Hi everyone,<div><br></div><div>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:</div>

<div><br></div><div>cctbx.xray.structure.as_pdb_file(self, remark=None, remarks=[], fractional_coordinates=False, resname=None, connect=None)</div><div><br></div><div>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:</div>

<div><br></div><div><div>ATOM      1 PDB= PDB     1      12.330  -6.948 -40.820  1.00 19.26           N</div><div>ATOM      2 PDB= PDB     2      49.988  55.370   3.948  1.00 19.26           N</div><div>ATOM      3 PDB= PDB     3      36.092  30.710  93.483  1.00 19.26           N</div>

<div>ATOM      4 PDB= PDB     4      55.370  49.988 175.123  1.00 19.26           N</div><div>ATOM      5 PDB= PDB     5      30.710  36.092  85.587  1.00 19.26           N</div><div><br></div><div>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:</div>

<div><br></div><div><div>ATOM      1 PDB= ALA     1      12.330  -6.948 -40.820  1.00 19.26           N</div><div>ATOM      2 PDB= ALA     2      49.988  55.370   3.948  1.00 19.26           N</div><div>ATOM      3 PDB= ALA     3      36.092  30.710  93.483  1.00 19.26           N</div>

<div>ATOM      4 PDB= ALA     4      55.370  49.988 175.123  1.00 19.26           N</div><div>ATOM      5 PDB= ALA     5      30.710  36.092  85.587  1.00 19.26           N</div><div><br></div><div>Up to this point, i don&#39;t get what is wrong. It may be that i&#39;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?</div>

<div><br></div><div><br></div><div>Thanks in advance!</div></div><div><br></div><div>Best regards,</div><div><br></div><div><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(34,34,34)"><p>

<font face="arial, helvetica, sans-serif">Claudia Millán (<a href="mailto:cmncri@ibmb.csic.es" style="color:rgb(17,85,204)" target="_blank">cmncri@ibmb.csic.es</a>)</font></p><p><font face="arial, helvetica, sans-serif">Institut de Biologia Molecular de Barcelona (IBMB-CSIC)</font></p>

<p><font face="arial, helvetica, sans-serif">Barcelona, Spain</font></p></span></div><br>
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