Dear Dr Emsley Many thanks for your reply.
I have now updated my Coot and am able to run refmac refinement using my ligand PDB and CIF generated from elbow2 under Phenix. This is indeed a lesson on the importance of keeping all softwares updated! Kind regards Sam On 24 January 2017 at 18:29, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > 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. >
