JLigand from this site
http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html
should be able to create link you want. And then you can add link
record on your pdb as in the template:
http://www.ysbl.york.ac.uk/refmac/data/template_link.txt
I hope it addresses the problem you are facing.
Garib
On 9 Oct 2009, at 10:07, Christian Rausch wrote:
Dear Sampath!
Refmac5's dictionary uses LLP to encode the "LYSINE-PYRIDOXAL-5*-
PHOSPHATE", a modified lysine residue with its NZ- amino group
covalently bound via a Schiff base to a pyridoxal phosphate.
See http://www.ccp4.ac.uk/html/refmac5/dictionary/list-of-ligands.html
Have a look at the attached file "LLP.pdb" (e.g. in PyMOL).
In Coot, move your PLP towards the NZ of the active site LYS.
Superimpose the aldehyde oxygen of PLP onto the NZ. Save both
structures and replace the ATOM coordinates of the modified LYS
with a HETATM record as you can see in the file "LLP.pdb" using the
coordinates of your LYS and PLP accordingly.
Wherever this modified LYS appears in three letter code in your PDB-
file replace it by LLP. You might need to correct the atom numbers
accordingly. The use this structure for refmac.
Greetings,
Christian
Biological Chemistry, TU Munich
<LLP.pdb>
