I would assume that the wrong chiralities were introduced during building. It is not very hard to change chiral centers around if you're dragging atoms around in and out of density...
Artem -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Dale Tronrud Sent: Saturday, August 02, 2008 2:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] D-Amino acids to L-Amino acids 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 >
