You could probably do this via a mutate option in coot . Or at least use  the 
sulfoxide as a new residue (not mutate)

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of amit gaur
Sent: Saturday, 30 November 2019 7:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] technical question

Hi everbody,
I want to replace a particular methionine in a pdb with methionine sulfoxide( 
an oxidized form of methionine). Can body please tell me how to do this? I am 
familiar with pymol, chimera and coot software.
--
Amit Gaur
Post Doctoral Researcher
Thomas Jefferson University
1020, Locust Street, Suite 418
Philadelphia, PA 19107



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