![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 hours ago
Last modified 10 minutes ago
#19879 feedback defect
Find Cavities: cavity KeyError
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface/Binding Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.3-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
find cativies is not working anymore
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/clmarino/Desktop/022326_RLNWT_ITGA2WT.cxs format session
Log from Mon Feb 23 10:36:03 2026You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/clmarino/Downloads/folds_2026_02_23_FN1-CTR_RLN/20260217_fn1_b7zle5_wt_ctrrln_wtb/fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_0.cif
Chain information for fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> open
> /Users/clmarino/Downloads/folds_2026_02_23_FN1-CTR_RLN/20260217_fn1_b7zle5_wt_ctrrln_wtb/fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_1.cif
Chain information for fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_1.cif #2
---
Chain | Description
A | .
B | .
> open
> /Users/clmarino/Downloads/folds_2026_02_23_FN1-CTR_RLN/20260217_fn1_b7zle5_wt_ctrrln_wtb/fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_2.cif
Chain information for fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_2.cif #3
---
Chain | Description
A | .
B | .
> open
> /Users/clmarino/Downloads/folds_2026_02_23_FN1-CTR_RLN/20260217_fn1_b7zle5_wt_ctrrln_wtb/fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_3.cif
Chain information for fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_3.cif #4
---
Chain | Description
A | .
B | .
> open
> /Users/clmarino/Downloads/folds_2026_02_23_FN1-CTR_RLN/20260217_fn1_b7zle5_wt_ctrrln_wtb/fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_4.cif
Chain information for fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_4.cif #5
---
Chain | Description
A | .
B | .
Computing secondary structure
[Repeated 3 time(s)]
> set bgColor white
> color bychain
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_0.cif, chain A (#1)
with fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_1.cif, chain A (#2),
sequence alignment score = 11680.5
RMSD between 147 pruned atom pairs is 1.090 angstroms; (across all 2240 pairs:
50.052)
Matchmaker fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_0.cif, chain A (#1)
with fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_2.cif, chain A (#3),
sequence alignment score = 11714.7
RMSD between 385 pruned atom pairs is 0.895 angstroms; (across all 2240 pairs:
28.924)
Matchmaker fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_0.cif, chain A (#1)
with fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_3.cif, chain A (#4),
sequence alignment score = 11639.1
RMSD between 98 pruned atom pairs is 0.500 angstroms; (across all 2240 pairs:
61.688)
Matchmaker fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_0.cif, chain A (#1)
with fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_4.cif, chain A (#5),
sequence alignment score = 11668.5
RMSD between 34 pruned atom pairs is 1.426 angstroms; (across all 2240 pairs:
49.185)
> ui tool show "Find Cavities"
> kvfinder
75 cavities found for fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_0.cif #1
fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_0.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.1.48 | | 3028.1 | 2052.1 | 14019 | 8.16 | 2.67
1.1.22 | | 2497.61 | 1766.7 | 11563 | 8.51 | 2.71
1.1.26 | | 1885.03 | 1387.54 | 8727 | 8.27 | 1.67
1.1.46 | | 1461.67 | 954.99 | 6767 | 8.42 | 1.83
1.1.36 | | 915.41 | 608.22 | 4238 | 4.84 | 0.88
1.1.3 | | 882.58 | 565.58 | 4086 | 4.24 | 1.24
1.1.15 | | 852.34 | 675.39 | 3946 | 4.69 | 1.34
1.1.68 | | 598.54 | 354.79 | 2771 | 4.8 | 1.25
1.1.24 | | 457.27 | 382.16 | 2117 | 7.22 | 2.01
1.1.9 | | 429.62 | 388 | 1989 | 6.73 | 1.87
1.1.12 | | 210.82 | 113.7 | 976 | 2.47 | 0.54
1.1.57 | | 160.27 | 166.14 | 742 | 2.47 | 0.69
1.1.17 | | 160.06 | 162.27 | 741 | 4.07 | 1.02
1.1.53 | | 119.45 | 140.82 | 553 | 3.93 | 1.3
1.1.8 | | 92.88 | 97.81 | 430 | 3.23 | 1.32
1.1.62 | | 82.73 | 81.06 | 383 | 3.06 | 0.9
1.1.20 | | 65.23 | 86.68 | 302 | 6.03 | 2.4
1.1.10 | | 60.7 | 66.04 | 281 | 1.7 | 0.48
1.1.58 | | 57.67 | 58.03 | 267 | 3 | 0.95
1.1.50 | | 54.43 | 60.4 | 252 | 3.12 | 1.31
1.1.49 | | 50.76 | 53.52 | 235 | 1.7 | 0.38
1.1.72 | | 47.95 | 53 | 222 | 1.8 | 0.46
1.1.33 | | 47.74 | 47.6 | 221 | 1.2 | 0.31
1.1.25 | | 47.52 | 65.37 | 220 | 1.8 | 0.47
