The easy way is Coot Extensions Link two atoms which should create a Link record in the pdb.
I think the better way is use jligand which creates a full dictionary describing the particular link with proper restraints. Load your ligand, load the Asp monomer link the two atoms in question create the dictionary (Regularize link) add the link record created by jligand to your pdb use the dictionary in subsequent refinements You might have to combine the link library with your dictionary of your ligand using the merge lib task (I'm not sure right now if jligand automatically creates the dictionary for the ligand as well) Cheers Christian On Fri, Oct 6, 2017 at 1:18 PM, Jiyong Su <[email protected]> wrote: > Dear CCP4 BB, > > We solved one co-crystal structure of a protein and a compound. We found > this compound could covalently modify an asparate residue of this protein. > A covalent bond formed between a oxygen atom of Asp carboxyl group and a > carbon atom of that compound. Does anyone knows how to draw a covalent bond > between the oxygen atom and the carbon atom and refined it? We tried coot, > pymol and chimera, but failed. Thank you in advance! > > Best regards, > > Jiyong Su > >
