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Opened 44 hours ago
Closed 13 hours ago
#20857 closed defect (fixed)
AlphaFold PAE: 'ra' is None
| 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
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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
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babel: 2.18.0
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blosc2: 4.4.3
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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
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ChimeraX-ColorKey: 1.5.8
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ChimeraX-Contacts: 1.0.1
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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
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ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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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
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ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
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ChimeraX-Meeting: 1.0.1
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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
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ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
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ChimeraX-RotamerLibsRichardson: 2.0
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ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
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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
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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
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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
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debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
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fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
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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
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ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
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nest-asyncio: 1.6.0
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PyOpenGL-accelerate: 3.1.10
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Change History (3)
comment:1 by , 21 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 |
comment:2 by , 17 hours ago
comment:3 by , 13 hours ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
Deleting some residues or atoms from predicted structure then mousing over PAE plot, then deleting more residues and atoms and mousing over PAE plot caused this error. It took two deletions and two mouse hovers to cause this error explaining why we have not seen it before. Fixed by making sure previously deleted atoms/residues handled correctly by PAE plot code.
Note:
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Appears that deleting some atoms of an alphafold structure and then mousing over a PAE plot for that structure can produce this error when it does not find the residue or atom corresponding to the mouse position on the PAE plot. Should be easy to fix.