Re: [PyMOL] PDB Format not correct for use in CHARMM

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 <
tho...@sc...> 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...@un...> 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.
>
>
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