On 09/29/2011 10:12 PM, Sam Arnosti wrote:
Hi every one
I have a problem with docking my ligand into the electron density map and make
the connections ( bonds ) with the protein.
It is a Lysine residue that makes a Schiff Base with a long chain aldehyde.
I do not know how to make the bonds and control the torsion angles of the
ligand.
I am using the CCP4 and Coot program for refining.
Thanks
Sam
If you build the ligand close to the LYS and run the review restraints
option in REFMAC it will suggest a LINK cif file. Check it carefully and
see if you agree with the supposed chemistry, then you can use it as
part of your dictionary. You will need the LINKR record the program will
have added to your pdb file
Eleanor
