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

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...

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

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

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 wrote: > Hi Marko, > > For the order of the atoms, check if

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

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

[PyMOL] PDB Format not correct for use in CHARMM

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