Dear Sam "double" bond is only used to find bon lengths and other parameters. Refmac uses bond length. As I see you would like to make a link between two residues. There is a tutorial written by Andrey Lebedev that addresses exactly this type of problems. Please have a look this site:
http://www.ysbl.york.ac.uk/mxstat/JLigand/index.html there are three tutorials: 1) simple ligand, 2) links (that is what you want) and 3) simple metal containing ligand treatment. I hope it helps. If it does not please let us know. regards Garib On 18 Jan 2012, at 21:07, Sam Arnosti wrote: > Hi every one > > I have made a Cif file for the restraints of my ligand with Jligand, which is > attached to my protein via a lysine-aldehyde Schiff base formation. > The problem is that whenever I run the refmac with the Cif file with torsions > and link description, it changes the distance of the Lysine and the Carbon of > my ligand. > > The density is there, but it does not recognize it as a C=N bond and puts > them up to 2 angstrom away from each other. > I do not know, if I should change the link description to make the Refmac > regonize the double bond or what else I can do. > > This is the description of link in my Cif file: > > _chem_link_bond.link_id > _chem_link_bond.atom_1_comp_id > _chem_link_bond.atom_id_1 > _chem_link_bond.atom_2_comp_id > _chem_link_bond.atom_id_2 > _chem_link_bond.type > _chem_link_bond.value_dist > _chem_link_bond.value_dist_esd > LYS-MER 1 NZ 2 C18 double 1.260 0.020 > > I appriciate your help beforehand. > > Regards > > Sam Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
