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 ------------------------------------------------------------------------------ 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
