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Thomas Stout wrote:
It seems to me that the best solution here would be to model what is
actually going on: disorder. For the example of a lysine where there is
limited or poor electron density beyond the C-beta, the best
representation of the physical model would be an ensemble of all
possible rotamers of what is physically present in the crystal. Having
"N" sidechains (alternate conformers) with occupancies of 1/N would be
extremely clear to all users (novice and expert alike) as well as most
if not all software.
I agree that it does represent what is (likely) going on when density is
missing. However, this multiple conformer representation will in fact
introduce a large blob of extremely low electron density. Again, the
issue is bulk solvent model, which will ignore occupancies. The
technical problem with this approach will be of course how to assign
B-factors. You can't refine them individually (there is no density and
therefore no density falloff). Also, such an algorithm should exclude
clashing conformers.
Even if it would model featureless density in the vicinity of a "missing
lysine" correctly (and I guess it can be done by tweaking bulk solvent
correction), it sounds too elaborate for the purpose of sending a
message to the potential non-crystallographer end-user. The information
about disorder is already there in form of high B-factor. It is just
one number the meaning of which needs to be conveyed, I suspect more
elaborate models will be more difficult to explain.
Ed.
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
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When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /
