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Hi Varun,<br>
<br>
ideally this needs to be accounted for at the level of target
function calculation, as explained here:<br>
<a class="moz-txt-link-freetext" href="http://journals.iucr.org/d/issues/2013/02/00/dz5268/dz5268.pdf">http://journals.iucr.org/d/issues/2013/02/00/dz5268/dz5268.pdf</a><br>
Intensity statistics in the presence of translational
noncrystallographic symmetry. Read RJ, Adams PD, McCoy AJ. Acta
Cryst. D69, 176-183 (2013).<br>
<br>
In reality, this is not yet implemented for refinement.<br>
<br>
It's not given that the minimum of ML coincides with the minimum of
R-factor, so in general minimization of ML does not guarantee drop
in R-factor, as explained here:<br>
<br>
<a class="moz-txt-link-freetext" href="ftp://ftp.ccp4.ac.uk/ccp4/newsletter/oct_99/08_ml.ps">ftp://ftp.ccp4.ac.uk/ccp4/newsletter/oct_99/08_ml.ps</a><br>
<br>
Also, the goal of ML-based refinement is not to obtain lowest R (as
explained in link above).<br>
<br>
I wonder what happens if after LS refinement you switch back to ML:
do R-factors remain around 27.3/29.8 or they increase?<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 9/29/14 4:38 AM, Varun Bhaskar
wrote:<br>
</div>
<blockquote
cite="mid:CANVxNfpKcQmZ2OZ7NCKZEO=VBTZRGUymx0c7GCB7e-0eO9FkNA@mail.gmail.com"
type="cite">
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<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">Hi,</div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><br>
</div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">I
collected a dataset for a binary complex (72kDa size) to 3.62A
resolution which could be processed in P3<span
style="font-size:9px">2</span>�2 1 space group.� Data
quality analysis with phenix.xtriage showed a presence of
Pseudotranslational symmetry (Non-origin peak in the patterson
with 60% intensity �at 0.33, -0.33, -0.013). I determined the
structure with MR. I have 6 copies in ASU. I tried Zanuda for
SG validation and this looks like the right space group.</div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><br>
</div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">For
refinement when I use Maximum likelihood (ML) as the target
function, my Rfactor/Rfree is around 31.3/32 but when I change
it to Least square (LS) my Rfactor/Rfree drops to 27.3/29.8.
The map quality after ML or LS refinement looks �very similar
for most of the molecule, except for few places where the map
from ML has slightly better features.</div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><br>
</div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">I
read people use LS instead of ML only in the case of twinning
but I am not sure if it could also be used in the case of
PST.� Would the use of LS as the target function for
refinement be right in this case?�</div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><br>
</div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><br>
</div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">Thanks
in advance<br>
</div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><br>
</div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">Best
Regards</div>
<div
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">Varun</div>
</div>
</blockquote>
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