-Just to make a note, there has actually been some discussion in the
published literature recently (ok maybe past ten years) about what
terms; simply steric (as originally) or hydrogen bonding etc
might be needed to explain observed backbone angular values.
Tommi
On Sep 26, 2011, at 5:44 PM, Dirk Kostrewa wrote:
Dear Nat,
yes, I fully agree - all these restraints that improve the geometry
either by restraining to high-resolution structures or by
introducing H-bond restraints for secondary structures are very
useful for low-resolution structures!
I see your argument with the Ramachandran plot. But imagine a set of
very strong non-bonding/bonding restraints that would result in an
absolutely clean Ramachandran plot for any structure, then the
Ramachandran plot would become useless even in the absence of any
phi/psi-restraints. So, I prefer to err a bit on the safe side here
by saying "not a truly independent measure".
Personally, I think, that ALL refinement programs, including the
real-space refinement in Coot, would benefit from inclusion of
proper H-bonding terms (something, that for instance the very old X-
Plor version did), since this would automatically restrain secondary
structures and other hydrophilic interactions to some reasonable
geometry, even at very low resolution.
Best regards,
Dirk.
Am 26.09.11 16:17, schrieb Nat Echols:
On Mon, Sep 26, 2011 at 1:53 AM, Dirk Kostrewa <[email protected]
> wrote:
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.
It depends on how strictly you assess the "independence" of
validation criteria. The Ramachandran plot is considered valid in
most cases because refinement programs traditionally do not
restrain phi and psi angles, so we need to rely on the accuracy of
the data (and our placement of atoms) and various complementary
geometry restraints (especially nonbonded) to keep residues in the
favorable regions of the plot. There are a variety of ways to make
the plot better by modification of the model and/or restraints
(adding hydrogens, increasing the weight on the nonbonded
restraints, secondary structure restraints, etc.), none of which
are as drastic as directly restraining the model to the plot. I
don't really view this as biasing the plot, for two reasons: a) the
quantity being measured is independent of the quantity restrained,
and b) at least in my hands, these modifications never completely
fix the problem of Ramachandran outliers. (It's the loop regions
that are really awful.)
Anyway, I don't think anyone should feel bad about using this kind
of restraint at low resolution. The caveat is that of all the
specialized restraints that we (Jeff Headd and I) have been testing
for low-resolution refinement (in Phenix), nothing works nearly as
well in preserving good geometry, and usually improving the R-
factors, as restraining model parameters to a related high-
resolution structure, when one is available. Fortunately, every
modern refinement program has this ability in some form, and I
expect that this is going to have the most impact in improving the
overall quality of low-resolution structures.
-Nat
--
*******************************************************
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
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D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [email protected]
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*******************************************************
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
[email protected]
