PyMOL doesn’t do this, in part because atoms in any given PDB file output from PyMOL could in principle derive from any loadead structure, from more than one structure, or be completely made up, and we wouldn’t want incorrect or conflicting meta information out there polluting the net.  Nevertheless, at present, PyMOL cannot even support the use case where all of the output atoms are indeed derived from a single PDB file with associated headers.  Thus, you will need to transfer them manually.





From: Sébastien Conilleau [mailto:sconilleau@chimie.u-strasbg.fr]
Sent: Tuesday, January 20, 2009 7:56 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] writing pdb files with headers



I noticed that pymol omits the headers (I mean the 5 first line) when you try to write a pdb file. At this point I do it using this command line in my script :

> cmd.save(newName+".pdb","tmp")

Is there an implemeted way to avoid this behaviour or do I have to play around with files ?



Sébastien Conilleau, PhD


Laboratoire d'Infochimie

Université Louis Pasteur

4, rue Blaise Pascal

67008 Strasbourg Cedex, France

Tel : +(33)3-90-24-15-63