1.1.43 | | 45.36 | 53.73 | 210 | 2.47 | 0.87
1.1.63 | | 42.34 | 46.75 | 196 | 1.7 | 0.44
1.1.42 | | 38.66 | 33.71 | 179 | 0.6 | 0.09
1.1.52 | | 37.15 | 48.91 | 172 | 1.8 | 0.47
1.1.38 | | 36.5 | 58.66 | 169 | 1.8 | 0.49
1.1.5 | | 34.78 | 41.95 | 161 | 1.8 | 0.63
1.1.55 | | 31.97 | 46.42 | 148 | 2.62 | 1.04
1.1.14 | | 30.46 | 43.4 | 141 | 1.8 | 0.64
1.1.37 | | 30.24 | 35.26 | 140 | 1.34 | 0.36
1.1.67 | | 26.35 | 39.77 | 122 | 0 | 0
1.1.59 | | 26.14 | 46.24 | 121 | 0 | 0
1.1.69 | | 24.84 | 38.2 | 115 | 1.7 | 0.48
1.1.19 | | 24.41 | 38.19 | 113 | 1.7 | 0.37
1.1.71 | | 22.9 | 49.81 | 106 | 4.24 | 1.94
1.1.13 | | 22.68 | 34.77 | 105 | 1.47 | 0.31
1.1.65 | | 22.25 | 34.99 | 103 | 2.55 | 1.07
1.1.73 | | 21.82 | 40.63 | 101 | 0 | 0
1.1.18 | | 21.17 | 29.25 | 98 | 1.34 | 0.39
1.1.28 | | 20.74 | 33.31 | 96 | 2.4 | 1.03
1.1.56 | | 20.52 | 34.36 | 95 | 3 | 1.27
1.1.11 | | 18.36 | 27.47 | 85 | 0.6 | 0.09
1.1.31 | | 18.36 | 26.94 | 85 | 0.85 | 0.29
1.1.30 | | 17.93 | 25.62 | 83 | 1.8 | 0.53
1.1.70 | | 17.93 | 27.99 | 83 | 1.2 | 0.34
1.1.51 | | 17.06 | 31.17 | 79 | 1.04 | 0.21
1.1.39 | | 16.85 | 32.3 | 78 | 0 | 0
1.1.64 | | 16.85 | 30.73 | 78 | 1.9 | 0.62
1.1.45 | | 16.2 | 26.61 | 75 | 1.34 | 0.52
1.1.44 | | 13.18 | 22.34 | 61 | 1.34 | 0.42
1.1.32 | | 12.96 | 26.54 | 60 | 1.7 | 0.63
1.1.2 | | 12.31 | 29.54 | 57 | 0 | 0
1.1.29 | | 12.1 | 23.24 | 56 | 0.85 | 0.21
1.1.1 | | 11.66 | 16.12 | 54 | 0.85 | 0.27
1.1.27 | | 10.8 | 19.85 | 50 | 0.85 | 0.34
1.1.54 | | 10.37 | 17.74 | 48 | 1.34 | 0.35
1.1.66 | | 10.37 | 23.28 | 48 | 1.7 | 0.74
1.1.75 | | 9.94 | 16.87 | 46 | 1.34 | 0.48
1.1.74 | | 9.72 | 21.3 | 45 | 1.34 | 0.49
1.1.4 | | 8.64 | 19.12 | 40 | 1.34 | 0.55
1.1.47 | | 8.64 | 20.22 | 40 | 1.2 | 0.49
1.1.34 | | 7.56 | 14.87 | 35 | 0.85 | 0.25
1.1.40 | | 7.34 | 17.1 | 34 | 0.6 | 0.12
1.1.61 | | 7.34 | 16.53 | 34 | 0.6 | 0.09
1.1.60 | | 7.13 | 13.75 | 33 | 1.04 | 0.38
1.1.7 | | 6.91 | 12.48 | 32 | 0.6 | 0.19
1.1.21 | | 6.7 | 14.85 | 31 | 0.6 | 0.19
1.1.23 | | 6.48 | 11.03 | 30 | 0.6 | 0.2
1.1.35 | | 6.48 | 12.64 | 30 | 0.85 | 0.22
1.1.16 | | 6.26 | 11.35 | 29 | 0.85 | 0.24
1.1.41 | | 5.62 | 13.21 | 26 | 0.6 | 0.12
1.1.6 | | 5.4 | 11.55 | 25 | 0.6 | 0.17
Populating font family aliases took 97 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
95 cavities found for fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_1.cif #2
fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_1.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
2.1.29 | | 5252.9 | 3934.01 | 24319 | 16.49 | 4.91
2.1.31 | | 2363.04 | 1625.91 | 10940 | 5.47 | 1.41
2.1.54 | | 987.55 | 650.22 | 4572 | 6.03 | 2.14
2.1.22 | | 829.22 | 624.86 | 3839 | 8.59 | 3.21
2.1.82 | | 510.84 | 401.39 | 2365 | 3.06 | 0.67
2.1.77 | | 460.73 | 331.17 | 2133 | 4.57 | 1.66
2.1.93 | | 372.17 | 364.26 | 1723 | 4.02 | 1.28
2.1.69 | | 368.93 | 442.9 | 1708 | 8.86 | 3.74
2.1.51 | | 349.27 | 348.68 | 1617 | 6.26 | 1.53
2.1.68 | | 281.88 | 258.65 | 1305 | 8.98 | 2.72
2.1.18 | | 235.44 | 257.6 | 1090 | 5.91 | 1.42
2.1.55 | | 220.97 | 207.34 | 1023 | 4.37 | 1.06
2.1.63 | | 220.54 | 207.05 | 1021 | 4.98 | 1.44
2.1.47 | | 214.7 | 226.11 | 994 | 3.6 | 1.13
2.1.12 | | 177.77 | 161.02 | 823 | 3.6 | 1.11
2.1.78 | | 164.38 | 150.26 | 761 | 2.47 | 0.76
2.1.27 | | 120.31 | 95.44 | 557 | 2.47 | 0.72
2.1.32 | | 115.13 | 131.72 | 533 | 3.65 | 0.94
2.1.60 | | 93.53 | 109.97 | 433 | 0 | 0
2.1.70 | | 93.1 | 118.62 | 431 | 3.84 | 1.06
2.1.61 | | 92.66 | 110.51 | 429 | 2.47 | 0.6
2.1.34 | | 86.4 | 105.79 | 400 | 4.02 | 1.38
2.1.94 | | 85.97 | 75.18 | 398 | 1.47 | 0.42
2.1.95 | | 85.75 | 105.73 | 397 | 3.06 | 1.22
2.1.5 | | 80.35 | 90.57 | 372 | 2.68 | 0.79
2.1.45 | | 77.11 | 104.09 | 357 | 4.41 | 1.41
2.1.66 | | 69.34 | 84.38 | 321 | 2.68 | 0.79
2.1.9 | | 62.86 | 61.52 | 291 | 3 | 0.8
2.1.86 | | 62.21 | 61.1 | 288 | 1.8 | 0.45
2.1.15 | | 57.67 | 64.48 | 267 | 2.47 | 0.71
2.1.40 | | 57.24 | 83.13 | 265 | 5.2 | 1.7
2.1.20 | | 56.38 | 60.76 | 261 | 2.55 | 0.7
2.1.56 | | 54.65 | 70.1 | 253 | 1.99 | 0.47
2.1.64 | | 53.57 | 66 | 248 | 3 | 1.02
2.1.83 | | 50.33 | 64.29 | 233 | 3 | 0.89
2.1.65 | | 50.11 | 59.3 | 232 | 1.9 | 0.44
2.1.30 | | 49.46 | 77.41 | 229 | 6.18 | 2.61
2.1.35 | | 46.01 | 55.81 | 213 | 3.06 | 1.27
2.1.90 | | 44.28 | 47.05 | 205 | 2.24 | 0.69
2.1.52 | | 36.07 | 54.32 | 167 | 0 | 0
2.1.25 | | 30.46 | 51.69 | 141 | 1.8 | 0.62
2.1.10 | | 27.43 | 41.63 | 127 | 3.06 | 1.39
2.1.62 | | 27 | 44.51 | 125 | 0 | 0
2.1.43 | | 26.14 | 36.57 | 121 | 1.7 | 0.52
