Problem solved. One must also switch to the "make sugar NO" keyword. Otherwise Refmac tries to use the discovered sugar and ion as if it was sugar-peptide bond.
Jan Dohnalek On Mon, Feb 1, 2010 at 2:52 PM, Jan Dohnalek <dohnalek...@gmail.com> wrote: > Dear all > I understand that when I use the Refmac keyword > make link no > Refmac should not apply found links. > It keeps finding links between ligands (Na+ and ligand OH) and (I think) > refines them as it issues a warning (not INFO), does not say "(not be used)" > for these and the output .pdb file contains the LINK records newly created > for these atoms. > > The actual distances look pretty much as if they were restrained ... > > Is there a way to make Refmac ignore these links? > > Jan Dohnalek > > -- > Jan Dohnalek, Ph.D > Institute of Macromolecular Chemistry > Academy of Sciences of the Czech Republic > Heyrovskeho nam. 2 > 16206 Praha 6 > Czech Republic > > Tel: +420 296 809 390 > Fax: +420 296 809 410 > -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
