[phenixbb] Phaser question : MR+SAD after refinement

Randy Read rjr27 at cam.ac.uk
Thu Apr 22 09:46:12 PDT 2010


If you want to be safe, you can remove the known/suspected anomalous scatterers from the PDB file and see if Phaser finds them back.  If you don't do this, Phaser will probably find them because they're treated as non-anomalous scatterers when they're part of the PARTIAL PDB model, and the LLG maps will look for places where the addition of anomalous scatterers will improve the likelihood target.  However, there will be a penalty because adding a heavy anomalous scatterer on top of a heavy atom will give too much real scattering.  If Phaser does find the site, then in subsequent refinements it omits the corresponding atom from the partial PDB file.

We're currently testing new ways of optimizing the use of Phaser to verify the anomalous scatterer sites from the final refined model, so things will probably change over the next few months, hopefully in a good way!


Randy Read

On 22 Apr 2010, at 16:08, Peter Grey wrote:

> Dear All,
> I solved a structure by MR+SAD in Phaser,  refined it,  and would like now to let Phaser locate additional heavy atom.
> Should I remove the anomalous scatterers from the  "PARTIAL PDB" I input to Phaser ?
> Thank you for your time,
> Peter
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Randy J. Read
Department of Haematology, University of Cambridge
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