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Hi Francis,<br>
<br>
<blockquote cite="mid:29DEE6F2-EE4D-4A28-9D60-23B48A7A9AF9@colorado.edu"
type="cite">
<pre wrap="">Filled and non filled maps? Kicked maps?
Is there documentation on what these are ?
</pre>
</blockquote>
<br>
<big><b>Kick maps:</b></big><br>
<br>
There will be a paper about it in one of the next coming Acta D. This
method was
introduced about 10-15 years ago by Dusan Turk in his program MAIN is
used since that. It is available in PHENIX too. Here is the copy-paste
from the manuscript:<br>
<br>
"(...) An average kick map (AK map) is computed as following (Gunčar et
al., 2000; Turk, 2007; Pražnikar et al., 2009): a large ensemble of
structures (several hundreds) is created where the coordinates of each
structure from the ensemble are all randomly shaken. The shake amount
(rmsd distortion introduced to coordinates) varies from 0 to 1.0 Å.
Then for each structure a map is computed ((mFobs-DFmodel)exp(iαmodel)
or (2mFobs-DFmodel)exp(iαmodel) or any other map, for example a
ligand-omit map). Finally, all maps are averaged out to produce one
averaged kick map. An AK map is expected to have less or no bias, less
noise, enhance existing signal and potentially can clear up some
initially bad densities. (...)"<br>
<br>
<br>
<big><b>Filled maps:</b></big><br>
<br>
By default, phenix.refine
outputs two types of maximum-likelihood weighted maps (or, in other
words, sigmaa-weighted maps): 2mFo-DFc and mFo-DFc.
<br>
<br>
The MTZ file with map coefficients
"_map_coeffs.mtz" contains in fact three maps: 2mFo-DFc and mFo-DFc,
and
"filled" 2mFo-DFc (also, it may contain an anomalous difference map if
F+/- are present). The first two maps are computed using original Fobs
(Fo), and
the last one is computed using "filled Fobs", that is the
original Fobs where missing reflections are "filled" with DFc. It is
well known (I can spell a long list or references) that the data
incompleteness affects the map quality, and sometimes, certain types of
data incompleteness can <span class="moz-txt-star"><span
class="moz-txt-tag"></span>severely<span class="moz-txt-tag"></span></span>
distort maps.
<br>
<br>
A possible solution (in order to reduce this negative effect) is to
"model" missing Fobs somehow. One possibility is just to put in DFc in
place where Fobs is missing, or as suggested by the classics, one can
use <Fobs> taken in a resolution bin around a missing reflection.
I even tried to use the random numbers and it was also better than
doing nothing. Obviously, there is a nearly invisible line between the
benefits of "filling in" missing Fobs and introducing bias. Where this
line goes - is the subject of a research that to my knowledge is not
done yet.
<br>
<br>
Anyway, this is why phenix.refine writes out "regular" and "filled"
maps: one is to give you unbiased but eventually lower quality map, and
the other one is to give you a better-looking map with a risk of being
biased. This way users have more options in exploring their maps.
<br>
<br>
I have to mention that to my knowledge REFMAC always writes "filled"
maps (those with missing Fobs substituted by DFc):
<br>
<br>
- it is mentioned in Maria Turkenburg's thesis:
<br>
<a class="moz-txt-link-freetext"
href="http://www.ysbl.york.ac.uk/%7Emgwt/thesis-tth/chapter2.html#tth_sEc2.6.5">http://www.ysbl.york.ac.uk/~mgwt/thesis-tth/chapter2.html#tth_sEc2.6.5</a>
<br>
<br>
- and in Refmac docs:
<br>
<a class="moz-txt-link-freetext"
href="http://www.ccp4.ac.uk/html/refmac5/keywords/xray-general.html">http://www.ccp4.ac.uk/html/refmac5/keywords/xray-general.html</a>
<br>
<br>
"Missing Data: For those reflections where the FP are missing, mFo is
set equal to dFc. (...)".
<br>
<br>
Pavel.<br>
<br>
<br>
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