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
