Thanks a lot, I will dig into it. S
> On 28 Feb 2018, at 17:37, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > > On 28/02/2018 16:26, Sebastiano Pasqualato wrote: >> Hi Paul, hi all, >> I have recently came across a case in which I have to refine a structure >> with a ligand covalently bound to a Cys of a protein. > >> I managed to input the geometric restrains for the refinement in phenix, and >> generate a pdb with a LINK line. >> However, I would like to real space refine the ligand against a map in coot, >> and I don’t know how to import the restrains for the ligand-Cys covalent >> bond. >> I have already generated and imported to Coot the CIF file for the ligand. >> Do I have to use JLigand? > > We know that this is a problematic process and what I would recommend will > change in a month or so. > > For now, yes, use JLigand - there is a nice tutorial here > > http://www.ysbl.york.ac.uk/mxstat/JLigand/tutorial_link.html > > Paul.
