If you will replace link line with the following
LINKR C1 NAG A1003 ND2 ASN A 611 NAG-ASN
Then it should be read by refmac and by coot. And restraints should be applied properly
regards
Garib
On 2 Dec 2010, at 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?
>
> many thanks in advance
>
> stephen
>
> --
> Dr. Stephen Sin-Yin Chui
> Research Assistant Professor,
> Department of Chemistry,
> The University of Hong Kong, Pokfulam Road,
> Hong Kong SAR, China.
> Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
> <611-ASN-view1><413-ASN-view2>
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