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Hi Paul: The map is 4.2 A, and if you download this in coot and display it, you will see what I am talking about. Also if I use your density fit validation, geometry validation, Ramachandran, and so on, it looks pretty reasonable for a 4.2 A structure. At that resolution, alpha helices are tubes of density. The side chain density in many cases (particularly the aromatics) is remarkably decent-looking, and it is less that obvious with an integral membrane protein that the Eisenberg analysis would be definitive. I've never met this guy in my life, but I think this is a genuine case of bad luck. I think that is what is so disturbing about this. Bill Paul Emsley wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > Their tool is available on the web: Verify3D: > http://nihserver.mbi.ucla.edu/Verify_3D/ > > Secondly, really, how *can* you build right-handed helices into > left-handed density with end up with a model that is "frighteningly > plausible-looking"? > > > [BR]> There got to be more to this story? > > I would agree... > > -- PE. > > > On Wed, 2006-12-27 at 12:17 -0500, EATON E LATTMAN wrote: >> Dear All, >> >> It is worth remembering the exemplary manner in which David Eisenberg >> and his group followed up on the flawed structure of >> rubisco that they published. First, David gave a long talk at the >> Diffraction Gordon Conference explaining in detail how the >> error arose, and offering clear suggestions to the community on how to >> avoid similar mistakes. Second, the rubisco structure >> led the group to develop 3-d profiling, sure one of the most powerful >> tools we have for evaluating a structure. >> >> Thus was a error transformed into a powerful methdologcal tool to >> minimize the frequency of errors in the future. > >> > >> > Boaz Shaanan, Ph.D. >> > Associate Professor >> > Dept. of Life Sciences >> > Ben-Gurion University of the Negev >> > Beer-Sheva 84105 >> > Israel >> > Phone: 972-8-647-2220 ; Fax: 646-1710 >> > Skype: boaz.shaananâ >
