[phenixbb] SAD + MR

Randy J. Read rjr27 at cam.ac.uk
Tue Jun 19 14:18:32 PDT 2007

Dear Lucas,

You'll need Phaser version 2.1, which will be in the next developer release 
of Phenix-1.3b. This has a new feature that exactly addresses your problem. 
You can start the SAD phasing using the molecular replacement model as an 
initial "substructure". Then log-likelihood-gradient maps are used to add 
in the anomalous scatterers. We've found that the resulting anomalous 
scatterer model is usually more accurate and, perhaps more importantly, is 
more complete. Often the S atoms can be found, even when the wavelength is 
not optimal for S-SAD. The map that comes out of this phasing process 
automatically combines the molecular replacement and anomalous scattering 
information, properly weighted and with a correction for model bias.

I'm in Grenoble right now at a phasing workshop, but when I get back I 
should be able to send you a statically-linked Linux executable of the 
beta-test version of Phaser-2.1.

Randy Read
On Jun 16 2007, Lucas Bleicher wrote:

>I have a dataset from a Cs-soaked crystal, and the
>protein has a domain solved in the PDB. The problem is
>that the map obtained just with the experimental
>phasing is not so easily interpreted, and the domain
>is just about 25% of the whole protein. Inspection of
>the map generated by MR suggests that it's a good
>solution, with residues fitting reasonably well on the
>Given the new features on Phaser 2.0, which I suppose
>is included in Phenix 1.3b, can anyone suggest a
>protocol to profit from both things (anomalous
>scattering + good search model)?
>Thanks in advance,
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