[Biopython] Problem writing a PDB with multiple models

[Claudia Millán Nebot]

Dear all,

I am trying to write a small function to fuse a number of pubs in a single
one,
by adding them as models to an structure object. The code looks like this:

def fuse_pdbs(list_of_filepaths,path_pdb):
    list_of_structures=[]
    parser=PDBParser()
    for pdb_file in list_of_filepaths:
        structure=parser.get_structure(pdb_file[:-4],pdb_file)
        list_of_structures.append(structure)
    main_structure=list_of_structures[0]
    for x,structure in enumerate(list_of_structures):
        #print "Processing ",structure," ",x
        model=structure[0]
        if x!=0:
            model.id=x
            main_structure.add(model)
    print Selection.unfold_entities(main_structure,'M')
    io=PDBIO()
    io.set_structure(main_structure)
    io.save(path_db)

The print statement shows the following output:

[<Model id=0>, <Model id=1>, <Model id=2>, <Model id=3>, <Model id=4>,
<Model id=5>, <Model id=6>, <Model id=7>, <Model id=8>, <Model id=9>,
<Model id=10>, <Model id=11>]


So I believe I have correctly generated the object. However, the pub file
generated is saving all models with id 0, plus it has some END keywords
that I think are not correct. It looks like this (I am showing the last
part of the first model and the first one from the second):


ATOM    168  N   ILE D  99      -5.026 -38.437  15.960  1.00 22.23
  N

ATOM    169  CA  ILE D  99      -5.870 -37.247  15.926  1.00 20.60
  C

ATOM    170  C   ILE D  99      -6.803 -37.455  14.742  1.00 20.32
  C

ATOM    171  O   ILE D  99      -6.378 -37.412  13.580  1.00 21.10
  O

ATOM    172  CB  ILE D  99      -5.028 -35.954  15.704  1.00 20.81
  C

TER

ENDMDL

END

MODEL      0

ATOM      1  N   ILE D  25      -4.486  28.320  36.177  1.00 13.13
  N

ATOM      2  CA  ILE D  25      -3.263  27.547  36.087  1.00 15.38
  C

ATOM      3  C   ILE D  25      -3.596  26.073  36.119  1.00 16.87
  C

ATOM      4  O   ILE D  25      -4.286  25.599  37.026  1.00 17.23
  O


I am not sure about what could be causing the problem, or if I can solve it
by adding some keyword to the write statement, indicating that it is like
an NMR model?  Maybe I am missing something obvious, but I would be glad to
know it :)


Best,


Claudia
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