[phenixbb] Phaser SAD question

Kitty Pattridge pattridg at umich.edu
Thu Dec 24 13:20:41 PST 2009

"Randy J. Read" <rjr27 at cam.ac.uk> wrote:

>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,
>phenixbb mailing list
>phenixbb at phenix-online.org

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