I dont think that isnt the correct format for a LINKR record. LINKR C LEU A -1 N CYG A 0 LEU-CYG LINKR C2 CYG A 0 N SER A 2 CYG-SER
It is like this - it points to a named LINK entry in your restraints library eg LEU-CYGun refmac with "Review restraints" option from the GUI it will create such an entry for you. You can then check whether you agree with t he chemistry imposed. Eleanor If you r On 12/02/2010 08:59 AM, Paul Emsley wrote: > 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.
