[phenixbb] Phaser SAD module - resolution question

Randy Read rjr27 at cam.ac.uk
Fri Aug 13 13:30:42 PDT 2010

In the MR+SAD procedure I usually just give all the data to the full resolution.  If there's too little anomalous signal, Phaser will tend to give you very few (or maybe even no) sites.  However, in some pathological data sets Phaser can end up fitting noise, so it's always a good idea to look at the sites in the context of a solvent-flattened map derived from the phases, to see if they look like what you expect (e.g. sites near the protein surface for a heavy-atom soak).

Of course, it never hurts to try something different and see what happens, so it would be good to try a control experiment varying the resolution as you propose.


Randy Read

On 13 Aug 2010, at 09:55, Peter Grey wrote:

> Dear Phenix community,
> I am using Phaser SAD module with a poor MR model to locate the initial heavy-atom sub-structure.
> I have a 3A dataset but the anomalous signal is weak at the higher resolution shells.
> I would like to ask for your advice regarding the resolution I should use in Phaser. 
> I thought that for the sake of just locating the sites I should use relatively low resolution (let's say 3.5 or even 4A) and then run Phaser a second time.
> In this second run I would use the highest-resolution and let Phaser only refine the sites (located in the first run) during one cycle and calculate the combined phases.
> Thank you in advance for your suggestions and advice,
> Peter
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Randy J. Read
Department of Haematology, University of Cambridge
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