[phenixbb] Phaser SAD question

Randy J. Read rjr27 at cam.ac.uk
Thu Dec 24 07:26:41 PST 2009

Dear Peter,

I'm interested in your observation that you get better signal from an 
anomalous difference map computed with density-modified phases than you get 
with an LLG map using the MR model. Presumably the density modification 
just started from the model phases as well? We've never tried that, so 
we'll have to look into that. Unfortunately, you can't at the moment start 
the LLG completion with a "model" specified through structure factors, 
though this is on our to-do list.

With the MR+SAD option, because it is iterative, there are sites found in 
subsequent cycles (where the information from some of the anomalous 
scatterers has become available) and you end up with a set of reliable 
sites that can be significantly larger than the set obtained from the first 
LLG map. Does your anomalous difference Fourier with density modified 
phases give you a larger apparently reliable substructure than the 
iterative completion? You could use phenix.emma to compare the two 
substructures and see how much they have in common.

You can indeed give Phaser the set of sites that you got from the anomalous 
difference map. One way to choose the cutoff would be to see how deep the 
deepest hole is (i.e. how many standard deviations the map goes in the 
negative direction), and choose a larger number in the positive direction. 
Or you could just use the peaks above 6-7 sigma.

I'd be interested in hearing how you get on with this approach, off-line if 
you prefer.

Good luck and Happy Christmas!

Randy Read

On Dec 24 2009, Peter Grey wrote:

>Dear Phenix Experts,
>I use the SAD+MR option in Phenix. The ASU is huge and the number of
>scatterres is in the few hundreds range. I try to minimize the number of
>runs of Phaser SAD+MR since they take long time on my computer and would
>appreciate your insight regarding the following :
> - I noticed that I get much higher signal and much larger number of sites 
> if I use density modified phases to calculate the anomalous difference 
> map. Is it possible to input these phases instead of the model to Phaser 
> ?
> - If not, do you recommend providing Phaser with the list of sites found 
> in this difference anomalous map. Should such a list include only the 
> sites you can be sure of (say above 7 sigma) or all possible sites (say 
> above 5 sigma) ?
> - Should I use the (peak height)/(sigma of map) as the first estimate of 
> occupancy ? if so do I have to normalize it (strongest site has occupancy 
> of 1) or can I leave the height/sigma values as they are ?
>Many thanks,

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