Error reading: 1h3i PDB

[loscati]

PDB file

The command:

singlechain.ge_from_pdb("1h3i.pdb", {"thr_min_len": 10, "loop_min_thr": 0}, {"model_id":1, "chain_id":"A", "threshold":4.5, "to_ignore":["HOH", "MG"]})

produce the following traceback:

File ~/pyge/pyge/singlechain.py:203, in ge_from_pdb(pdb_file, ge_options, cm_options, selection_options)
    200 else:
    201     loop_min_len = 0
--> 203 ge_loops_result = gent.ge_loops(cm, ca_positions, thr_min_len)
    204 ge_config_max = gent.ge_configuration(ge_loops_result, loop_min_len, "max")
    205 ge_config_w = gent.ge_configuration(
    206     ge_list_complete=ge_loops_result,
    207     loop_min_len=loop_min_len,
    208     mode="weighted",
    209     kwards={"hill_coeff": 3, "threshold": 0.5},
    210 )

File ~/pyge/pyge/gent.py:158, in ge_loops(contact_map, bead_position, thr_min_len, backend)
    156 len_chain = bead_position.shape[0]
    157 if contact_map.shape[0] != len_chain:
--> 158     raise ValueError("Contact map and bead position have different length")
    159 loops = _loop_list(contact_map)
    160 # note: first index is 0
    161 # note: second index > first index, for construction

Expected behavior: cm and bead_position should have the same len

Moreover, MDAnalysis warn that the chain is discontinuous where the HOH and the MG starts, despite being ignored by the PDB parser,