Hello everyone, When I refine in CCP4 a structure with Glc units attached every few of them as a ligand and there are several of them in the same file, I start off with a PDB that shows the LINK records between the GLC units as LINKR because I add the links by > Extensions > Modelling > Make Link (2 atoms) in COOT.
What does LINKR mean? why not just LINK? More importantly, when I refine, the output PDB file does not contain the LINK records, why do they go away? and in PyMol I see only GLC that are close enough to make a covalent bond stay connected, the others become detached, in CCP4 they all show detached, but if I do a real space refinement for those sugars of the same ligand in the output file, they come close together and attached? Any suggestions? Thank you very much in advance. Remie
