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.

Pavel

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
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