First you should look into why your chiral centers flipped. In my experience the most common cause is that the neighboring peptide bond needs to be flipped.
If you just want to flip a chiral center in Coot, I think the easiest way is to "real space refine" the residue and before accepting the result, drag the CA to the side you want. You may have over-drag to get it to stay. It only takes a moment. But don't assume that your refinement program is just doing something stupid. Look for the primal cause. Dale Tronrud Yusuf Akhter wrote:
Hi Everybody, I am refining structure of a protein at 3 Angstrom. I am doing model building in Coot. After several rounds of refinement using Refmac when I tried to run PROCHECK on my partially build model I found that some of the residues are D-amino acids. How to change these D-amino acids to L-amino acids?? Is there any option in Coot for that?? Thanks in advance, yusuf
