Dear Phenix Experts,<br><br>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 :<br>
<br>- 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 ?<br><br>-  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) ?<br>
<br>- 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 ? <br><br clear="all">
<br>Many thanks,<br><br>Peter.<br><br><br>