Hi Stefano,
The PDB chain IDs in relax are treated as separate molecules, as that
is how the chain IDs are defined in the PDB standard. In testing all
3 PDB files, I see:
"""
script = 'test.py'
----------------------------------------------------------------------------------------------------
pipe.create('bug_21814', 'mf')
structure.read_pdb('SpUreE_dimer_H.pdb')
structure.read_pdb('SpUreE_dimer_H_new.pdb')
structure.read_pdb('hadded_2_test.pdb')
----------------------------------------------------------------------------------------------------
relax> pipe.create(pipe_name='bug_21814', pipe_type='mf', bundle=None)
relax> structure.read_pdb(file='SpUreE_dimer_H.pdb', dir=None,
read_mol=None, set_mol_name=None, read_model=None, set_model_num=None,
alt_loc=None, merge=False)
Internal relax PDB parser.
Opening the file 'SpUreE_dimer_H.pdb' for reading.
Adding molecule 'SpUreE_dimer_H_mol1' to model None (from the original
molecule number 1 of model None)
Adding molecule 'SpUreE_dimer_H_mol2' to model None (from the original
molecule number 2 of model None)
relax> structure.read_pdb(file='SpUreE_dimer_H_new.pdb', dir=None,
read_mol=None, set_mol_name=None, read_model=None, set_model_num=None,
alt_loc=None, merge=False)
Internal relax PDB parser.
Opening the file 'SpUreE_dimer_H_new.pdb.bz2' for reading.
Adding molecule 'SpUreE_dimer_H_new.pdb_mol3' to model None (from the
original molecule number 1 of model None)
Adding molecule 'SpUreE_dimer_H_new.pdb_mol4' to model None (from the
original molecule number 2 of model None)
relax> structure.read_pdb(file='hadded_2_test.pdb', dir=None,
read_mol=None, set_mol_name=None, read_model=None, set_model_num=None,
alt_loc=None, merge=False)
Internal relax PDB parser.
Opening the file 'hadded_2_test.pdb' for reading.
Adding molecule 'hadded_2_test_mol5' to model None (from the original
molecule number 1 of model None)
"""
Therefore everything appears to be working correctly now - from the
aspect of reading PDB files anyway.
Regards,
Edward
On 19 March 2014 13:29, Stefano Luciano Ciurli <stefano.ciurli@xxxxxxxx>
wrote:
Hi Edward,
The following error occurs when loading the SpUreE_dimer_H_new.pdb and
hadded_2.pdb PDB files (but not the SpUreE_dimer_H.pdb file)
OK at least now I know where to look for error.
In the "good" file SpUreE_dimer_H.pdb, I have no headers, the two chains
are labeled A and B, and the residue numbering continues on after the end
of chain A; same thing for another file that also works, generated using
MODELLER and that contains three lines made by MODELLER itself, two chains
labeled A and B and residue numbering continuing after chain A, the zinc
atom is also present;
In the "bad" file SpUreE_dimer_H_new.pdb, I have the PDB headers, chains
labeled A and B, and the residue numbering restarts from 1 after the end of
chain A; so, restarting residue numbering is "bad"
In the "bad" file hadded_2.pdb, I have the PDB headers, I have only one
chain that reaches only up to residue 143 (missing four residues) and the
Zn ion and water molecules are still there; here the problem is probably
the number of residues.
Stefano
Re: [bug #21814] PDB file format