On 17/03/11 12:55, Garib N Murshudov wrote:
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.
Sadly not as easy as that.
First, Coot uses the "old-style" filenames - i.e. the .cif files [1] are
in lettered subdirectories, not all files in one directory
(straightforward for me to fix if you mean to keep the new naming style).
Secondly (and more importantly), the PDB version 3.x has a " H "
hydrogen atom on the peptide N - so did the old-style dictionary. The
new Refmac dictionary does not (it does have HN1 and HN2 - presumably
non-polymer) - hence we still get flying hydrogens - different ones :-/.
So, do I take it that with the new dictionary I now need to apply the
mon_lib_list's data_mod_list items for the peptides (in this case
DEL-NH1 and DEL-OXT) when Coot finds a peptide link? It seems to me
that if this dictionary is out in the wild I'll need to sort this out
pretty sharpish.
Paul.
[1] the Corina manual calls CIF files "CCP4 dictionary files" :-)
