PDB format dictates that TER records are present at the end of a polymer chain. Chain breaks or non-sequential numbering do not introduce TER records. A TER record is required between the polymer and non-polymer chain - even with same chain ID. TER records should not be between non-polymers...
Of course, there have been many different flavors of PDB files produced by different programs... http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER On 11/28/2016 10:31 AM, Spencer Bliven wrote: > It would be nice to have a setting that adds TER records only where the chain > or segi change (as opposed to whenever the residue numbers are > non-sequential). I believe that better captures the original intent for > terminating polymers. Of course, the real answer is that everyone should > switch to mmCIF. > > On Mon, Nov 28, 2016 at 4:01 PM, Thomas Holder <thomas.hol...@schrodinger.com > <mailto:thomas.hol...@schrodinger.com>> wrote: > > Hi Marko and Rui, > > The TER records can also be prevented with "set pdb_use_ter_records, off". > > https://pymolwiki.org/index.php/pdb_use_ter_records > <https://pymolwiki.org/index.php/pdb_use_ter_records> > > Cheers, > Thomas > > On 28 Nov 2016, at 05:03, Rui Sousa <rui.so...@univ-nantes.fr > <mailto:rui.so...@univ-nantes.fr>> wrote: > > > Hi Marko, > > > > For the order of the atoms, check if "retain_order" is set to 1; if not, > > use "set retain_order, 1" before importing your PDB file. For the rest > > of your problem, what exactly is being changed from the imported PDB > > file and the saved one? Apart from the addition of TER, which is a > > fairly trivial problem to solve. > > > > Best regards, > > > > Rui > > > > Le 28/11/2016 10:41, Marko Sever a écrit : > >> Hello everybody, > >> > >> I'm working with a protein-protein complex and am fixing some stuff. > >> > >> When I save the fixed complex as a pdb the PDB format is not the same > as it was in the imported pdb files (there it was the same as the CHARMM > default pdb format). > >> > >> In the saved pdb it changed the line position of atoms in the pdb file. > Residues are ok but atoms in a given residue are mixed up. It also added > addition TER's which I had to manually delete. > >> > >> So how would I specify the output PDB format to be the same as in the > original imported pdbs (before manipulation), so same as CHARMM pdb > format. > >> > >> Please help, > >> > >> Marko > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > > > ------------------------------------------------------------------------------ > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net > <mailto:PyMOL-users@lists.sourceforge.net>) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > <https://lists.sourceforge.net/lists/listinfo/pymol-users> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> > > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > 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 ------------------------------------------------------------------------------ _______________________________________________ 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
