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Hi Maia,<br>
<br>
<blockquote cite="mid:DDBF4DCE1DB5497A8B82D0484D466FD8@LEO" type="cite">
<div><font face="Arial" size="2">Now that Randy sent you a reference
about the effect of very weak reflections will you include the changes
in the refiment procedure? <br>
</font></div>
</blockquote>
<br>
My question was rather to satisfy my curiosity and not to convince me
that removing of data is harmless (thanks Randy for pointing out that
paper!). It is pretty obvious that removing any data is bad. It is in
my to-do list to add intensity based ML target, but the users should do
the right job from the start as well, by not setting negative
intensities to zero amplitudes when at refinement stage you can't do
anything good with those.<br>
<br>
<blockquote cite="mid:DDBF4DCE1DB5497A8B82D0484D466FD8@LEO" type="cite">
<div><font face="Arial" size="2">I am wondering about that because I
get different maps from the phenix refinement and from the refmac
refinement. </font></div>
</blockquote>
<br>
I guess you need to make sure which maps you are looking at, taht is
make sure you compare apples with apples and not with oranges.
phenix.refine outputs various maps, namely with and w/o filling missing
Fobs, it rejects Fobs outliers (according to Randy's paper as
implemented by Peter Zwart), it may or may not include test reflections
into map calculations, and does a whole lot of other things that are
different from any other refinement program. <br>
If you have a specific problem case that I can reproduce, I would
appreciate if you send it to me, so I do analyze it, and improve
software if turns out to be necessary.<br>
<br>
<blockquote cite="mid:DDBF4DCE1DB5497A8B82D0484D466FD8@LEO" type="cite">
<div><font face="Arial" size="2">In one case I see the isoalloxazine
ring of the FAD cofactor flat, in the other case this ring is bent. The
same story with the densities for ligands. Is it about geometry
restraints or effects of exclusion of very weak reflections?</font></div>
</blockquote>
<br>
Compare regular and missing-Fobs-filled maps for these regions
(phenix.refine outputs both): are they different? <br>
<br>
Pavel.<br>
<br>
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