2.1.79 | | 24.84 | 34.38 | 115 | 1.8 | 0.59
2.1.73 | | 23.11 | 42.35 | 107 | 0 | 0
2.1.19 | | 22.68 | 33.62 | 105 | 0.85 | 0.25
2.1.36 | | 22.46 | 37.85 | 104 | 1.34 | 0.33
2.1.6 | | 22.03 | 30.76 | 102 | 1.8 | 0.48
2.1.42 | | 19.01 | 30.99 | 88 | 2.16 | 0.94
2.1.81 | | 19.01 | 38.34 | 88 | 0 | 0
2.1.3 | | 17.28 | 28.85 | 80 | 2.16 | 0.99
2.1.49 | | 17.28 | 36.68 | 80 | 0 | 0
2.1.17 | | 16.42 | 25.77 | 76 | 1.7 | 0.64
2.1.33 | | 16.42 | 23.44 | 76 | 1.34 | 0.46
2.1.11 | | 16.2 | 24.45 | 75 | 1.34 | 0.44
2.1.14 | | 15.77 | 23.63 | 73 | 1.2 | 0.34
2.1.67 | | 15.77 | 25.49 | 73 | 1.8 | 0.81
2.1.24 | | 14.04 | 21.5 | 65 | 1.34 | 0.34
2.1.80 | | 13.82 | 34.21 | 64 | 3.5 | 2.1
2.1.89 | | 13.82 | 25.85 | 64 | 1.7 | 0.51
2.1.39 | | 13.39 | 23.7 | 62 | 1.2 | 0.28
2.1.91 | | 12.74 | 17.85 | 59 | 1.2 | 0.23
2.1.4 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.38 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.41 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.44 | | 12.31 | 23.43 | 57 | 0.6 | 0.15
2.1.75 | | 12.31 | 22.21 | 57 | 1.7 | 0.74
2.1.88 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.37 | | 11.45 | 26.09 | 53 | 1.8 | 0.99
2.1.84 | | 11.23 | 12.86 | 52 | 0.85 | 0.23
2.1.76 | | 11.02 | 20.04 | 51 | 0.85 | 0.22
2.1.13 | | 9.94 | 16.03 | 46 | 1.2 | 0.25
2.1.1 | | 9.72 | 17.48 | 45 | 1.2 | 0.33
2.1.92 | | 9.72 | 15.57 | 45 | 1.2 | 0.29
2.1.85 | | 9.29 | 20.19 | 43 | 1.2 | 0.41
2.1.16 | | 8.64 | 18.64 | 40 | 1.34 | 0.53
2.1.7 | | 8.42 | 16.15 | 39 | 1.2 | 0.35
2.1.50 | | 7.78 | 13.06 | 36 | 0.85 | 0.26
2.1.87 | | 7.34 | 12.86 | 34 | 0.6 | 0.21
2.1.57 | | 7.13 | 11.95 | 33 | 0.6 | 0.15
2.1.8 | | 6.91 | 16.12 | 32 | 1.04 | 0.41
2.1.72 | | 6.91 | 12.77 | 32 | 0.6 | 0.19
2.1.23 | | 6.48 | 13.58 | 30 | 0.6 | 0.04
2.1.58 | | 6.48 | 11.63 | 30 | 0.6 | 0.12
2.1.59 | | 6.48 | 13.19 | 30 | 0.6 | 0.16
2.1.26 | | 6.26 | 14.36 | 29 | 0.85 | 0.27
2.1.28 | | 6.26 | 13.04 | 29 | 0.6 | 0.08
2.1.71 | | 6.05 | 11.7 | 28 | 0.6 | 0.13
2.1.74 | | 6.05 | 12.43 | 28 | 0.85 | 0.24
2.1.2 | | 5.83 | 12.41 | 27 | 0 | 0
2.1.21 | | 5.83 | 11.18 | 27 | 0.6 | 0.13
2.1.46 | | 5.62 | 10.97 | 26 | 0.6 | 0.18
2.1.53 | | 5.4 | 10.77 | 25 | 0.6 | 0.19
2.1.48 | | 5.18 | 11.09 | 24 | 0.6 | 0.1
99 cavities found for fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_2.cif #3
fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_2.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
3.1.36 | | 9416.3 | 7298.15 | 43594 | 9.49 | 2.64
3.1.47 | | 656.64 | 510.11 | 3040 | 7.02 | 2.11
3.1.17 | | 655.56 | 495.64 | 3035 | 4.84 | 1.46
3.1.48 | | 427.03 | 344.5 | 1977 | 6.49 | 1.54
3.1.58 | | 338.04 | 334.03 | 1565 | 3.06 | 1.01
3.1.29 | | 230.69 | 199.34 | 1068 | 3.23 | 1.18
3.1.55 | | 193.1 | 124.78 | 894 | 2.68 | 0.85
3.1.38 | | 161.78 | 145.33 | 749 | 4.24 | 1.33
3.1.43 | | 159.41 | 182.75 | 738 | 4.87 | 1.27
3.1.6 | | 149.04 | 128.01 | 690 | 2.16 | 0.46
3.1.23 | | 145.58 | 171.56 | 674 | 5.16 | 1.85
3.1.50 | | 143.64 | 138.85 | 665 | 2.55 | 0.79
3.1.86 | | 135.22 | 143.93 | 626 | 3 | 0.75
3.1.28 | | 131.98 | 107.75 | 611 | 3 | 0.85
3.1.69 | | 120.96 | 112.06 | 560 | 1.9 | 0.61
3.1.74 | | 117.94 | 120.21 | 546 | 3 | 0.74
3.1.92 | | 108.86 | 121.39 | 504 | 4.33 | 1.72
3.1.22 | | 101.95 | 98.81 | 472 | 3 | 0.76
3.1.25 | | 98.28 | 88.09 | 455 | 2.75 | 0.8
3.1.84 | | 96.98 | 97.74 | 449 | 3.79 | 1.19
3.1.19 | | 87.05 | 110.01 | 403 | 3.5 | 1.03
3.1.63 | | 82.3 | 76.72 | 381 | 2.68 | 0.74
3.1.75 | | 82.3 | 75.36 | 381 | 3 | 0.72
3.1.61 | | 81.22 | 101.02 | 376 | 0 | 0
3.1.35 | | 73.22 | 86.25 | 339 | 2.62 | 0.61
3.1.79 | | 68.26 | 64.73 | 316 | 3.5 | 1.04
3.1.85 | | 68.04 | 98.8 | 315 | 0 | 0
3.1.14 | | 60.91 | 62.59 | 282 | 1.34 | 0.39
3.1.73 | | 56.16 | 96.93 | 260 | 0 | 0
3.1.98 | | 56.16 | 63.65 | 260 | 2.16 | 0.55
3.1.93 | | 54.65 | 77.44 | 253 | 1.9 | 0.58
3.1.68 | | 51.41 | 75.75 | 238 | 3.5 | 1.55
3.1.41 | | 47.95 | 46.17 | 222 | 1.9 | 0.59
3.1.46 | | 44.5 | 77.82 | 206 | 4.07 | 1.38
3.1.56 | | 39.74 | 51.82 | 184 | 1.9 | 0.55
3.1.59 | | 37.15 | 53.22 | 172 | 1.7 | 0.53
3.1.77 | | 36.94 | 51.75 | 171 | 3.6 | 1.59
3.1.67 | | 36.07 | 44.89 | 167 | 2.16 | 0.83
3.1.90 | | 34.56 | 50.29 | 160 | 3.23 | 1.33
3.1.18 | | 33.05 | 43 | 153 | 2.81 | 1.17
3.1.10 | | 32.4 | 37.09 | 150 | 1.2 | 0.45
3.1.95 | | 29.38 | 35.21 | 136 | 1.7 | 0.32
3.1.34 | | 28.51 | 44.21 | 132 | 0 | 0
3.1.96 | | 28.3 | 42 | 131 | 1.34 | 0.3
3.1.87 | | 25.27 | 51.8 | 117 | 3.84 | 1.65
3.1.13 | | 23.11 | 35.66 | 107 | 1.34 | 0.42
