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.
