List index out of range error for `8ixa`

[yingyue2030699]

cg_model ============== 1
{'chains': [<Chain id=A>, <Chain id=B>, <Chain id=C>, <Chain id=D>, <Chain id=E>, <Chain id=F>, <Chain id=G>, <Chain id=H>, <Chain id=I>, <Chain id=J>, <Chain id=K>, <Chain id=L>, <Chain id=M>, <Chain id=N>, <Chain id=O>, <Chain id=P>, <Chain id=Q>, <Chain id=R>, <Chain id=S>, <Chain id=T>, <Chain id=U>, <Chain id=V>, <Chain id=W>, <Chain id=X>, <Chain id=Y>, <Chain id=Z>, <Chain id=a>], 'COMs': [Coords(x=291.288, y=445.357, z=438.413), Coords(x=289.733, y=444.784, z=272.814), Coords(x=247.839, y=413.394, z=264.013), Coords(x=248.411, y=413.959, z=346.832), Coords(x=249.007, y=414.573, z=429.601), Coords(x=341.090, y=454.851, z=281.676), Coords(x=341.897, y=454.761, z=364.513), Coords(x=342.758, y=454.701, z=447.304), Coords(x=290.501, y=445.047, z=355.636), Coords(x=290.799, y=444.940, z=398.290), Coords(x=289.237, y=444.356, z=232.691), Coords(x=247.566, y=412.805, z=223.891), Coords(x=248.119, y=413.395, z=306.709), Coords(x=248.728, y=414.007, z=389.479), Coords(x=340.462, y=454.666, z=241.555), Coords(x=341.286, y=454.627, z=324.391), Coords(x=289.988, y=444.674, z=315.514), Coords(x=342.144, y=454.515, z=407.181), Coords(x=262.000, y=473.092, z=408.676), Coords(x=260.042, y=472.096, z=243.084), Coords(x=209.231, y=425.131, z=234.300), Coords(x=209.876, y=425.987, z=317.139), Coords(x=210.582, y=426.903, z=399.891), Coords(x=326.239, y=492.346, z=251.931), Coords(x=260.997, y=472.610, z=325.953), Coords(x=327.317, y=492.391, z=334.806), Coords(x=328.487, y=492.408, z=417.544)], 'radii': [np.float32(21.101877), np.float32(21.10188), np.float32(21.101873), np.float32(21.101868), np.float32(21.101873), np.float32(21.101871), np.float32(21.101877), np.float32(21.10187), np.float32(21.101881), np.float32(21.064085), np.float32(21.064075), np.float32(21.06408), np.float32(21.064087), np.float32(21.06408), np.float32(21.064083), np.float32(21.064081), np.float32(21.064087), np.float32(21.064077), np.float32(19.51111), np.float32(19.511097), np.float32(19.511116), np.float32(19.511108), np.float32(19.51111), np.float32(19.511116), np.float32(19.511114), np.float32(19.511108), np.float32(19.511105)], 'interfaces': [['E', 'H', 'J', 'S'], ['C', 'K', 'Q', 'T'], ['B', 'L', 'M', 'U'], ['I', 'M', 'N', 'V'], ['A', 'N', 'W'], ['O', 'P', 'X'], ['I', 'P', 'R', 'Z'], ['A', 'R', 'a'], ['D', 'G', 'J', 'Q', 'Y'], ['A', 'I'], ['B'], ['C'], ['C', 'D'], ['D', 'E'], ['F'], ['F', 'G'], ['B', 'I'], ['G', 'H'], ['A'], ['B'], ['C'], ['D'], ['E'], ['F'], ['I'], ['G'], ['H']], 'interface_coords': [[Coords(x=279.563, y=420.134, z=440.284), Coords(x=319.131, y=438.722, z=447.571), Coords(x=291.541, y=450.894, z=419.875), Coords(x=274.345, y=458.074, z=417.894)], [Coords(x=278.370, y=419.398, z=274.692), Coords(x=289.901, y=450.323, z=254.275), Coords(x=291.391, y=453.693, z=290.570), Coords(x=272.603, y=457.257, z=252.299)], [Coords(x=275.720, y=419.891, z=273.157), Coords(x=245.582, y=418.462, z=245.477), Coords(x=245.474, y=422.134, z=281.773), Coords(x=226.988, y=417.206, z=243.507)], [Coords(x=276.341, y=420.254, z=355.968), Coords(x=246.183, y=419.054, z=328.299), Coords(x=246.115, y=422.706, z=364.597), Coords(x=227.580, y=417.931, z=326.335)], [Coords(x=276.982, y=420.646, z=438.749), Coords(x=246.829, y=419.683, z=411.067), Coords(x=228.218, y=418.708, z=409.095)], [Coords(x=343.653, y=459.757, z=263.137), Coords(x=346.456, y=462.157, z=299.431), Coords(x=331.093, y=473.524, z=261.154)], [Coords