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Opened 7 hours ago
#19879 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
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
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