Hi George,
On Wed, Oct 20, 2010 at 04:58:34PM -0700, 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).
What do you need FOM values for - apart from just looking at them? You
don't need them for calculating maps since both SIGMAA and Phaser (I
assume) output map-coefficients directly (an amplitude and
weight). And you don't need them in refinement since both programs
probably output Hendrickson-Lattmann coefficients - which are a much
better description of phase probability. Density-modification: same
thing.
> 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.
Are you using the FOM columns in density modification? Why? Most
modern programs will allow you input of Hendrickson-Lattmann
coefficients (and also output those). And the initial map can be
calculated with the map coefficients anyway.
> It also saves me from having to blur the phase probability
> distribution in order to down weight FOM when FOM is too high.
FOM columns in a MTZ file are maybe useful to calculate statistics
versus resolution ... but nearly everything you would do with FOM
(attach it to an amplitude and phase) can be done much better with
Hendrickson-Lattmann coefficients.
E.g. running DM after a MR solution, I would use
LABIN FP=F SIGFP=SIGF PHIO=PHWT FOMO=FOM -
HLA=HLA HLB=HLB HLC=HLC HLD=HLD -
FDM=FWT PHIDM=PHWT
It still reads the FOM column - but only to analyse it against
resolution to determine a good phase-extension scheme. Internally, it
will always use the HLA-D values ... afaik.
Cheers
Clemens
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