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 1.2600.020
>
> 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
