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

[Thomas H. <tho...@sc...>]

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.