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. It may be inconvenient for post-processing with some other tools, but that is easily taken care of by changing a setting (unset use_ter_records), or by post-processing (sed -i /TER/d file.pdb).
Cheers, Tsjerk On Tue, Mar 20, 2012 at 1:14 PM, Thomas Holder <spel...@users.sourceforge.net> wrote: > On 03/20/2012 11:35 AM, Tsjerk Wassenaar wrote: >> >> In addition to Thomas' answer... What is _wrong_ about the TER >> statement? Your chain is broken, indicated by the nonconsecutive >> numbers. That means you have two distinct molecules, and they are >> separated by a TER statement. Doesn't seem wrong. Yeah, they might be >> the same chain, but having a broken chain without considering them as >> separate molecules seems more wrong to me. > > > depends on circumstances. Many algorithms (like alignment/superposition) > work fine even with gapped chains. There are some applications which stop > reading a PDB file on the first TER record, like TMalign. So when preparing > input for TMalign with PyMOL, you most likely want to skip any TER records. > > Cheers, > Thomas > > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen -- 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
