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Hi Jouko,<br>
<br>
a few points to be aware of:<br>
<br>
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.<br>
<br>
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. <br>
<br>
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.<br>
<br>
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.<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 7/11/14, 2:48 PM, Jouko Virtanen
wrote:<br>
</div>
<blockquote
cite="mid:CAPaUbfX0+iK-kn2Nt3jDQt8qA5EppABQt5fu_0mM=2he9=9Wjw@mail.gmail.com"
type="cite">
<div dir="ltr"><span
style="font-family:arial,sans-serif;font-size:13px">Hi all,</span>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">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.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">Best
regards,</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">
Jouko</div>
</div>
<br>
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<br>
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