Shucks! So much for trying to keep the developer out of the wind. But he's a wrongdoer by PDB definitions anyway! So it would be best to modify the behaviour concerning writing of TER records. Feel free to file it as suggestion.
Gotta love polemics! -- Next time I'll manage, David. Next time... :p Tsjerk On Tue, Mar 20, 2012 at 2:48 PM, David Hall <li...@cowsandmilk.net> wrote: > On Tue, Mar 20, 2012 at 8:44 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> Hi Thomas, >> >> 'Wrong', certainly in the context it was given in, is a statement of >> judgment. It suggest that there is a failure in the functioning, and >> is a criticism to the developer, becoming a wrongdoer. My argument is, >> that the answer given (with TER statements) is not wrong, but from a >> chemical and biological point of view, and in light of the PDB format, >> is actually more correct. > > The PDB format says: > The TER records occur in the coordinate section of the entry, and > indicate the last residue presented for each polypeptide and/or > nucleic acid chain for which there are determined coordinates. For > proteins, the residue defined on the TER record is the > carboxy-terminal residue; for nucleic acids it is the 3'-terminal > residue. > ( http://www.wwpdb.org/documentation/format33/sect9.html#TER ) > > Chain breaks in crystal structures are generally not the > carboxy-terminal residues. > > -David -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
