deleted'
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1044, in
self._row_residues_or_atoms = tuple((None if ra.deleted else ra)
^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 885, in mouseMoveEvent
self._report_residues_and_atoms_callback(int(x),int(y))
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 695, in _report_residues_or_atoms
column_name, row_name = [pae.row_residue_or_atom_name(i) for i in
(column_index, row_index)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 695, in <listcomp>
column_name, row_name = [pae.row_residue_or_atom_name(i) for i in
(column_index, row_index)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1091, in row_residue_or_atom_name
ra = self.row_residues_or_atoms()[row]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1044, in row_residues_or_atoms
self._row_residues_or_atoms = tuple((None if ra.deleted else ra)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1044, in <genexpr>
self._row_residues_or_atoms = tuple((None if ra.deleted else ra)
^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'deleted'
AttributeError: 'NoneType' object has no attribute 'deleted'
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1044, in
self._row_residues_or_atoms = tuple((None if ra.deleted else ra)
^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63LA/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 6 days, 8 hours, 6 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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
sse-starlette: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.24.2
Change History (1)
comment:1 by , 24 hours ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → AlphaFold PAE: 'ra' is None |
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