(x=320.499, y=436.988, z=366.366), Coords(x=344.502, y=459.671, z=345.980), Coords(x=347.305, y=462.009, z=382.278), Coords(x=332.037, y=473.526, z=344.008)], [Coords(x=321.215, y=437.107, z=449.182), Coords(x=345.402, y=459.563, z=428.764), Coords(x=333.052, y=473.517, z=426.772)], [Coords(x=278.956, y=419.739, z=357.486), Coords(x=318.396, y=438.598, z=364.768), Coords(x=292.229, y=453.920, z=373.404), Coords(x=290.703, y=450.608, z=337.105), Coords(x=273.454, y=457.668, z=335.144)], [Coords(x=292.814, y=450.473, z=415.813), Coords(x=290.177, y=455.883, z=377.142)], [Coords(x=291.178, y=449.920, z=250.213)], [Coords(x=246.907, y=418.654, z=241.415)], [Coords(x=242.722, y=422.960, z=285.572), Coords(x=247.508, y=419.239, z=324.237)], [Coords(x=243.417, y=423.613, z=368.338), Coords(x=248.156, y=419.857, z=407.006)], [Coords(x=344.628, y=458.837, z=259.075)], [Coords(x=344.772, y=465.543, z=302.799), Coords(x=345.472, y=458.749, z=341.918)], [Coords(x=289.274, y=455.638, z=294.379), Coords(x=291.975, y=450.200, z=333.043)], [Coords(x=346.356, y=464.624, z=386.028), Coords(x=346.365, y=458.627, z=424.703)], [Coords(x=270.180, y=460.148, z=416.460)], [Coords(x=268.409, y=459.271, z=250.866)], [Coords(x=222.335, y=417.203, z=242.075)], [Coords(x=222.927, y=417.961, z=324.905)], [Coords(x=223.565, y=418.775, z=407.664)], [Coords(x=328.193, y=477.162, z=259.719)], [Coords(x=269.275, y=459.715, z=333.715)], [Coords(x=329.164, y=477.185, z=342.577)], [Coords(x=330.208, y=477.198, z=425.336)]], 'interface_residues': [[[62, 63, 94], [289, 290, 291], [102, 103, 106, 107, 185, 186, 187, 227, 228, 229, 400, 403, 404, 409, 410], [415, 416, 417, 418, 422]], [[62, 63, 94], [102, 103, 106, 107, 185, 186, 187, 227, 228, 229, 400, 403, 404, 409, 410], [259, 260, 267, 352, 353, 355, 356, 357, 358, 359], [415, 416, 417, 418, 422]], [[289, 290, 291], [102, 103, 106, 107, 185, 186, 187, 227, 228, 229, 400, 403, 404, 409, 410], [259, 260, 267, 352, 353, 355, 356, 357, 358, 359], [415, 416, 417, 418, 422]], [[289, 290, 291], [102, 103, 106, 107, 185, 186, 187, 227, 228, 229, 400, 403, 404, 409, 410], [259, 260, 267, 352, 353, 355, 356, 357, 358, 359], [415, 416, 417, 418, 422]], [[289, 290, 291], [102, 103, 106, 107, 185, 186, 187, 227, 228, 229, 400, 403, 404, 409, 410], [415, 416, 417, 418, 422]], [[102, 103, 106, 107, 185, 186, 187, 227, 228, 229, 400, 403, 404, 409, 410], [259, 260, 267, 352, 353, 355, 356, 357, 358, 359], [415, 416, 417, 418, 422]], [[62, 63, 94], [102, 103, 106, 107, 185, 186, 187, 227, 228, 229, 400, 403, 404, 409, 410], [259, 260, 267, 352, 353, 355, 356, 357, 358, 359], [415, 416, 417, 418, 422]], [[62, 63, 94], [102, 103, 106, 107, 185, 186, 187, 227, 228, 229, 400, 403, 404, 409, 410], [415, 416, 417, 418, 422]], [[62, 63, 94], [289, 290, 291], [259, 260, 267, 352, 353, 355, 356, 357, 358, 359], [102, 103, 106, 107, 185, 186, 187, 227, 228, 229, 400, 403, 404, 409, 410], [415, 416, 417, 418, 422]], [[1, 2, 251, 252, 259, 322, 323, 344, 345, 346, 347, 348, 350, 351], [98, 176, 177, 178, 179, 387, 388, 393, 394]], [[1, 2, 251, 252, 259, 322, 323, 344, 345, 346, 347, 348, 350, 351]], [[1, 2, 251, 252, 259, 322, 323, 344, 345, 346, 347, 348, 350, 351]], [[98, 176, 177, 178, 179, 387, 388, 393, 394], [1, 2, 251, 252, 259, 322, 323, 344, 345, 346, 347, 348, 350, 351]], [[98, 176, 177, 178, 179, 387, 388, 393, 394], [1, 2, 251, 252, 259, 322, 323, 344, 345, 346, 347, 348, 350, 351]], [[1, 2, 251, 252, 259, 322, 323, 344, 345, 346, 347, 348, 350, 351]], [[98, 