If you feed it into REFMAC with review restraints mode - it will create a bond between two atoms within bonding distance and write a LINKR record into the output PDB.
You can then use that coordinate file and the LINK dictionary to refine the model There are other ways using the up-to-the-moment COOT. Eleanor Dodson On 6 October 2017 at 13:18, Jiyong Su <sujy...@nenu.edu.cn> 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 > >
