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
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