To answer your question... On 10/04/17 08:44, Mohamed Noor wrote:
Is it possible to directly build a ligand in real space (in Coot?) and then generate a SMILES string for restraint generation.
I think that you are describing a 3D editor. It is not possible to do this in Coot (Coot's molecular editor is 2D). If you want to use Coot I would do as Johannes says, use File -> Get Monomer.
PG4 (first choice), PGE, PEG, PE8. These are fun to refine in Coot, they wriggle around.
I think that SMILES is a bit of side-issue.
I am already using Polder and omit maps that confirm these are not noise.
:-) Paul.
