[phenixbb] SAD + MR
Randy J. Read
rjr27 at cam.ac.uk
Tue Jun 19 14:18:32 PDT 2007
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.
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,
> Novo Yahoo! Cadê? - Experimente uma nova busca.
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