[phenixbb] Maximum Entropy Maps

Pavel Afonine pafonine at lbl.gov
Fri Feb 22 07:49:36 PST 2013

Hi Morten,

thanks for feedback.

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.


On 2/22/13 2:18 AM, Morten Groftehauge wrote:
> Hi Pavel,
> 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.
> Cheers,
> Morten
> On 14 February 2013 19:46, Nathaniel Echols <nechols at lbl.gov 
> <mailto:nechols at lbl.gov>> wrote:
>     On Thu, Feb 14, 2013 at 7:50 AM, Pavel Afonine <pafonine at lbl.gov
>     <mailto:pafonine at lbl.gov>> wrote:
>     > The algorithm implemented in Phenix is fast: it should take from
>     a few
>     > seconds for small structures to a few minutes for large ones. I
>     do not
>     > understand why it should take long time to run (as pointed out
>     in that Acta
>     > D paper).
>     I suspect that's because they're running a much different algorithm.
>     The Phenix implementation doesn't reproduce the difference densities
>     they display, for what it's worth, but since neither the code or even
>     the binaries for the ENIGMA program are available (!), it's hard to
>     know exactly what they're doing differently.
>     >> I see that phenix.maximum_entropy_map is now a command in Phenix.
>     >> Some quick questions: Where is this likely to be must useful
>     and does it
>     >> take ridiculously long to run? From the Nishibori 2008 paper in
>     Acta D it
>     >> seems like this would mainly be useful for very high resolution
>     structures
>     >> that you would normally call complete - and that it would take
>     a very long
>     >> time to compute.
>     I must say, I find that paper very misleading - the conventional maps
>     from Phenix are sufficient to identify the alternate conformation of
>     Tyr33 in Figure 2, for instance.  The published structure doesn't have
>     *any* alternate conformations, which at 1.3Å resolution is absurd, so
>     it's very easy to produce an improved model without doing anything
>     fancy.  In Figure 5 they compare a conventional omit map with the MEM
>     version, but they're using much different grid spacings, so of course
>     they look different!
>     Maximum entropy tends to be used most frequently by small-molecule
>     crystallographers looking at charge densities, which is partly what
>     the Nishibori paper is doing.  For proteins, this is what Nicholas
>     Glykos (author of GraphEnt) told me about its use:
>     "For well behaved and complete data the maps look very similar. But in
>     other cases the ability of the maxent map to alleviate the problems
>     arising from series termination errors made a difference. We had
>     one case
>     of [redacted] that diffracted to ~0.8A. Four passes were made to
>     measure
>     both high and low resolution data. Unfortunately, for one of the
>     passes the
>     time-per-frame was completely wrong and we ended-up with a data
>     set missing
>     all terms between ~4 and ~3 Angstrom. The conventional FFT had
>     numerous
>     peaks arising from the series termination errors, the maxent map was
>     significantly better. In other cases, we use maxent to
>     artificially sharpen
>     maps (by reducing the esd's) while avoiding the noise introduced
>     by normal
>     (E-value-based) sharpening."
>     -Nat
>     _______________________________________________
>     phenixbb mailing list
>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>     http://phenix-online.org/mailman/listinfo/phenixbb
> -- 
> Morten K Grøftehauge, PhD
> Pohl Group
> Durham University
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> phenixbb at phenix-online.org
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