3.1.9 | | 22.46 | 25.87 | 104 | 1.7 | 0.55
3.1.5 | | 21.6 | 31.09 | 100 | 1.47 | 0.35
3.1.31 | | 21.38 | 29.79 | 99 | 1.34 | 0.38
3.1.32 | | 19.44 | 26.66 | 90 | 1.7 | 0.47
3.1.88 | | 19.01 | 38.34 | 88 | 0 | 0
3.1.12 | | 18.36 | 23.99 | 85 | 0.85 | 0.21
3.1.60 | | 17.93 | 22.9 | 83 | 1.2 | 0.28
3.1.37 | | 17.71 | 28.25 | 82 | 1.8 | 0.57
3.1.42 | | 17.5 | 25.82 | 81 | 1.7 | 0.48
3.1.49 | | 17.5 | 34.64 | 81 | 2.16 | 0.83
3.1.33 | | 17.28 | 36.68 | 80 | 0 | 0
3.1.66 | | 17.28 | 36.68 | 80 | 0 | 0
3.1.3 | | 17.06 | 30.23 | 79 | 1.2 | 0.28
3.1.44 | | 16.85 | 32.3 | 78 | 0 | 0
3.1.52 | | 16.85 | 32.3 | 78 | 0 | 0
3.1.80 | | 16.85 | 32.3 | 78 | 0 | 0
3.1.26 | | 16.42 | 25.42 | 76 | 1.8 | 0.6
3.1.30 | | 15.12 | 25.43 | 70 | 1.2 | 0.31
3.1.39 | | 14.47 | 30.81 | 67 | 2.16 | 0.93
3.1.4 | | 13.82 | 26.94 | 64 | 0.85 | 0.2
3.1.89 | | 13.39 | 26.4 | 62 | 0.85 | 0.28
3.1.8 | | 12.96 | 25.33 | 60 | 0.6 | 0.04
3.1.51 | | 12.74 | 22.14 | 59 | 1.34 | 0.62
3.1.2 | | 12.31 | 29.54 | 57 | 0 | 0
3.1.78 | | 12.31 | 29.54 | 57 | 0 | 0
3.1.91 | | 12.31 | 29.54 | 57 | 0 | 0
3.1.7 | | 11.88 | 27.62 | 55 | 2.16 | 1.18
3.1.71 | | 10.8 | 21.22 | 50 | 1.2 | 0.32
3.1.65 | | 10.37 | 17.6 | 48 | 1.34 | 0.43
3.1.40 | | 9.72 | 18.35 | 45 | 0.6 | 0.09
3.1.20 | | 9.29 | 21.36 | 43 | 1.34 | 0.56
3.1.94 | | 9.29 | 19.51 | 43 | 1.34 | 0.59
3.1.64 | | 9.07 | 13.91 | 42 | 0.6 | 0.13
3.1.1 | | 8.86 | 13.89 | 41 | 0.6 | 0.16
3.1.15 | | 8.86 | 20.79 | 41 | 1.2 | 0.5
3.1.21 | | 8.86 | 15.47 | 41 | 0.85 | 0.34
3.1.81 | | 8.86 | 17.52 | 41 | 1.2 | 0.39
3.1.16 | | 8.42 | 16.65 | 39 | 1.34 | 0.45
3.1.62 | | 8.21 | 15.47 | 38 | 0.85 | 0.25
3.1.82 | | 8.21 | 16.33 | 38 | 0.85 | 0.28
3.1.57 | | 7.99 | 13.48 | 37 | 1.04 | 0.33
3.1.99 | | 7.99 | 16.68 | 37 | 0.85 | 0.24
3.1.54 | | 7.78 | 17.25 | 36 | 0.6 | 0.08
3.1.11 | | 7.56 | 15 | 35 | 1.2 | 0.32
3.1.24 | | 7.34 | 16.05 | 34 | 1.2 | 0.43
3.1.72 | | 6.91 | 12.95 | 32 | 0.6 | 0.19
3.1.53 | | 6.7 | 12.81 | 31 | 0.6 | 0.19
3.1.45 | | 6.05 | 14.3 | 28 | 0.6 | 0.17
3.1.76 | | 6.05 | 12.54 | 28 | 0.6 | 0.17
3.1.83 | | 5.83 | 12.58 | 27 | 0.85 | 0.25
3.1.70 | | 5.62 | 12.37 | 26 | 0 | 0
3.1.27 | | 5.4 | 14.21 | 25 | 0.6 | 0.02
3.1.97 | | 5.4 | 12.04 | 25 | 0 | 0
98 cavities found for fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_3.cif #4
fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_3.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
4.1.27 | | 767.02 | 603.75 | 3551 | 11.85 | 3.65
4.1.14 | | 723.38 | 660.43 | 3349 | 6.73 | 1.81
4.1.85 | | 594.86 | 438.49 | 2754 | 6.46 | 2.35
4.1.33 | | 502.85 | 499.65 | 2328 | 3.79 | 0.92
4.1.51 | | 405.43 | 340.73 | 1877 | 5.47 | 1.38
4.1.26 | | 276.7 | 292.74 | 1281 | 6.81 | 2.54
4.1.8 | | 258.55 | 220.02 | 1197 | 3.06 | 1.07
4.1.55 | | 243.86 | 227.41 | 1129 | 7.05 | 2.41
4.1.83 | | 233.5 | 175.82 | 1081 | 3.45 | 1.02
4.1.47 | | 228.31 | 239.17 | 1057 | 0 | 0
4.1.21 | | 225.5 | 238.56 | 1044 | 3.12 | 0.89
4.1.25 | | 180.58 | 166.9 | 836 | 1.99 | 0.48
4.1.59 | | 170.42 | 207.96 | 789 | 9.66 | 3.21
4.1.17 | | 169.99 | 189.1 | 787 | 4.57 | 1.13
4.1.57 | | 158.33 | 132.02 | 733 | 3.12 | 1.05
4.1.66 | | 148.61 | 204.49 | 688 | 8.25 | 2.38
4.1.71 | | 130.25 | 110.23 | 603 | 4.61 | 1.59
4.1.49 | | 123.77 | 107.35 | 573 | 3 | 0.63
4.1.60 | | 122.26 | 144.64 | 566 | 7.91 | 4.11
4.1.92 | | 115.78 | 92.43 | 536 | 2.55 | 0.57
4.1.67 | | 112.54 | 127.02 | 521 | 4.57 | 2.3
4.1.86 | | 99.36 | 78.9 | 460 | 1.7 | 0.35
4.1.73 | | 98.93 | 111.86 | 458 | 5.13 | 2.06
4.1.4 | | 97.2 | 65.71 | 450 | 1.9 | 0.38
4.1.44 | | 87.91 | 112.92 | 407 | 3 | 0.79
4.1.9 | | 85.32 | 91.9 | 395 | 2.24 | 0.62
4.1.30 | | 80.57 | 89.85 | 373 | 6.38 | 2.79
4.1.29 | | 69.12 | 77.13 | 320 | 1.8 | 0.49
4.1.52 | | 67.18 | 91.59 | 311 | 0 | 0
4.1.61 | | 66.74 | 68.07 | 309 | 2.4 | 0.61
4.1.15 | | 60.48 | 76.19 | 280 | 2.16 | 0.62
4.1.58 | | 59.18 | 55.49 | 274 | 2.81 | 0.84
4.1.88 | | 58.75 | 60.36 | 272 | 2.4 | 0.67
4.1.22 | | 55.51 | 57.84 | 257 | 3.06 | 1.05
4.1.34 | | 55.51 | 73.31 | 257 | 2.47 | 0.74
4.1.43 | | 54.86 | 77.85 | 254 | 0 | 0
4.1.89 | | 50.98 | 65.72 | 236 | 1.9 | 0.81
4.1.10 | | 50.76 | 67.74 | 235 | 4.95 | 2.1
4.1.82 | | 44.06 | 84.66 | 204 | 0 | 0
4.1.35 | | 43.42 | 59.15 | 201 | 0 | 0
4.1.63 | | 42.77 | 48.19 | 198 | 2.47 | 0.58
4.1.39 | | 40.39 | 43.49 | 187 | 1.2 | 0.31
4.1.18 | | 40.18 | 64.36 | 186 | 4.02 | 1.73
4.1.54 | | 38.02 | 53.8 | 176 | 2.81 | 0.95
4.1.72 | | 36.29 | 46.7 | 168 | 2.08 | 0.64
4.1.7 | | 36.07 | 58.87 | 167 | 0 | 0
