Dear Yuri,
In addition to the other good options that have been presented, you can use
the log-likelihood gradient maps in Phaser to find anomalous scatterers. We
find this to be very sensitive, and it has the advantage of being iterative
(i.e. when you find some anomalous scatterers, this improves your model and
thus the sensitivity for finding additional sites).
When you're starting from a refined model, we think it is best to look for
purely imaginary scatterers to add to the real scattering in your model. In
the ccp4i GUI, choose the "SAD with molecular replacement partial
structure" mode, provide the data (with F+ and F-), the wavelength, and the
current model, then turn on LLG-map completion and select the "Complete
with purely anomalous scatterer" option.
If you want to see the initial LLG map, set the number of completion cycles
to 0 and turn on the option to output log-likelihood-gradient map
coefficients. Open these in coot as a difference map, choosing the columns
FLLG_AX and PHLLG_AX. If you let Phaser complete the sites, then the final
LLG map should be nearly flat and you have to look at the PDB file
containing the sites that it found.
Best wishes,
Randy Read
On Nov 26 2011, Yuri Pompeu wrote:
Hi Boaz, Yes indeed, the phosphate group of the molecule looks quite
beautiful at 1.17A and it has a really big peak 18sigma! Is there a
utility for calculating anomalous maps, or is it simply an option in the
refinement program?
--
Randy J. Read
