X-PLOR vs Hydrogens
puius at aecom.yu.edu
Tue Feb 4 12:28:44 EST 1997
Thomas J. Stout wrote:
> The reason I am concerned is that the B-factors assigned
> to the protons appear to be the 'refined overall B-factor'
> from the beginning of the job, which isn't particularly
> appropriate. Shouldn't the assigned value more closely
> approximate a 'riding model' under the assumption that
> the B-factor of a particular proton will be pretty closely
> related to the B-factor of the heavier atom to which it
> is attached?
While that would make sense, there's really no way to judge the
B-factor of a hydrogen, so X-PLOR will refine them with the
"group" B-factor at the beginning and then leave them alone.
B-factors estimate how the atom in question is "smeared" over
space. Since protein crystallographers almost *never* see
hydrogens, they never estimate the B-factors for them. I suspect
the hydrogens won't affect the R-factor anyway. (Anyway, lots of
hydrogens -- on the ends of lysines, or methyl groups -- are
The new X-PLOR allows you to run "generate.inp" without
building hydrogens. It makes refinements run a bit faster.
If you are doing an NMR structure, or anything other than
protein X-ray crystallography above 1.5 A resolution, everything
I say is null and void and does not apply <grin>, and you might
want to ask the question again specifying exactly what sort of
structure you're doing.
By the way, you could have X-PLOR assign the B-factor from
the amide nitrogen to the amide hydrogen at various points in
the refinement (create your own 'riding model').
COntact me if you want help writing the
Yoram A. Puius Albert Einstein College of Medicine
mailto:puius at aecom.yu.edu Department of Biochemistry
5th year M.D.-Ph.D. 1300 Morris Park Avenue, Bronx, NY 10461
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