In this lab there are as many takes on this as there are
crystallographers I think! It seems to depend on personality - are you a
wild optimist who traces connectivity at 0.5 Sigma - or a cautious soul
who hates to be wrong..
It seems to me that there are often disordered regions we can never
model and they should simply be omitted with a comment.
There are loops where you can build a reasonable model, although the B
factors will go sky-high, and really we need to get better tools to
communicate with "the greater scientific community who have no way to
judge this. They do not know what a b-factor is or where to look for an
occupancy."
Our crystallographic models are less useful if they dont..
And another proglem - what do people do about LYS and other wobblt side
chains which fade out into the solvent!
Eleanor
SIPPEL,KATHERINE H wrote:
Dear Crystallographic Community,
Dr. Holton made a comment today that got me thinking on the issue of
modeling. This has been a hotly debated topic in our own lab but I would
like to hear the current opinions of the community as a whole. It is a
question of two parts.
First, what do you think about modeling into regions of poor density? Do
you (A) model something in as best you can while conforming to ideal
geometry/chemistry with full disclosure about b-factors in the region,
(B) reduce the occupancies of the poorly modeled loops/side chains, or
(C) truncate your model, removing loops and side chains from the model
at the cost of statistical numbers? From a crystallographers point of
view we can assess the quality of the model and make informed decisions
as to what conclusions to draw, however most of the greater scientific
community has no way to judge this. They do not know what a b-factor is
or where to look for an occupancy. Are we doing a disservice to science
by emphasizing the minimization of Rwork and Rfree over full disclosure
of what we can legitimately see?
Secondly, on a similar vein, what is the community's opinion on modeling
hydrogens? I have read a lot on the subject and can see both sides of
the argument. From a crystallographer's point of view these are very
helpful in maintaining geometry and ensuring the model makes chemical
sense. I can also see the necessity of submitting them to the pdb so
that the statistics can be recreated. On the other hand most biologist
has no comprehension of the concept of riding hydrogens. They assume
that if the hydrogen is in the pdb, that the crystallographer saw it and
use that information to develop experiments.
I realize that I may be kicking a hornet nest here but I would genuinely
like to know what people think.
Thanks,
Katherine Sippel
SIPPEL,KATHERINE H
Ph. D. candidate
Department of Biochemistry and Molecular Biology
College of Medicine
University of Florida