4.1.5 | | 29.16 | 37.44 | 135 | 1.7 | 0.44
4.1.93 | | 28.94 | 33.33 | 134 | 1.8 | 0.37
4.1.81 | | 28.73 | 59.51 | 133 | 0 | 0
4.1.56 | | 25.92 | 36.74 | 120 | 2.16 | 0.74
4.1.68 | | 25.7 | 35.83 | 119 | 1.7 | 0.47
4.1.42 | | 25.27 | 43.38 | 117 | 0 | 0
4.1.38 | | 24.62 | 39.54 | 114 | 0 | 0
4.1.3 | | 24.19 | 35.82 | 112 | 1.34 | 0.35
4.1.69 | | 24.19 | 29.82 | 112 | 1.47 | 0.47
4.1.96 | | 22.46 | 29.46 | 104 | 2.16 | 0.92
4.1.46 | | 22.25 | 29.01 | 103 | 1.34 | 0.44
4.1.40 | | 21.38 | 27.21 | 99 | 1.7 | 0.51
4.1.76 | | 20.74 | 43.87 | 96 | 0 | 0
4.1.80 | | 20.09 | 24.83 | 93 | 1.34 | 0.43
4.1.23 | | 19.87 | 44.36 | 92 | 1.7 | 0.49
4.1.41 | | 18.79 | 29.71 | 87 | 1.99 | 0.81
4.1.95 | | 18.58 | 27.24 | 86 | 1.2 | 0.29
4.1.98 | | 15.98 | 22.78 | 74 | 1.2 | 0.42
4.1.6 | | 15.55 | 26.8 | 72 | 1.2 | 0.28
4.1.65 | | 14.9 | 24.84 | 69 | 1.8 | 0.46
4.1.70 | | 14.04 | 27.21 | 65 | 0.85 | 0.29
4.1.91 | | 13.82 | 23.36 | 64 | 1.2 | 0.32
4.1.87 | | 12.74 | 23.47 | 59 | 1.2 | 0.32
4.1.36 | | 12.53 | 19.43 | 58 | 0.6 | 0.11
4.1.2 | | 12.31 | 29.54 | 57 | 0 | 0
4.1.31 | | 12.31 | 29.54 | 57 | 0 | 0
4.1.50 | | 12.31 | 29.54 | 57 | 0 | 0
4.1.74 | | 12.31 | 29.54 | 57 | 0 | 0
4.1.79 | | 12.31 | 29.54 | 57 | 0 | 0
4.1.53 | | 12.1 | 22.85 | 56 | 1.2 | 0.35
4.1.37 | | 11.66 | 20.42 | 54 | 0.85 | 0.2
4.1.16 | | 11.45 | 19.68 | 53 | 1.2 | 0.3
4.1.12 | | 10.8 | 11.07 | 50 | 0.6 | 0.07
4.1.64 | | 10.8 | 15.09 | 50 | 1.2 | 0.29
4.1.28 | | 10.58 | 22.54 | 49 | 1.2 | 0.36
4.1.19 | | 9.94 | 11.21 | 46 | 0.85 | 0.21
4.1.97 | | 9.72 | 19.86 | 45 | 0.6 | 0.19
4.1.90 | | 9.5 | 13.17 | 44 | 0.85 | 0.24
4.1.11 | | 8.64 | 18.34 | 40 | 1.2 | 0.4
4.1.13 | | 8.64 | 18.73 | 40 | 1.34 | 0.53
4.1.24 | | 8.64 | 14.09 | 40 | 0.85 | 0.16
4.1.1 | | 8.42 | 18.31 | 39 | 1.34 | 0.48
4.1.62 | | 8.42 | 19.12 | 39 | 1.34 | 0.52
4.1.78 | | 7.78 | 16.35 | 36 | 1.2 | 0.37
4.1.20 | | 7.56 | 12.84 | 35 | 0.6 | 0.19
4.1.32 | | 7.56 | 14.74 | 35 | 0.85 | 0.25
4.1.84 | | 7.13 | 13.29 | 33 | 0.85 | 0.29
4.1.45 | | 6.7 | 13.87 | 31 | 0.6 | 0.19
4.1.48 | | 6.26 | 12.55 | 29 | 0.6 | 0.1
4.1.75 | | 5.4 | 11.12 | 25 | 0.85 | 0.2
4.1.77 | | 5.4 | 11.94 | 25 | 0.85 | 0.23
4.1.94 | | 5.18 | 10.98 | 24 | 0.6 | 0.2
75 cavities found for fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_4.cif #5
fold_20260217_fn1_b7zle5_wt_ctrrln_wtb_model_4.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
5.1.18 | | 4823.93 | 3458.82 | 22333 | 13.23 | 3.01
5.1.22 | | 2138.83 | 1434.3 | 9902 | 9.08 | 2.25
5.1.36 | | 975.46 | 699.52 | 4516 | 7.52 | 2.09
5.1.6 | | 409.1 | 295.8 | 1894 | 5.09 | 1.27
5.1.10 | | 277.13 | 260.27 | 1283 | 4.41 | 1.25
5.1.66 | | 255.1 | 120.1 | 1181 | 1.7 | 0.38
5.1.5 | | 192.67 | 155.31 | 892 | 2.55 | 0.7
5.1.62 | | 190.3 | 137.23 | 881 | 3.7 | 0.83
5.1.9 | | 182.74 | 208.66 | 846 | 6.73 | 2.45
5.1.52 | | 154.01 | 145.25 | 713 | 4.16 | 1.01
5.1.11 | | 152.28 | 174.28 | 705 | 0 | 0
5.1.7 | | 135.86 | 91 | 629 | 1.34 | 0.26
5.1.50 | | 130.9 | 153.74 | 606 | 5.56 | 2.52
5.1.30 | | 114.26 | 120.3 | 529 | 3.84 | 1.03
5.1.29 | | 107.78 | 98.13 | 499 | 4.41 | 1.51
5.1.67 | | 93.53 | 67.55 | 433 | 1.9 | 0.28
5.1.68 | | 91.37 | 103.18 | 423 | 3 | 0.87
5.1.39 | | 71.06 | 87.84 | 329 | 2.62 | 0.55
5.1.2 | | 58.32 | 80.36 | 270 | 4.07 | 1.59
5.1.19 | | 56.16 | 79.48 | 260 | 2.68 | 1.03
5.1.38 | | 55.08 | 57.58 | 255 | 2.08 | 0.53
5.1.65 | | 49.68 | 55.03 | 230 | 2.16 | 0.57
5.1.73 | | 49.68 | 55.06 | 230 | 3 | 0.99
5.1.44 | | 41.69 | 60.57 | 193 | 2.24 | 0.81
5.1.15 | | 40.18 | 42.93 | 186 | 2.24 | 0.64
5.1.56 | | 34.34 | 39.42 | 159 | 1.9 | 0.59
5.1.59 | | 33.26 | 63.85 | 154 | 3.6 | 1.33
5.1.32 | | 33.05 | 39.96 | 153 | 1.8 | 0.51
5.1.8 | | 31.1 | 52.77 | 144 | 3.06 | 0.98
5.1.31 | | 29.16 | 41.84 | 135 | 3.06 | 1.29
5.1.20 | | 27.65 | 41.78 | 128 | 1.34 | 0.37
5.1.35 | | 27.22 | 35.13 | 126 | 1.9 | 0.56
5.1.40 | | 27 | 47.25 | 125 | 3 | 1.01
5.1.46 | | 26.78 | 38.8 | 124 | 2.16 | 0.77
5.1.14 | | 25.92 | 36.34 | 120 | 1.7 | 0.42
5.1.55 | | 25.92 | 17.77 | 120 | 1.2 | 0.2
5.1.47 | | 24.84 | 32.06 | 115 | 1.2 | 0.32
5.1.54 | | 24.62 | 51.93 | 114 | 0 | 0
5.1.27 | | 23.11 | 42.35 | 107 | 0 | 0
5.1.70 | | 22.03 | 33.54 | 102 | 2.55 | 1.11
5.1.26 | | 19.22 | 31.33 | 89 | 1.2 | 0.26
5.1.12 | | 18.58 | 32.6 | 86 | 0.85 | 0.18
5.1.4 | | 17.28 | 32.27 | 80 | 1.7 | 0.46
5.1.37 | | 17.28 | 23.98 | 80 | 1.99 | 0.6
5.1.45 | | 17.28 | 24.09 | 80 | 1.2 | 0.41
5.1.23 | | 16.85 | 32.3 | 78 | 0 | 0
5.1.41 | | 14.47 | 25.97 | 67 | 1.04 | 0.24
