Hi Raya, My reply comes late but maybe it is still relevant to you. I have a few suggestions for molecular replacement in phaser:
* Input both protein models in your search (define both known structures as ensembles and search for both) * Give higher values (let's say 1.0, 1.2, 1.4) for the "rms difference" in "Similarity of PDB" * Allow a number of clashes as packing tolerance (check your log files how many clashes the "top solutions" have) * Run phaser with "all choices of alternative space group" (as mentioned before) Good luck, christian Raja Dey wrote: > Hello, > I am trying to solve a multi-protein DNA complex structure from a > 3.6 A native data set. The target structure is a dimer (95 aa in each > monomer) in complex with DNA( 15 base pairs) plus a second protein of 131 aa. > The data has been scaled to P6(1)22 sp. gr. and one target structure is > expected to be in the asymmetric unit that corresponds to 68% solvent > content. 70 % of the target structure is known in two parts(two different pdb > structures previously solved contributing 55% and 15% of the target > structure). I tried with molrep and phaser considering the first part(55%) as > the search model but it turned out to no good solution which all clashes with > symmetry related copies. If I assume the sp. gr. is not the case what else I > can try. Any suggestion is well appreciated. > Thanks... > Raja > _______________________________________________________________________ Dr. Christian Biertümpfel Laboratory of Molecular Biology NIDDK/National Institutes of Health phone: +1 301 402 4647 9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201 Bethesda, MD 20892-0580 USA _______________________________________________________________________