177, 178, 179, 387, 388, 393, 394], [1, 2, 251, 252, 259, 322, 323, 344, 345, 346, 347, 348, 350, 351]], [[98, 176, 177, 178, 179, 387, 388, 393, 394], [1, 2, 251, 252, 259, 322, 323, 344, 345, 346, 347, 348, 350, 351]], [[98, 176, 177, 178, 179, 387, 388, 393, 394], [1, 2, 251, 252, 259, 322, 323, 344, 345, 346, 347, 348, 350, 351]], [[251, 252, 255, 256, 311]], [[251, 252, 255, 256, 311]], [[251, 252, 255, 256, 311]], [[251, 252, 255, 256, 311]], [[251, 252, 255, 256, 311]], [[251, 252, 255, 256, 311]], [[251, 252, 255, 256, 311]], [[251, 252, 255, 256, 311]], [[251, 252, 255, 256, 311]]], 'interface_energies': [[0.0, 0.0, -4.7, -3.0], [0.0, -4.7, -4.0, -3.0], [0.0, -4.7, -4.0, -3.0], [0.0, -4.7, -4.0, -3.0], [0.0, -4.7, -3.0], [-4.7, -2.8, -3.0], [0.0, -4.7, -4.0, -3.0], [0.0, -4.7, -3.0], [0.0, 0.0, -4.0, -4.7, -3.0], [-4.7, -4.0], [-4.7], [-4.7], [-4.0, -4.7], [-4.0, -4.7], [-4.7], [-2.8, -4.7], [-4.0, -4.7], [-4.0, -4.7], [-3.0], [-3.0], [-3.0], [-3.0], [-3.0], [-3.0], [-3.0], [-3.0], [-3.0]]}
/Users/yueying/Workspace/ionerdss/ionerdss/model/pdb/detect_repeats.py:88: UserWarning: /Users/yueying/Workspace/ionerdss/8ixa.cif: Missing mmCIF entity_poly info. Falling back to sequence alignment.
  warnings.warn(f"{pdb_id}: Missing mmCIF entity_poly info. Falling back to sequence alignment.")
3 homologous chain groups identified:
{'I': 'I', 'A': 'I', 'B': 'I', 'C': 'I', 'D': 'I', 'E': 'I', 'F': 'I', 'G': 'I', 'H': 'I', 'Q': 'Q', 'J': 'Q', 'K': 'Q', 'L': 'Q', 'M': 'Q', 'N': 'Q', 'O': 'Q', 'P': 'Q', 'R': 'Q', 'Y': 'Y', 'S': 'Y', 'T': 'Y', 'U': 'Y', 'V': 'Y', 'W': 'Y', 'X': 'Y', 'Z': 'Y', 'a': 'Y'}
[DEBUG] I_1 offset = (-11.725, -25.223, 1.872)
[DEBUG] I_2 offset = (27.843, -6.635, 9.158)
[DEBUG] Q_1 offset = (0.253, 5.537, -18.538)
Traceback (most recent call last):
  File "/Users/yueying/Workspace/ionerdss/./test_8y7s.py", line 5, in <module>
    pdbmodel.run_pipeline()
  File "/Users/yueying/Workspace/ionerdss/ionerdss/model/pdb/core.py", line 83, in run_pipeline
    regularized_model_data = regularize_repeated_chains(
  File "/Users/yueying/Workspace/ionerdss/ionerdss/model/pdb/regularize_repeats.py", line 540, in regularize_repeated_chains
    sigs, templates, interfaces, pairs = process_chain_group(
  File "/Users/yueying/Workspace/ionerdss/ionerdss/model/pdb/regularize_repeats.py", line 89, in process_chain_group
    process_interfaces_for_chain(
  File "/Users/yueying/Workspace/ionerdss/ionerdss/model/pdb/regularize_repeats.py", line 233, in process_interfaces_for_chain
    interface_templates = build_new_interface_templates(
  File "/Users/yueying/Workspace/ionerdss/ionerdss/model/pdb/regularize_repeats.py", line 333, in build_new_interface_templates
    offset = compute_interface_offset(j, i, group, side_chain_id, cg_model)
  File "/Users/yueying/Workspace/ionerdss/ionerdss/model/pdb/regularize_repeats.py", line 362, in compute_interface_offset
    pt = get_chain_data(chain_id, cg_model, "interface_coords")[i]
IndexError: list index out of range

[yingyue2030699]

1DLH does not work because some chains are just small molecules (so binding site = COM on those molecules). Force ignore the short chains amino acids (tunable hyperparameter)?

[yingyue2030699]

(FIXED) 8y7s

Parser bug truncating sequences Problem: Chains with multiple peptides (breaks) only returned first peptide sequence

Chain E had 2 peptides (171 + 383 = 554) but parser returned only 171
This caused alignment to fail and chains to not group together

Fix: concatenate multiple peptides