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Francis: When I had a similar issue, Paul told me that one had to mutate a residue to be sure that the stereochemistry is correct. Moreover, as of the last time I checked with Paul, COOT does look at the chiral volumes for pseudo-chiral centers such as Leu and Val, so it is no surprise that COOT doesn't catch it. Try either Simple Mutate or Mutate & Auto Fit ... Steven >-----Original Message----- >From: Mailing list for users of COOT Crystallographic Software >[mailto:[log in to unmask]] On Behalf Of Francis E Reyes >Sent: Thursday, March 05, 2009 6:36 PM >To: [log in to unmask] >Subject: Re: stereochemical violations in real space refinement? > >Actually i just checked my structure with the Validate -> Incorrect >Chiral Volumes. It seems to check out OK, but the PDB doesn't like it? >Anyone? > >thanks >FR >On Mar 5, 2009, at 4:25 PM, Francis E Reyes wrote: > >> Hi all, >> >> Just tried to submit a PDB and it seems that LEU is not correctly >> positioned (CG/CD1,CD2). I real space refined this residue, does the >> real space refinement take into account stereochemical considerations? >> >> Thanks >> FR >> >> --------------------------------------------- >> Francis Reyes M.Sc. >> 215 UCB >> University of Colorado at Boulder >> >> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D >> >> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D > >--------------------------------------------- >Francis Reyes M.Sc. >215 UCB >University of Colorado at Boulder > >gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D > >8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D