Hi Pietro,
There are monomer library entries for Ca in various states of
coordination by water, entries, OC1, OC2,OC3 etc but unfortunately
these are incomplete (no distances or angles with sd's), at least in
our CCP4 installation. The entry for octahedral MG-O6, file MO6, is
complete so you could use that as a model if you want to. The
advantage of these entries is that they restrain angles as well as
distances (eg O-MG-O, or O-CA-O in your case), ie it will keep it
octahedral.
Andrew
On 10 Sep 2010, at 14:56, Pietro Roversi wrote:
Dear all,
How do I set up a Refmac dictionary to constrain octahedrally
coordinated Ca++?
Refmac5 seems to detect the potential bond between the Ca++ and the
ligands:
INFO: link is found (not be used) dist= 2.229 ideal_dist=
2.320
ch:AA res: 263 GLU at:O .->ch:Ag res: 600
CA at:CA .
but it does not enforce them, and I cannot figure out what the
CCP4 convention for a O-Ca++ bond is.
Thanks for any suggestions!
Pietro
