Re: [phenixbb] LINK records, sugars, and a question in two parts

Hi Engin,

I was wondering if phenix.refine does or does not write out LINK records in the output pdb.

phenix.refine does not output LINK records.

Also, are carbohydrate groups written out as ATOM or HETATMs?

I think whatever you have in input PDB file will be preserved in output file (waters may be exception). I hope someone else could answer your other questions. Pavel.