Be aware that WASP does not take into account symmetry-related atoms when analysing the co-ordination sphere of a potential ion; this becomes clear when you look at the source code (http://biochem.wustl.edu/~enrico/wasp.htm) & see that it only reads the ATOM & HETATM records from the PDB file, and it never asks you for cell & space group info (see http://biochem.wustl.edu/~enrico/README.htm - scroll down to the end). In my view this is a serious deficiency considering that most ions (at least the ones that are likely to be confused with water molecules) reside on the surface of a protein where at least some of the contacts are likely to be to symmetry-related atoms.
Caveat emptor!
-- Ian
> -----Original Message-----
> From: [log in to unmask]
> [mailto:[log in to unmask]] On Behalf Of Jacob Keller
> Sent: 21 August 2007 16:55
> To: [log in to unmask]
> Subject: Re: [ccp4bb] Wasp web server
>
> There is a nice web server which does wasp et al:
>
> http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl
> JPK
>
>
> ==============Original message text===============
> On Tue, 21 Aug 2007 10:48:00 am CDT Marko Hyvonen wrote:
>
> >
> > 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:
>
> ##############################################################
> ###########
> ##############################################################
> ###########
>
>
> 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
> _______________________________________
> ===========End of original message text===========
>
>
>
> ***********************************
> Jacob Keller
> Northwestern University
> 6541 N. Francisco #3
> Chicago IL 60645
> (847)467-4049
> [log in to unmask]
> ***********************************
>
>
>
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