The December issue of Structure, due out next week, contains a
Ways & Means article concerning Ramachandran plots, describing
(among other things) a tighter definition of "core" areas based
on an analysis of high-resolution crystal structures.
A WWW page with supplementary material is available at URL:
This page includes list of outlier percentages for ~3,000
PDB entries sorted by different criteria, as well as some
Fortran source code for programmers who want to include
the new core definition into their own programs. The new
definition has already been implemented in the relevant
Uppsala software (O, OOPS, LSQMAN, MOLEMAN2). For example,
in O there is a Ramachandran command in the Graph menu
which will produce a Ramachandran plot which is pickable
(i.e., you can click on an outlier, and O will centre
on that residue).
In addition, Tom Taylor has set up a WWW server to produce
these Ramachandran plots for any PDB entry, or for your own
model(s). The URL is:
Tom would appreciate feedback regarding the time it takes
in various parts of the world to use this service (his
E-mail address is: tom at xray.bmc.uu.se).
--Gerard Kleywegt & Alwyn Jones