[cctbxbb] Writing a pdb file from an xray_structure object

[Claudia Millán Nebot]

Hi everyone,

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

so i guessed that something must be wrong with the residues.... and went to
check the code. That as_pdb_file method calls
to iotbx.pdb.xray_structure.as_pdb_file(), and on that code i realised that
as i was calling it whithout any resname, it was retrieving it from some
information on the scatterers that could be wrong. Putting the value of
resname to ALA, as a trial, produced almost the same output except for the
name:

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

Up to this point, i don't get what is wrong. It may be that i'm using a too
simple method and without the correct parameters (xray_structure_simple()),
as i guess part of the error is that the assignation of the types of atoms
and residues is going crazy. There are other ways of performing this step
from a pdb to an xray_structure and viceversa?


Thanks in advance!

Best regards,

Claudia Millán (cmncri at ibmb.csic.es)

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain
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