On 3/10/23 4:05 AM, Julia Griese wrote:
Hi all,
My impression has been that the most common approach these days is to
“let the B-factors take care of it”, but I might be wrong. Maybe it’s
time to run another poll?
Personally, I call any other approach R-factor cosmetics. The goal in
model building is not to achieve the lowest possible R-factors, it’s to
build the most physically meaningful, most likely to be correct, model.
And I could call your approach "model cosmetics".
If you can't see the side-chain, you don't know where it is and you
probably don't even know where the centroid of the distribution is.
Only in the case of very short side-chains with few rotamers can you
make a reasonable volume approximation to where the side-chain is and
"let the B-factors" smear out the density to cover a range of the
projected conformations.
For longer side-chains, if you put it in a single conformation, you are
very likely NOT coming close to correctly modeling the actual
distribution of the conformations. So let's circle back on "most likely
to be correct model" and ask what we *actually* know about where the
atoms are.
Put your disordered Arg in with 10 alternate conformations, each with a
refined relative occupancy, and then let the B-factors smear that lot
out, and that's your better model.
Phil Jeffrey
Princeton
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