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On Jan 10, 2007, at 11:01 AM, Marc SCHILTZ wrote:
So the criterion of atoms that should be modelled because they "are
in the crystal" has now been narrowed down to atoms that should be
modelled because they are "covalently connected to the rest of the
protein".
If this concept is taken further, one could ask why we are not
explicitly refining hydrogen atoms ? Clearly, they are quite often
important for the biological function of a macromolecule. Clearly,
they are in the crystal, covalently connected to the rest of the
protein and we also have a pretty good idea about where they are.
But we are not refining hydrogen atoms because the experimental
data does not warrant this ! (unless we got very high-resolution
data). Shouldn't the same criterion apply for the refinement of
disordered non-hydrogen atoms ?
Actually, hydrogens are usually taken into account, not explicitly,
but as riding hydrogens.
If we always had ultra-high resolution data, we could model and
refine many of the hydrogen atoms. But if the resolution of the
data is limited, we don't do that, event though we know that these
atoms are there. Similarly, if we had ultra-high resolution data,
we could possibly model and refine many of the disordered side-
chains because the low-occupancy alternate positions would probably
show up in the maps. But not so if the resolution of the data is
limited.
The low-occupancy conformations also often show up at lower
resolution, just contour at, say, 0.3 sigma.
Anyway, I'd be perfectly willing to look at any proposed criteria
that define when to omit an atom and when not. That should be an even
more interesting discussion ;)
Best - MM
------------------------------------------------------------------------
--------
Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353
