I actually chose 3dko because it is a kinase (with a ligand), and therefore an interesting candidate for a molecular replacement "score". I have not set this up yet, but I think if you look for PDB entries that contain the word "kinase" and try to molecular-replace all of them into the 3dko dataset, what fraction of them will "work"? I think that fraction would make a good "score" for a given molecular replacement pipeline.
But, if you want to bootstrap S-SAD phasing with a homolog, then I'd say its definitely "cheating" if you use a homolog close enough to build your way out of the resulting density without any anomalous information at all. Perhaps the "fairest" way to do this would be to make a 2-dimensional score? The "frac" of the dataset you used, plus the BLAST2 E-value of the model you started with vs the 3dko sequence? -James Holton MAD Scientist On Mon, Jan 14, 2013 at 2:31 PM, Nat Echols <nathaniel.ech...@gmail.com> wrote: > On Mon, Jan 14, 2013 at 11:18 AM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> > wrote: >> I admit not having read all contributions to this thread. I understand >> the "John Henry Challenge" as whether there is an 'automated way of >> producing a model from impossible.mtz'. From looking at it and without >> having gone all the way to a PDB-file my feeling is one could without >> too much effort from the baton mode in e.g. coot. > > This should be even more possible if one also uses existing knowledge > about the expected structure of the protein: a kinase domain is quite > distinctive. So, James, how much external information from homologous > structures are we allowed to use? Running Phaser would certainly be > cheating, but if I take (for instance) a 25% identical kinase > structure, manually align it to the map and/or a partial model, and > use that as a guide to manually rebuild the target model, does that > meet the terms of the challenge? > > -Nat
