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'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?</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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