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.
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