Yes, real space refinement takes into account stereochemical restraints, that is what all the traffic lights are about.
What, exactly, is the PDB complaining about? If it is the chirality of atom CG, then you should realize that this is not a real chiral center. CG becomes chiral when the two CD atoms are given numbers. There are two ways to do it but a convention has been adopted to make all Leu CG atoms look the same. If your residue is being flagged as backwards, simply edit the PDB file and swap the numbers on the two CD atoms. Some programs monitor fake chiral centers but others do not. The PDB certainly does, at least for amino acids. Check the labeling of oxygen atoms in phosphates if you want a scare. If this isn't your problem please add details. Dale Tronrud Francis E Reyes wrote: > 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
