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Hi Mohamed,<br>
<br>
MEM = maximum entropy method. This was a quick attempt to implement
MEM-based map modification, as described here (admittedly quite
sketchy):<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/presentations/mem.pdf">http://phenix-online.org/presentations/mem.pdf</a><br>
All in all, this works great with very high resolution data (better
than 1A), compare usual 2mFo-DFc (blue) vs MEM (red) maps (this is a
0.6A resolution data set):<br>
<a class="moz-txt-link-freetext" href="https://www.dropbox.com/sh/0js402ab87779e0/AAAOpEMN5iDa2Z5qniKpatARa?dl=0">https://www.dropbox.com/sh/0js402ab87779e0/AAAOpEMN5iDa2Z5qniKpatARa?dl=0</a><br>
To make it work similarly well at lower resolutions more work is
required; so in this sense this is an unfinished project.<br>
<br>
FEM = Feature Enhanced Map:<br>
<br>
Acta Cryst. (2015). D71, 646-666.<br>
FEM: feature-enhanced map<br>
P. V. Afonine, N. W. Moriarty, M. Mustyakimov, O. V. Sobolev, T. C.
Terwilliger, D. Turk, A. Urzhumtsev and P. D. Adams<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/presentations/fem_06MAY2014.pdf">http://phenix-online.org/presentations/fem_06MAY2014.pdf</a><br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 3/31/15 5:19 PM, mohamed noor wrote:<br>
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<div>Dear developers<br>
<br>
</div>
What is the difference between MEM and FEM maps? I read
the documentation and my understanding is both are
supposed to create beautiful maps :)<br>
<br>
</div>
My problem is I have a structure at 1.9 A (a different
protein than the one referred to in my previous question),
the Rfactor is around 20/22 %, Rms bonds is 0.03 and Rms
angles is 1.845. If the bonds/angles get lower, the Rfactor
jumps up (same problem as the other structure).<br>
<br>
</div>
Looking in Coot, there are positive and negative density and
missing density for the side chains of residues with high B
factor. For some reason, phenix.refine keeps on adding water
at strange places even at regions that I suspect to be just
noise. For this reason, I want to see if the noise is really
noise. A second reason is I have density that seem to be too
big for a water molecule but waters were placed anyway, so I
want to know if these are real positive density.<br>
<br>
</div>
<div>The dataset was obtained from only 50 degrees, SG is P 61 2
2. Including more images brought up the Rmerge to 30-40% and
Rfactor being stuck at 30 %. For some reason, I don't find the
X-ray statistics from the phenix.model_vs_data logfile but in
essence, I have:<br>
<br>
28-1.9: 82 %<br>
</div>
<div>6 A - infinity: 95 %<br>
</div>
<div>in the shells (2.25-2.14, 2.14-2.04, 2.04-1.97, 1.97-1.9)
my completeness is around 85-62 % and CCwork is at least 70 %
and CC1/2 of the dataset is 60 % at the highest resolution
shell.<br>
<br>
</div>
<div>Thanks.<br>
</div>
</div>
<br>
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