On 02/12/10 06:49, Dr. STEPHEN SIN-YIN, CHUI wrote: > Dear All, > > Please see the maps for the ASN residues of the protein, As suggested by > colleague, they are NAG which are connected to the N atom of ASN413 & ASN611. > I put the NAG molecule to those density and try to use the following command > line in PDB, > > LINKR C1 NAG A1003 ND2 ASN A 611 1555 1555 1.45 > > > but after restrained refinement using REFMAC5 (quite latest version), the bond > distance between N of ASN and C1 of NAG seems to be off (1.28 A) from the > value > I set for this restraint. > > My question is related to the true command of bond restraint for this > situation? > Also if I want to show a "link or line" between N atom of the ASN and C1 atom > of > NAG in COOT, any idea how to do this? >
The distance is controlled by the Refmac restraints library, specifically (in this case) the NAG-ASN bond (found in lib/data/monomers/list/mon_lib_list.cif). If you look at data_link_NAG-ASN you will see that the ideal distance is 1.439. You can tighten the restraint by adjusting the bond_value_dist_esd (although I would not recommend this). If you want to see it in Coot you should use a LINK line - careful with the formating. I believe that recent pre-release builds will display a (compatibly/correctly formatted) LINKR line too. Paul.
