Sorry for the late reply -- I've been travelling.
You're correct, the current version of Phaser produces figures of merit
(and HL coefficients) based entirely on the initial guess about the quality
of model. The version currently in Phenix (and coming soon to the upcoming
CCP4 release) can refine the RMS values, which will give results similar to
those from SIGMAA or Refmac. This will be turned on by default when we're
happy that it's almost always best to carry out the refinement. (The worry
is that it might be unstable when the model is very incomplete, which might
be the case with your helices.)
Regards,
Randy Read
On Oct 21 2010, 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
