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> 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 > > Cheers, > Thomas > > On 28 Nov 2016, at 05:03, Rui Sousa <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) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >
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