Does the mtz file you are using for refinement have the correct
spacegroup in it? Sometimes it gets left as the pointgroup P222 and
causes disasters
(you just need to run
mtzutils hklin1 now.mtz hklout x.mtz
SYMM P21212
end
Eleanor
Satinder K. Singh wrote:
Hello,
I have a SAD data set to 2.9A and a native data set on the same
protein to 2.3A. I have built 70% of the model (polyalanine) into the
SAD experimental map that has been subjected to 2-fold NCS averaging
and phase-extended to 2.3 A. From the maps, the model looks like it
fits the density fine, but when I try to refine (either rigid-body or
positional refinement in REFMAC or simulated annealing in CNS), I get
an R-factor of ~60%, worse than random. Similarly, a SigmaA run
("combine isomorphous phase with partial structure") on the model
yields an R-factor of ~60%. However, when I run DM on the
original phase-combined file (before NCS averaging and phase
extension) in omit mode, I get an R-free of 34.6%, which suggests that
the map files itself is okay.
I also checked the space group of the processed data, and it is
definitely P21212.
Does anyone have any suggestions of what I may be doing wrong?
Thanks in advance for your help.
Kind regards,
Satinder
