2012/12/12 Pavel Afonine <pafonine@lbl.gov>

Hi Claudia,

i have been using the xray_structure_simple() method to get an xray.structure object from a pdb object and use it to perform some calculations on it, one of them being expand it to P1. After, i tried to write a new pdb out of this xray_structure in P1. For that purpose, i used the following method:

cctbx.xray.structure.as_pdb_file(self, remark=None, remarks=[], fractional_coordinates=False, resname=None, connect=None)

but using it both with the original xray structure and with the one on P1 I get very bad lookings pdbs, with incorrect formating, like that for the case of the one in P1:

ATOM 1 PDB= PDB 1 12.330 -6.948 -40.820 1.00 19.26 N
ATOM 2 PDB= PDB 2 49.988 55.370 3.948 1.00 19.26 N
ATOM 3 PDB= PDB 3 36.092 30.710 93.483 1.00 19.26 N
ATOM 4 PDB= PDB 4 55.370 49.988 175.123 1.00 19.26 N
ATOM 5 PDB= PDB 5 30.710 36.092 85.587 1.00 19.26 N

xray_structure object does not have information about atom/residue/chain/etc labels. Conceptually, it is supposed to contain minimally necessary amount amount of data in order to calculate Fcalc. It gets stripped off the moment you go from pdb input object to xray_structure_simple().

To write a meaningful PDB file you need to use PDB hierarchy machinery. For details, see "cctbx PDB handling tools" article here:
http://phenix-online.org/newsletter/CCN_2010_07.pdf

There are numerous examples scattered across cctbx code of going back and forth between xray_structure object and pdb files.

Pavel

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