"Randy J. Read" 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,

Peter.

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