<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Hi Morten,<br>
<br>
thanks for feedback.<br>
<br>
This is exactly why the program outputs two maps in one file: the
original one that you supplied to the program and MEM map. When
you open them in Coot they will be calculated and displayed using
the same gridding. Also, the maps are re-scaled such that if you
contour them at the same level the maps will show identical
volumes, which means you don't need to play with sigma levels for
both maps to make them comparable.<br>
<br>
Pavel<br>
<br>
On 2/22/13 2:18 AM, Morten Groftehauge wrote:<br>
</div>
<blockquote
cite="mid:CAEAG6YTO-Ezucvt0Ojon+K=d3Xt2VhDG--7Kns8_2=5ZMc_HKQ@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Pavel,
<div><br>
</div>
<div style="">The maximum entropy maps look wonderful and it
looks like they might be useful in the doubtful cases. It is
however hard to compare them to the standard 2Fo-Fc when the
grid sampling isn't the same.</div>
<div style=""><br>
</div>
<div style="">Cheers,</div>
<div style="">Morten</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 14 February 2013 19:46, Nathaniel
Echols <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On Thu, Feb 14, 2013 at 7:50 AM, Pavel
Afonine <<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>>
wrote:<br>
> The algorithm implemented in Phenix is fast: it
should take from a few<br>
> seconds for small structures to a few minutes for
large ones. I do not<br>
> understand why it should take long time to run (as
pointed out in that Acta<br>
> D paper).<br>
<br>
</div>
I suspect that's because they're running a much different
algorithm.<br>
The Phenix implementation doesn't reproduce the difference
densities<br>
they display, for what it's worth, but since neither the
code or even<br>
the binaries for the ENIGMA program are available (!), it's
hard to<br>
know exactly what they're doing differently.<br>
<div class="im"><br>
>> I see that phenix.maximum_entropy_map is now a
command in Phenix.<br>
>> Some quick questions: Where is this likely to be
must useful and does it<br>
>> take ridiculously long to run? From the Nishibori
2008 paper in Acta D it<br>
>> seems like this would mainly be useful for very
high resolution structures<br>
>> that you would normally call complete - and that
it would take a very long<br>
>> time to compute.<br>
<br>
</div>
I must say, I find that paper very misleading - the
conventional maps<br>
from Phenix are sufficient to identify the alternate
conformation of<br>
Tyr33 in Figure 2, for instance. The published structure
doesn't have<br>
*any* alternate conformations, which at 1.3Å resolution is
absurd, so<br>
it's very easy to produce an improved model without doing
anything<br>
fancy. In Figure 5 they compare a conventional omit map
with the MEM<br>
version, but they're using much different grid spacings, so
of course<br>
they look different!<br>
<br>
Maximum entropy tends to be used most frequently by
small-molecule<br>
crystallographers looking at charge densities, which is
partly what<br>
the Nishibori paper is doing. For proteins, this is what
Nicholas<br>
Glykos (author of GraphEnt) told me about its use:<br>
<br>
"For well behaved and complete data the maps look very
similar. But in<br>
other cases the ability of the maxent map to alleviate the
problems<br>
arising from series termination errors made a difference. We
had one case<br>
of [redacted] that diffracted to ~0.8A. Four passes were
made to measure<br>
both high and low resolution data. Unfortunately, for one of
the passes the<br>
time-per-frame was completely wrong and we ended-up with a
data set missing<br>
all terms between ~4 and ~3 Angstrom. The conventional FFT
had numerous<br>
peaks arising from the series termination errors, the maxent
map was<br>
significantly better. In other cases, we use maxent to
artificially sharpen<br>
maps (by reducing the esd's) while avoiding the noise
introduced by normal<br>
(E-value-based) sharpening."<br>
<br>
-Nat<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a moz-do-not-send="true"
href="http://phenix-online.org/mailman/listinfo/phenixbb"
target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
Morten K Grøftehauge, PhD
<div>Pohl Group</div>
<div>Durham University</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</body>
</html>