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 <[email protected]> Date: Friday, December 18, 2009 11:20 Subject: [ccp4bb] mystery-blob-itis To: [email protected] > 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: [email protected] > 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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