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

[Ezra P. <ezr...@rc...>]

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 <tho...@sc... 
> <mailto: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
>     <https://pymolwiki.org/index.php/pdb_use_ter_records>
>
>     Cheers,
>       Thomas
>
>     On 28 Nov 2016, at 05:03, Rui Sousa <Rui...@un...
>     <mailto: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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