Upgrading dictionary should be just matter of downloading from this site: www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac_dictionary_v5.6.0023.tar.gz
or from the latest ccp4 (6.1.24 or something like that) Garib On 17 Mar 2011, at 12:54, Paul Emsley wrote: > On 16/03/11 18:45, Dr. Mark Mayer wrote: >> Dear all, >> >> I'm rebuilding structure refined using phenix -1.7-650 using coot >> 0.6.2-pre-1-250. >> When I use the rotamers command to select new rotamers (flagged as >> bad by molprobity) some of the riding H atoms get left behind, which >> means the file is no good for further crystallographic refinement. >> Likewise, real space refinement produces the infamous flying hydrogens >> problem. >> >> Any ideas on fixing this? Our current work around is to remove H and >> then run reduce again prior to refinement in phenix. >> >> > > > This is not a Coot problem. There is a mismatch between the model and the > dictionary (presumably version 3.x and 2.3). > > The dictionary needs to be upgraded to 3.x - it is not hard work but needs to > be done. I have scheduled it for 0.7 if it is not done before I do it - for > standard protein residues, RNA and DNA at least. > > You are using the approved work-around. > > Paul.
