[phenixbb] Maximum-likelihood score calculation

Pavel Afonine pafonine at lbl.gov
Fri Jul 11 16:57:46 PDT 2014

Hi Jouko,

a few points to be aware of:

1) ML targets used in phenix.refine and Phaser are essentially the same 
but parametrized differently (alpha/beta vs sigmaA). You can see this if 
you check corresponding publications.

2) Parameters of ML targets used in phenix.refine (alpha/beta) and 
Phaser (sigmaA) are estimated differently mainly because these program 
work at very different range of model-data discrepancy.

At MR stage (Phaser) model errors are usually gross and deriving 
alpha/beta or sigmaA from comparison of Fcalc and Fobs may not be 
reliable; this is why Phaser asks the user to provide an approximate 
information about how large the model errors are (as rmsd or sequence 
identity). This information is then used to estimate sigmaA, and in turn 
calculate ML target.

At refinement stage (phenix.refine) model-data discrepancy is smaller, 
and sigmaA or alpha/beta can be reliably estimated from comparison of 
Fcalc and Fobs. This is what phenix.refine does, and this is the target 
that you get from fmodel object that Nat mentioned earlier.


On 7/11/14, 2:48 PM, Jouko Virtanen wrote:
> Hi all,
> I would like to calculate the maximum-likelihood score given an input 
> structure and an mtz file.  How can I do that?  Thanks in advance.
> Best regards,
> Jouko
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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