Being lazy I would just do refinement with REFMAC and let it generate
the SigmaA values.. then try rebuilding with either buccaneer or
Arp/Warp.They willboth generate weighting terms based on the Rfactors.
Eleanor
On 10/21/2010 12:58 AM, Goragot Wisedchaisri wrote:
Hi,
I have helices that I did rigid body refinement with Phaser (after phased
rotation and phased translation in Molrep). I compare FOM output by Phaser to
the FOM computed by sigmaA using the Phaser refined coordinates and found that
FOM from Phaser is only about half (~0.25) of FOM from SigmaA (~0.5). I'm
running Phaser using ccp4 version 6.1.13. I remember a while back that Phaser
used to calculate a priori sigmaA estimation based on assumed model rmsd error.
I am not sure if this a priori SigmaA weight is also output in the FOM column.
If this is not the case, could anyone point me to a documentation of how Phaser
calculates FOM. The Phaser wiki and J App Crys paper does not seem to have
detail information on this.
I could just use SigmaA or do refinement in Refmac but I have to say that I
like the low FOM from Phaser because model bias seem to be much less after
density modification. It also saves me from having to blur the phase
probability distribution in order to down weight FOM when FOM is too high. But
I still would like to know how Phaser currently calculates the unusually low
output FOM.
Many thanks,
George Wisedchaisri
