Even with SHELX, at 1.2A you should use a riding model for hydrogens and not refine them freely. SHELX has a useful facility (OMIT $H or OMIT followed by specific hydrogen atom names) to keep the hydrogen atoms in the atom list but not include their contributions to the structure factors. Then you can very easily see in a difference map (e.g. with COOT) if there is density near their expected positions.
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Tue, 23 Nov 2010, Ed Pozharski wrote: > Not sure if all the sirs will concur (and it might be a good idea to ask > madams also), but the answer is probably no. As far as protonation > state goes (guess that is what you are after, not oxidation), a better > strategy may be to look into the bond lengths between the appropriate > heavy atoms that are affected by it. Make sure that you refine without > restraints imposed on a particular bond and see if its length is closer > to the one corresponding to protonated or deprotonated state. > > Cheers, > > Ed. > > On Mon, 2010-11-22 at 23:18 -0600, Kenneth Satyshur wrote: > > Sirs: > > > > We are attempting to refine hydrogens on a ligand (which is 100 % occupied) > > and > > has ~ 40 heavy atoms (CNO). The data is 1.2 A, 325 AA, 83335 data points in > > C2. > > We have refined aniso and with H riding along (Rf= 17, R = 15) in CCP4. Can > > we individually > > refine the protons on the ligand? Let them run free with the others along > > for the ride? > > Or will they just run away at this > > resolution? Can CCP4 even do this? Should we switch to Shelx or Phenix? > > It is important to find out what the oxidation state is for the ligand at > > the pH > > we crystallized the protein and complex. > > > > thanks > > > >