5.1.42 | | 14.26 | 25.83 | 66 | 1.9 | 0.68
5.1.75 | | 14.26 | 24.23 | 66 | 1.2 | 0.39
5.1.17 | | 13.82 | 21.72 | 64 | 1.34 | 0.4
5.1.51 | | 13.82 | 22.83 | 64 | 1.7 | 0.51
5.1.49 | | 13.61 | 26.43 | 63 | 1.34 | 0.39
5.1.69 | | 13.61 | 22.33 | 63 | 1.2 | 0.44
5.1.71 | | 13.61 | 21.28 | 63 | 1.04 | 0.22
5.1.24 | | 12.96 | 21.2 | 60 | 1.2 | 0.29
5.1.64 | | 12.96 | 26.14 | 60 | 0.6 | 0.08
5.1.33 | | 12.31 | 22.01 | 57 | 1.7 | 0.56
5.1.58 | | 12.31 | 20.11 | 57 | 1.34 | 0.37
5.1.16 | | 11.66 | 18.99 | 54 | 1.34 | 0.54
5.1.72 | | 11.45 | 18.61 | 53 | 1.2 | 0.33
5.1.48 | | 11.02 | 18.71 | 51 | 0.85 | 0.24
5.1.3 | | 10.58 | 17.3 | 49 | 0.6 | 0.2
5.1.1 | | 10.15 | 19.66 | 47 | 0.6 | 0.15
5.1.25 | | 8.42 | 13.67 | 39 | 0.85 | 0.31
5.1.34 | | 8.42 | 19.26 | 39 | 1.2 | 0.48
5.1.74 | | 8.21 | 18.7 | 38 | 0.85 | 0.2
5.1.53 | | 7.78 | 16.1 | 36 | 1.34 | 0.49
5.1.60 | | 7.78 | 7.5 | 36 | 0.6 | 0.03
5.1.61 | | 5.83 | 7.64 | 27 | 0.6 | 0.04
5.1.13 | | 5.62 | 13.43 | 26 | 0.6 | 0.16
5.1.21 | | 5.62 | 14.45 | 26 | 0.85 | 0.26
5.1.43 | | 5.62 | 10.68 | 26 | 0.6 | 0.23
5.1.57 | | 5.62 | 14.45 | 26 | 0.85 | 0.3
5.1.63 | | 5.62 | 8.36 | 26 | 0 | 0
5.1.28 | | 5.18 | 10.17 | 24 | 0.6 | 0.1
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> color #1.1 #fffb00ff models
> view #1.1.1 @< 3.5
> zoom 0.75
moved plane near -14.09929995745584 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -14.09929995745584 [-0.07341029 -0.37408681 -0.92448364]
> surface #1.1.1-75 transparency 50
> ~surface #1.1
> surface #1.1.1
> show #!1/A:620-623,700,702-704
> hide #!1.1 models
> view #!1.1.2 @< 3.5
> zoom 0.75
moved plane near -11.873044875765245 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -11.873044875765245 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.2
> show #!1/A:620,622-623,625,699-700
> view #1
> view #!1.1.2 @< 3.5
> zoom 0.75
moved plane near -12.417614975056546 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -12.417614975056546 [-0.07341029 -0.37408681 -0.92448364]
> view #!1.1.3 @< 3.5
> zoom 0.75
moved plane near -30.08405651573123 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -30.08405651573123 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.3
> show
> #!1/A:622,624-625,645,655,657,659-660,663,665-671,719-722,724,727,739-744,746,792-795,798,800-804
> view #!1.1.4 @< 3.5
> zoom 0.75
moved plane near -11.034930930564025 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -11.034930930564025 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.4
> show #!1/A:753-755,787-789
> show #!1.1 models
> hide #!1.1.1 models
> hide #!1.1.2 models
> view #!1.1.5 @< 3.5
> zoom 0.75
moved plane near -14.303903718674263 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -14.303903718674263 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.5
> show #!1/A:754-756,761-764,780,786
> hide #!1.1.3 models
> view #!1.1.6 @< 3.5
> zoom 0.75
moved plane near -11.024843661474847 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -11.024843661474847 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.6
> show #!1/A:630,632,641,661,663-664
> view #!1.1.7 @< 3.5
> zoom 0.75
moved plane near -9.230274819193978 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -9.230274819193978 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.7
> show #!1/A:808,884,887
> view #!1.1.8 @< 3.5
> zoom 0.75
moved plane near -15.931669029142748 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -15.931669029142748 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.8
> show #!1/A:609-612,633,635-638,683,685,691
> view #!1.1.9 @< 3.5
> zoom 0.75
moved plane near -26.507377500847195 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -26.507377500847195 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.9
> show
> #!1/A:205-206,208-209,227-228,230-235,264-268,312-313,828,839-842,856-859,862,864-866,883,888
> view #!1.1.10 @< 3.5
> zoom 0.75
moved plane near -16.34996156206868 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -16.34996156206868 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.10
> show #!1/A:1459-1461,1464,1510-1511,1538-1543,1567
> view #!1.1.11 @< 3.5
> zoom 0.75
moved plane near -15.04245303898422 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -15.04245303898422 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.11
> show #!1/A:516,549,731-733,810-811,881,888-891
> view #!1.1.12 @< 3.5
> zoom 0.75
