Jungfraujoch/tools/battery/nullmodel.json

{
 "about": "Wrong-model null step (README: 'The wrong-model null'): each set runs once without --model and once with each of five WRONG models - the deposited coordinates of other open-arm entries, from the site's pdb_cache. Every wrong model is a real protein of similar size (residue count of the asymmetric unit), unrelated in sequence (local BLOSUM62 alignment, identities / residues of the shorter chain, chains of 30 residues or more) and in fold (gesamt Q-score between the longest chains; a homologue sits above 0.5). size = residues of the model / of the set's own deposited model. One model per set is the hard-ish one (same secondary-structure class, similar size), one shares the space group or a similar cell where the open arm has one, and the two sets in an enantiomorphic group each have a model in the other enantiomorph, which is the one decision a model may write into the reflection files (MODEL_ENANTIOMORPH_ADOPTED).",
 "sets": [
  {"set": "8u0i", "why": "P4(3)2(1)2 deposited, which rugnux determines as the enantiomorph pair; its own model adopts P4(3)2(1)2 (ACCEPTED), so a wrong model must not; all-beta, 86 residues",
   "models": [
    {"pdb": "6v2r", "size": -0.30, "seq_id": 0.06, "q": 0.13, "why": "same space group P4(1)2(1)2 and a tetragonal cell of similar size (40/83 against 50/91); alpha+beta"},
    {"pdb": "7l84", "size": 0.50, "seq_id": 0.05, "q": 0.05, "why": "the other enantiomorph, P4(3)2(1)2, of the group rugnux writes without a model: the hand gate. Lysozyme; larger than +30% because no smaller open-arm entry is in that group"},
    {"pdb": "6cs9", "size": -0.05, "seq_id": 0.20, "q": 0.15, "why": "hard-ish: beta-rich, same size"},
    {"pdb": "9vyb", "size": 0.20, "seq_id": 0.12, "q": 0.11, "why": "beta-rich, P2(1)2(1)2(1)"},
    {"pdb": "6cee", "size": 0.16, "seq_id": 0.08, "q": 0.08, "why": "alpha/beta, P2(1)2(1)2(1)"}]},
  {"set": "6iu5", "why": "P3(1), enantiomorphic and with a merohedral twin law, so a model can both claim the hand and probe the indexing; eight helical chains, 585 residues",
   "models": [
    {"pdb": "6pxb", "size": 0.04, "seq_id": 0.11, "q": 0.12, "why": "the other enantiomorph P3(2), trigonal: the hand gate and the indexing probe at once"},
    {"pdb": "7raa", "size": -0.15, "seq_id": 0.18, "q": 0.11, "why": "hard-ish: all-alpha, similar size"},
    {"pdb": "7q6j", "size": -0.14, "seq_id": 0.21, "q": 0.06, "why": "mainly alpha"},
    {"pdb": "9rci", "size": -0.08, "seq_id": 0.14, "q": 0.05, "why": "mainly alpha, P1"},
    {"pdb": "8pqd", "size": 0.02, "seq_id": 0.15, "q": 0.06, "why": "alpha/beta, same size"}]},
  {"set": "9khr", "why": "P2(1)2(1)2(1), alpha/beta, 169 residues (9jq9 in the open arm is the same protein - 100% identity - and is NOT a wrong model)",
   "models": [
    {"pdb": "8dz7", "size": -0.24, "seq_id": 0.05, "q": 0.06, "why": "same space group P2(1)2(1)2(1); lysozyme"},
    {"pdb": "11if", "size": 0.06, "seq_id": 0.14, "q": 0.05, "why": "hard-ish: alpha/beta in the same proportions, same size"},
    {"pdb": "6nen", "size": 0.04, "seq_id": 0.17, "q": 0.20, "why": "hard-ish: alpha/beta, the closest fold of the set (100 residues within 2.5 A)"},
    {"pdb": "8v2t", "size": 0.13, "seq_id": 0.04, "q": 0.08, "why": "mainly alpha, tetragonal"},
    {"pdb": "6hv2", "size": 0.01, "seq_id": 0.06, "q": 0.09, "why": "same size, hexagonal P6(1)22"}]},
  {"set": "9b22", "why": "P2(1), alpha+beta, two chains, 407 residues",
   "models": [
    {"pdb": "5jk4", "size": -0.08, "seq_id": 0.16, "q": 0.04, "why": "same space group P2(1) and a similar cell (37.7/77.9/56.3, beta 102 against 39.8/92.7/57.7, beta 92)"},
    {"pdb": "9qw2", "size": 0.08, "seq_id": 0.19, "q": 0.05, "why": "same space group P2(1)"},
    {"pdb": "9sl0", "size": -0.06, "seq_id": 0.16, "q": 0.05, "why": "hard-ish: alpha+beta, similar size"},
    {"pdb": "9w3y", "size": 0.20, "seq_id": 0.13, "q": 0.07, "why": "alpha+beta"},
    {"pdb": "9rcs", "size": 0.01, "seq_id": 0.20, "q": 0.03, "why": "P2(1), beta-rich, same size"}]},
  {"set": "6pxc", "why": "I222, a centred lattice, alpha+beta, 117 residues",
   "models": [
    {"pdb": "6cee", "size": -0.15, "seq_id": 0.10, "q": 0.08, "why": "orthorhombic P2(1)2(1)2(1)"},
    {"pdb": "9vyb", "size": -0.12, "seq_id": 0.12, "q": 0.10, "why": "hard-ish: alpha+beta, similar size"},
    {"pdb": "6rym", "size": 0.04, "seq_id": 0.08, "q": 0.15, "why": "alpha+beta, same size"},
    {"pdb": "6h5t", "size": 0.13, "seq_id": 0.11, "q": 0.10, "why": "centred, I422; all-beta"},
    {"pdb": "7orr", "size": 0.06, "seq_id": 0.10, "q": 0.08, "why": "centred, I2(1)3"}]}
 ]
}