Dear Nat and other interested colleagues,
when I played with H-bond restraints for secondary structures for the
refinement of a 4.3 A structure (only a few weeks before they were
introduced in phenix), I've made the following observation: at low
resolution without H-bond restraints for secondary structures, the
carbonyl groups of these secondary structures take the liberty within
their globbish electron densities to deviate from their ideal H-bond
conformation, resulting in a tight "belt" of outliers around the
preferred Ramachandran regions, with typical deviations of only a few
degrees. Introducing the additional H-bond restraints for maintaining
secondary structures pulls these outlier carbonyl groups back into the
preferred Ramachandran regions. In my case, the number of Ramachandran
outliers was reduced to less than one half! Although, these H-bond
restraints do not directly include information about allowed
Ramachandran regions, the Ramachandran plot is actually affected by
these restraints. Thus, at least in my opinion, the Ramachandran plot is
then not a truly independent measure for model quality, anymore. The
same holds true for all geometrical restraints, of course.
Best regards,
Dirk.
Am 22.09.11 22:49, schrieb Nat Echols:
On Thu, Sep 22, 2011 at 4:18 PM, Pete Meyer <pame...@mcw.edu
<mailto:pame...@mcw.edu>> wrote:
In short, the effective observation to parameter ratio improves by
~4%. This seems like a relatively small improvement, especially
if the trade-off is that Ramachandran statistics can't be used for
validation anymore. It also seems like the improvement would
decrease with larger proteins (the number of additional parameters
from adding a residues increase faster than the number of
secondary structure restraints that residue could provide).
There is nothing preventing you from using Ramachandran statistics for
validation if the secondary structure restraints only restrain the
distances between hydrogen-bonded atoms. (This is what the
implementation of S.S. restraints in phenix.refine does.) This
actually contributes significantly fewer than two extra restraints per
residue on average. And it doesn't actually have much of an effect on
Ramachandran statistics; the number of outliers is slightly reduced,
as is the clashscore. I suspect (although I haven't examined this in
detail) that this is mostly keeping the ends of helices and sheets
from unraveling, which is what they're most useful for. (The change
in R-factors is negligible in our tests, although they sometimes
reduce overfitting a little bit.)
This is an entirely different issue from Ramachandran (i.e. phi/psi)
restraints, which should only be used as a last resort at low
resolution at the end of refinement, and after fixing all outliers
manually in Coot. (Restraining to a high-resolution model, if one is
available, is a much better option.)
-Nat
--
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW: www.genzentrum.lmu.de
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