moved plane near -19.34193896428151 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -19.34193896428151 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.12
> show #!1/A:527-529,729-730,737,739,774,1728-1729,1745-1748
> view #!1.1.13 @< 3.5
> zoom 0.75
moved plane near -10.311177890999138 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -10.311177890999138 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.13
> show #!1/A:588,590,639,684-688
> view #!1.1.14 @< 3.5
> zoom 0.75
moved plane near -14.114275217131736 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -14.114275217131736 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.14
> show #!1/A:352-353,356,1547,1549,1561-1563
> view #!1.1.15 @< 3.5
> zoom 0.75
moved plane near -30.966769468722845 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -30.966769468722845 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.15
> show
> #!1/A:310-312,316,322-325,333,340,342,409-414,416-417,443,458,460,463,468-471,499,501,503-507,819-822,830,873,875,895-901,2220,2222-2223
> view #!1.1.16 @< 3.5
> zoom 0.75
moved plane near -12.346968531503547 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -12.346968531503547 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.16
> show #!1/A:1511,1539,1541-1542,1621
> view #!1.1.17 @< 3.5
> zoom 0.75
moved plane near -20.562527705746266 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -20.562527705746266 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.17
> show #!1/A:323,330,345-348,350,359-360,362,372-374,403-407
> view #!1.1.18 @< 3.5
> zoom 0.75
moved plane near -12.34416513487023 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -12.34416513487023 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.18
> show #!1/A:1578,1583-1584,1586,1602,1606,1608
> view #!1.1.19 @< 3.5
> zoom 0.75
moved plane near -13.843910842465633 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -13.843910842465633 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.19
> show #!1/A:1482-1484,1489-1492,1508,1514
> view #!1.1.20 @< 3.5
> zoom 0.75
moved plane near -16.103131782994037 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -16.103131782994037 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.20
> show #!1/A:575,586-588,590,598-600,687-689
> view #!1.1.21 @< 3.5
> zoom 0.75
moved plane near -11.53382511813374 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -11.53382511813374 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.21
> show #!1/A:353-354,1547-1549
> view #!1.1.22 @< 3.5
> zoom 0.75
moved plane near -43.53782706049093 [-0.07341029 -0.37408681 -0.92448364]
moved plane far -43.53782706049093 [-0.07341029 -0.37408681 -0.92448364]
> ~surface #1.1
> surface #!1.1.22
> show
> #!1/A:158,160-164,182-190,201,203,205,211,213,216,218-225,486,488-492,494,506,508-510,512-513,518-522,533,549-553,844-855,868-872,874-879,881,895,902-905,907-908,912,914,926-937,958,960,981-982,984/B:18
> hide #!1.1.4 models
> view #1
> hide #!1.1.75 models
> hide #!1.1.74 models
> show #!1.1.74 models
> hide #!1.1.74 models
> hide #!1.1.73 models
> hide #!1.1.72 models
> hide #!1.1.71 models
> hide #!1.1.70 models
> hide #!1.1 models
> show #!1.1.3 models
> hide #!1.1.3 models
> hide #!1.1.5 models
> hide #!1.1.6 models
> hide #!1.1.7 models
> hide #!1.1.8 models
> hide #!1.1.9 models
> hide #!1.1.10 models
> hide #!1.1.11 models
> hide #!1.1.12 models
> hide #!1.1.13 models
> hide #!1.1.14 models
> hide #!1.1.24 models
> hide #!1.1.25 models
> hide #!1.1.23 models
> hide #!1.1.22 models
> show #!1.1.23 models
> hide #!1.1.23 models
> show #!1.1.22 models
> hide #!1.1.22 models
> hide #!1.1.26 models
> show #!1.1.26 models
> hide #!1.1.27 models
> show #!1.1.27 models
> hide #!1.1.27 models
> hide #!1.1.21 models
> hide #!1.1.20 models
> hide #!1.1.19 models
> hide #!1.1.18 models
> hide #!1.1.17 models
> hide #!1.1.16 models
> hide #!1.1.15 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1.28 models
> hide #!1.1.29 models
> hide #!1.1.30 models
> save /Users/clmarino/Desktop/022326_FN1_CTR_ReelinWT.cxs
> close
> open
> /Users/clmarino/Downloads/fold_20260217_reln_wt_itga2wt/fold_20260217_reln_wt_itga2wt_model_0.cif
Chain information for fold_20260217_reln_wt_itga2wt_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> open
> /Users/clmarino/Downloads/fold_20260217_reln_wt_itga2wt/fold_20260217_reln_wt_itga2wt_model_1.cif
Chain information for fold_20260217_reln_wt_itga2wt_model_1.cif #2
---
Chain | Description
A | .
