Fwd: [ccp4bb] How to tell Refmac it is a fixed double bond?

From: Sam Arnosti
Date: 18 January 2012 21:07


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      1.260    0.020

I appriciate your help beforehand.

Regards

Sam

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From: Garib N Murshudov

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

Garib N Murshudov