Dear Jiyong Su, The go-to program for this is currently jligand from CCP4. To define a link you load both compounds (ASP and your thing), delete the leaving atoms (don't forget the hydrogens), define the bond (right click to change the bond order if needed). Then you can save the definition (there is a refinement step here) as mmCIF and you also get a template LINK record to put in your PDB file.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Jiyong Su > Sent: Friday, October 06, 2017 14:19 > To: [email protected] > Subject: [ccp4bb] Creating a covalent bond > > 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