B | .
> open
> /Users/clmarino/Downloads/fold_20260217_reln_wt_itga2wt/fold_20260217_reln_wt_itga2wt_model_2.cif
Chain information for fold_20260217_reln_wt_itga2wt_model_2.cif #3
---
Chain | Description
A | .
B | .
> open
> /Users/clmarino/Downloads/fold_20260217_reln_wt_itga2wt/fold_20260217_reln_wt_itga2wt_model_3.cif
Chain information for fold_20260217_reln_wt_itga2wt_model_3.cif #4
---
Chain | Description
A | .
B | .
> open
> /Users/clmarino/Downloads/fold_20260217_reln_wt_itga2wt/fold_20260217_reln_wt_itga2wt_model_4.cif
Chain information for fold_20260217_reln_wt_itga2wt_model_4.cif #5
---
Chain | Description
A | .
B | .
Computing secondary structure
[Repeated 3 time(s)]
> color bychain
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_20260217_reln_wt_itga2wt_model_0.cif, chain A (#1) with
fold_20260217_reln_wt_itga2wt_model_1.cif, chain A (#2), sequence alignment
score = 18019.3
RMSD between 1862 pruned atom pairs is 1.050 angstroms; (across all 3460
pairs: 5.667)
Matchmaker fold_20260217_reln_wt_itga2wt_model_0.cif, chain A (#1) with
fold_20260217_reln_wt_itga2wt_model_2.cif, chain A (#3), sequence alignment
score = 18027.1
RMSD between 1432 pruned atom pairs is 1.019 angstroms; (across all 3460
pairs: 7.081)
Matchmaker fold_20260217_reln_wt_itga2wt_model_0.cif, chain A (#1) with
fold_20260217_reln_wt_itga2wt_model_3.cif, chain A (#4), sequence alignment
score = 18018.7
RMSD between 2337 pruned atom pairs is 1.075 angstroms; (across all 3460
pairs: 7.008)
Matchmaker fold_20260217_reln_wt_itga2wt_model_0.cif, chain A (#1) with
fold_20260217_reln_wt_itga2wt_model_4.cif, chain A (#5), sequence alignment
score = 17968.9
RMSD between 1572 pruned atom pairs is 0.930 angstroms; (across all 3460
pairs: 9.611)
> ui tool show "Find Cavities"
> kvfinder
219 cavities found for fold_20260217_reln_wt_itga2wt_model_0.cif #1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 136, in find_cavities
run(self.session, cmd)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 119, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'KIK'
KeyError: 'KIK'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 119, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
> ui tool show "Find Cavities"
> kvfinder #1
219 cavities found for fold_20260217_reln_wt_itga2wt_model_0.cif #1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 136, in find_cavities
run(self.session, cmd)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 119, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'KIK'
KeyError: 'KIK'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 119, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
> save /Users/clmarino/Desktop/022326_RLNWT_ITGA2WT.cxs
——— End of log from Mon Feb 23 10:36:03 2026 ———
> view name session-start
opened ChimeraX session
> ui tool show "Find Cavities"
> kvfinder #1
219 cavities found for fold_20260217_reln_wt_itga2wt_model_0.cif #1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 136, in find_cavities
run(self.session, cmd)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 119, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'KIK'
KeyError: 'KIK'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 119, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,1
Model Number: MCX04LL/A
Chip: Apple M4
Total Number of Cores: 10 (4 Performance and 6 Efficiency)
Memory: 24 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3 (25D125)
Kernel Version: Darwin 25.3.0
Time since boot: 2 minutes, 12 seconds
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
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: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
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: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.3
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: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
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-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
finufft: 2.3.1
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
narwhals: 1.34.1
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 2.2.6
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
plotly: 6.0.1
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pyKVFinder: 0.8.1
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
toml: 0.10.2
tomlkit: 0.13.2
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (4)
comment:1 by , 15 minutes ago
| Component: | Unassigned → Surface/Binding Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Find Cavities: cavity KeyError |
comment:2 by , 14 minutes ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
comment:3 by , 14 minutes ago
| Resolution: | can't reproduce |
|---|---|
| Status: | closed → reopened |
comment:4 by , 10 minutes ago
| Status: | reopened → feedback |
|---|
Hi Claudia,
Thanks for reporting this problem. Find Cavities uses the pyKVFinder package to actually find the cavities and there is a newer version of that package available. To get ChimeraX to use the newer package type the command "pip uninstall pyKVFinder" and then run Find Cavities (which will then install the newer version itself).
If that does not fix the problem, then I would need access to your fold_20260217_reln_wt_itga2wt_model_0.cif file in order to investigate the error.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
Note:
See TracTickets
for help on using tickets.
*Possibly* a duplicate of #19532, but I would expect the key to be KAA rather than KIK.