Something else you need to be aware of when using WASP, even if the symmetry
contact problem isn't an issue, e.g. as a work-around for that you could
generate a PDB file containing a complete unit cell with a small border of say
3.5 Ang around it - I've no idea if the server does that for you.
The second problem is that WASP does not by default take account of nitrogen
ligands, only oxygens: this is controlled by the following statements in the
code:
C60 write (6, *) 'Select ligands in the coordination shell'
C write (6, *) '1- O'
C write (6, *) '2- N'
C write (6, *) '3- O and N'
C read (5, '(A)') response
C o_lig = .false.
C n_lig = .false.
C if (response.eq.'1') then
C o_lig = .true.
C elseif (response.eq.'2') then
C n_lig = .true.
C elseif (response.eq.'3') then
C o_lig = .true.
C n_lig = .true.
C else
C write(6,*) 'choice ', response, ' was unrecognized.'
C goto 60
C endif
C The only ligating atoms are oxygens.
o_lig = .true.
n_lig = .false.
i.e. activate the commented-out statements and delete the last 3 statements
above. AFAIK this change has not been made in the code on the server. I did
an analysis of Na+ ligands in the CSD and although it's true that around 2/3
are O atoms, I was surprised to find that most of the remaining 1/3 are N
atoms. WASP essentially identifies ions by working out the distance-weighted
co-ordination number, so clearly if the apparent co-ordination number is
reduced either by omitting symmetry contacts or omitting potential ligands then
it's not going to make the correct identification!
-- Ian
> -----Original Message-----
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle
> Sent: 21 August 2007 17:25
> To: Jacob Keller
> Cc: [email protected]
> Subject: RE: [ccp4bb] Wasp web server
>
> 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: [EMAIL PROTECTED]
> > [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller
> > Sent: 21 August 2007 16:55
> > To: [email protected]
> > 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
> > [EMAIL PROTECTED]
> > ***********************************
> >
> >
> >
>
>
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