Dear Jacob,
The signal for weak anomalous sites can be stronger in Phaser SAD LLG maps than
in model-phased anomalous difference Fouriers, especially if the substructure
already contains the stronger sites, so that you're just looking for what is
still left to be explained in the SAD data.
It is quite possible that the S- and Cl- signal is being lost under that
from the Se sites. Could be:
1) simply noise that would swamp the S-SAD signal anyway
2) you just aren't contouring your map low enough (sigma is not on an
absolute scale)
3) trigonometry. Remember, with SAD you are not
Dear Jacob,
... or you could use the anomalous residual map in SHARP, the first
program to offer this kind of calculation 15 years ago or so: see
La Fortelle, E. de Bricogne, G. (1997). Methods Enzymol. 276, 472–494.
and/or the SHARP manual at
Where in refinement of your model are you ?
At an early stage I wouldn't be surprised to only see SeMets but once you've
refined your structure and go back to calculate an anomalous map with the
improved phases you might double your signal for SeMet and start seeing sulfurs.
An alternative
Hi Jacob
I agree with Juergen, and just add that your Cys and Cl might not be
fully occupied.
cheers
Preben
On 9/1/11 10:03 PM, Jacob Keller wrote:
Dear Crystallographers,
I recently have been working with a 2.5 Ang SeMet peak wavelength
dataset which contains 2 cys's and also a couple of
