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Hi Roger, personally, I would take the four dimers from Phaser, strip off all side chains (make a poly-ala/gly), do a ML refinement with tight NCS restraints. The resulting map could then be on-the-fly real-space-averaged with Coot. At your resolution, I would expect to see the real register of at least some side chains either in the 2mfodfc-map or in one of the real-space-averaged 2mfodfc-maps. Good luck, Dirk. Am 01.09.10 17:12, schrieb Roger Rowlett: > I am trying to find a MR solution for a large unit cell (R3:H, > 158x158x196) with a relatively poor, but I think workable search model > (30% identity, 50% similarity). The data set is decent to 2.4 A. I > might be able to get better if necessary. I submitted the sequence of > the target to the Phyre server, and it returned a PDB file derived > from what I had already identified as the most likely successful > search model. Phaser finds a reasonable solution with four dimers > (Z=9-15 depending on the data set) for which the unit cell packing > looks good. Phaser even assembles what looks like "correct" biological > tetramers in the ASU and across the symmetry interfaces. The main > chain appears to be mostly traceable, but the side chains are not all > well-resolved, and I suspect from the better-defined regions, that the > chain is misregistered by a residue or two throughout most of the > structure. > > Assuming that an MR solution is possible, what is a good approach from > here? FWIW, Phaser does not correctly place a poly-Ala/Gly model, > although it may place three chains similarly to the MR solution I have > with the Phyre model. My first thought is to: > > 1. Chainsaw the currrent solution, and attempt to identify and build > in the correct register of the side chains. after refinement. > 2. Do a low resolution refinement of the poly-Ala/Gly model to better > thread the main chain? > 3. Try EPMR with the Phyre model or the poly-Ala/Gly model > 4. Give up and get real phases (but I'm so close now!?) > > Thanks in advance. > > -- > Roger S. Rowlett > Professor > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 > fax: (315)-228-7935 > email: [log in to unmask] <mailto:[log in to unmask]> -- ******************************************************* Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: [log in to unmask] WWW: www.genzentrum.lmu.de *******************************************************