Thank you very much. I am in total agreement with you that HL coefficients are better description of the phase probability and in fact I have been using the HL coeffs all these times for phase combination and density modification. My earlier post was just to make it easy for a comparison between weights calculated by sigmaA and Phaser. If I take HL coeffs from Phaser and calculate FOM, I will also get the same unusually low FOM. (I am not familiar with how to compare HL coeffs directly but based on the HL equation, the higher the coeff values for the same phase set, the higher the phase probability. The HL coeffs from Phaser are much smaller (A=0.3, B=0.28, C,D=0) than HL coeffs converted from SigmaA (A=0.95, B=0.88). The values are mean abs. from the mtz files.)
The reason I am curious about the low FOM (or HL coeffs as you prefer) from Phaser is because I am trying to compare phase combination results between the partial structure and low resolution experimental phases. I use poly alanine alpha-helices as a partial structure and apparently when using HL coeffs calculated from sigmaA or Refmac results, the model phases contribute quite a large model bias after phase combination which also get carried through density modification. The model bias seems less (obviously because of lower weight from the model) when I use result from Phaser and and the map after density modification somehow seems more satisfying. BTW, I am testing a method to solve previously determined strutures starting with experimental low resolution phases and that is why I was curious to know how Phaser gives so much different weight and HL coeffs from sigmaA. I know that you can
change weight by using a scale factor during phase combination (also available in CCP4 clipper utility) or bluring the phase probability. The easiest would be to arbitarily scale it down by half. But if anybody knows a good criteria to properly down weight phase probability, please let me know.
Many thanks,
George Wisedchaisri
On Thu, 21 Oct 2010, Clemens Vonrhein wrote:
> 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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> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> *
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