In general, it requires a LINK record to add the required bond. I don't know how to set up refinement parameters. I had a similar case once (see 1ECC), and created a big non-standard residue containing both the amino acid and ligand as one residue. (But, that was done in X-PLOR.) If setting up link paramaters become a hassle, you might try the single-residue approach.
Joe Hall Gareth wrote: > Dear ccp4bb users, > > I am currently refining a crystal structure of a protein with a > drug molecule in the active site. The drug molecule is seen, as > expected, to covalently bind to the active site. Therefore, can anyone > tell me what I need to do to alter the pdb file so as to form a covalent > bond between the protein and my drug molecule? > > Cheers in advance, > > Gareth Hall > > This message has been checked for viruses but the contents of an > attachment may still contain software viruses, which could damage your > computer system: you are advised to perform your own checks. Email > communications with the University of Nottingham may be monitored as > permitted by UK legislation. >
