On 24/01/2017 08:04, Sam Tang wrote:
I am trying to fit a small molecule ligand into a protein complex using Coot.
The data was
processed to P212121, at 2.6 A. What I did was to input a SMILES string, fit
the ligand,
merge the ligand into the protein molecule using 'Merge Molecules' and save
coordinates.
After fitting the ligand (now as chain O) I ran restrained refinement in
Refmac5 and the
following error returns:
Into what did you input a SMILES? If the answer is Coot, then you have an Old Coot and will
be lead down the garden path.
> I believe it is due to the nomenclature of the ligand wherein Refmac mistook
atoms as DUM
I think that you're more or less right.
The modern approach is to use Acedrg to generate the ligand either via a GUI or the command
line. That will give you a PDB file which you can fit, and a dictionary that you can use in
Refmac, Coot (and, I believe, Phenix).
Paul.
