[ccp4bb]

[Roger Rowlett]

For finding multiple copies of protein assemblies in the ASU, Phaser or OpenEPMR are the best choices based on our experience. If your Matthews probability prediction is correct (it definitely not foolproof) then I would try searching for two trimers per ASU. Phaser or OpenEPMR should be able to handle that. Alternatively, you could try to place 6 monomers, but this number of protein assemblies is usually extremely challenging for either program. You will have to search all alternative space groups of P622 [e.g., P6(1)22, etc.] and see which one generates appropriate packing and sensible electron density maps. Both Phaser and OpenEPMR will search all alternative space groups in one go if you set the option. We just solved an MR structure recently where three dimers gave the perfect Matthews number, but alas, there was no way to fit three dimers in the ASU with the proper symmetry. Two or four dimers were wayyyyy out on the fringe of the Matthews probability, but it turns out that the ASU actually has only two dimers (a biological unit tetramer), and the solvent content of the crystal is a whopping 67%. So you might have to consider alternative packings. Phaser will usually complain about clashes or lack of unit cell volume if you try to stuff too much into the ASU. Do be pretty liberal with allowed clashes in Phaser or you won't get any solutions. We usually allow 30 or more clashes for initial searches, as required, to allow for solutions to be revealed. This is especially important if your search models are significantly different from your protein. In worst cases, you might want to trim your search model back from the N- or C-terminus to a more compact domain to avoid clashes that are present in the search model but not your target protein. Cheers, Roger Rowlett Vandana Kukshal wrote: hello sir , recently i have collected one data of 3.0 A of a protein having no sequence homology with any known PDB . but while fold prediction i got 100 %  identical fold with some of the protein . space group of my protein is P622 and showing 6 molecule in a assymetric unit. the homologous fold proteins are trimer protein. can i run MR in this case . how i should proceed. i m trying for MIR also . regards vandana -- 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: rrowl...@mail.colgate.edu