>
> Are there any methods that allow one to input such ions as possible
> candidates? What would be ideal is to have a program that says something
> like "The density peak at x,y,z, has a .0973 chance of being real. It is
> only 2.2 Å from N7 of G12, precluding water. Based on the mother liquor
> ingredient list you provided, there is a 0.75 chance that this is Mg++,
> 0.25 chance it is Na+ (or whatever), based on a
> crystallographically-derived library of 40,000 structural variants of the
> ribosome.
Not quite what you ask for, but WASP does something along those lines.
From the output of the program:
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WASP --- WAter Screening Program
Version 1.0 1995
Copyright (c) Murad Nayal & Enrico Di Cera 1995
This program will take a Protein Data Bank structural file with solvent
electron density peaks designated as water oxygens. Based on simple
structural criteria it will pick out the peaks that could be metal ions
(Na+, Li+, Mg+2, Ca+2). The chosen peaks are subsequently written to 4
pdb-formatted files one for each ion. The temperature factor field is
replaced by the calculated ion-specific valence of that solvent peak.
Reference: Nayal, M., & Di Cera, E. (1996) J. Mol. Biol. 256: 228-234
#########################################################################
#########################################################################
See http://biochem.wustl.edu/~enrico/
Marko
>
> Bill
>
_____________________________________
Marko Hyvönen
Department of Biochemistry
University of Cambridge
http://www-cryst.bioc.cam.ac.uk/~marko
tel: +44-(0)1223-766 044 / 760 468, fax: 766 002
_______________________________________
