Dear modeller users,
I have a question concerning the phi/psi distribution in the alpha
region. The homology models which I generate seem to have a curious
phi/psi distribution within the allowed alpha region. Almost all the
residues within procheck's red region are sharply clustered into two
peaks (one at the classical alpha helical angles of
around -60, -40) and the other at the gamma region ( -90, 0). I often
get a couple of minor lateral peaks as well. This is very different
from crystal structures (including my template), where there is a more
homogenous spread within the allowed region, although obviously showing
a greater density of points towards -60, -40. I wonder why this happens
and if I am doing something obviously stupid. It would seem that the
sigmas on binormal restrainsts for phi/psis are very small. Can I
easily adjust these values and what is the easiest way?
This question is related to a similar one concerning proline phis
angles which I note have a tendancy to drift away from -65. I have in
the past used special restraints on all prolines in order to reduce
sigma(phi) for which the default value seems to be rather generous.
I would be most grateful for any comments/suggestions/help.
Thanks,
Richard Garratt
University of Sao Paulo