[phenixbb] Phaser SAD question

Peter Grey petgxray at gmail.com
Wed Dec 23 16:13:33 PST 2009

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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