Thank you very much for your suggestions. The truth is that I am
following more or less the usual pathways for ligand identification as
you Boaz suggested but I was just wondering if there was something to
identify ligands in a bit less intuitive/classical manner (some sort
of pattern recognition, etc...).
Well, I will continue with the trial/error stuff... you cannot
escape ... :-).
Cheers
Isabel
Le 18 déc. 09 à 12:03, Boaz Shaanan a écrit :
> Hi Isabel,
>
> I don't have a direct answer about ways to find potential ligands
> (by the way, Arp/wArp and coot have a tool for that, and probably
> phenix too, which you may have already tried) beyond what you've
> already tried. But what has worked for me many times is to start by
> putting waters into those blobs and refine them. If these blobs hide
> some ligands, or components of crystallization buffer, these waters
> will cluster and give you better hints, in most cases. On different
> occasions I located this way peg molecules (waters arranged in a
> circle), Mg+2 with the coordination sheel, phosphates, sulfates
> which weren't obvious to begin with. I think it's worth trying.
>
> Cheers,
>
> Boaz
>
>
>
> ----- Original Message -----
> From: Isabel Garcia-Saez <[log in to unmask]>
> Date: Friday, December 18, 2009 11:20
> Subject: [ccp4bb] mystery-blob-itis
> To: [log in to unmask]
>
> > Dear all,
> > Curiously, I think I am just suffering an acute attack of
> > mystery-
> > blob-itis as well. I try to finish up the refinement of two
> > structures
> > and I am puzzled about a few blobs I found (from waters than
> > could be
> > ions to density that could be PEG). I have been digging out
> > ligands
> > from PDBSum, HICup, try to find ions with WASP, etc, but does
> > anyone
> > know a better way to identified misterious blobs densities (sort
> > of
> > database of ligand densities, pattern recognition...)?.
> >
> > Thanks a lot,
> >
> > Isabel
> >
> >
> >
> >
> >
> > Isabel Garcia-Saez PhD
> > Institut de Biologie Structurale Jean-Pierre Ebel
> > Laboratoire des Protéines du Cytosquelette
> > 41, rue Jules Horowitz
> > F-38027 Grenoble CEDEX 1
> > France
> > tel.: 00-33-438 789615
> > FAX: 00-33-438 785494
> > e-mail: [log in to unmask]
> > http://www.ibs.fr
> >
> >
> >
> >
> >
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
> Phone: 972-8-647-2220 ; Fax: 646-1710
> Skype: boaz.shaanan
>
>
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