I think you are probably asking the wrong question, and what you are eventually going to want to know is how do I get a modified amino acid recognized in PHENIX or REFMAC so that it makes proper peptide bonds. The making and breaking of bonds in COOT (or O for ligands) is not something that gets utilized downstream in PHENIX or REFMAC, that is better done in ligand construction programs.
As far as making the modified amino acid I would use Chemdraw/Chemdraw3d then export and use PRODRG to make a cif file, though there are many nice ligand construction tools out there today (including one in PHENIX I believe). Matt Vetting On Tue, Dec 6, 2011 at 5:10 PM, Saugata Hazra <[email protected]>wrote: > Hello Everyone, > > I'm sorry if its a silly question. I used to use "O" and recently started > working with "COOT". I am wondering how to make covalent bond in coot, > between a modified substrate and regular protien residue. I can not > figure out how to make the bond. > > Thanks & Regards, > Saugata > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- Matthew W Vetting Albert Einstein College of Medicine [email protected] Enzyme Function Initiative Structure Core
