[phenixbb] strange MR problem

Nathaniel Echols nechols at lbl.gov
Mon Dec 12 20:38:50 PST 2011

On Mon, Dec 12, 2011 at 8:26 PM, intekhab alam <faisaldbg at gmail.com> wrote:
> I have a 3.0A dataset of a protein-protein complex. I used one of the
> protein structure solved previously as a template and used phaser in CCP4 as
> well as in phenix. I used the sca file in phenix which gave a solution with
> 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used the
> converted .mtz file which gave 6 molecules in ASU but with a different
> packing. In both the cases map fits well in the model and there is some
> extra density that may correspond to second protein partner of the complex
> molecule. when i tried to use the MR solution generated in phenix with the
> mtz file from ccp4 the model shows a lot of clashes.

The two solutions are probably equivalent under crystallographic
symmetry - they simply represent different versions of the ASU.  It's
possible that they also have different origins, but I can't tell from
your description whether this is the case.  What kind of refinement
are you running that results in clashes, and what is the clashscore
for the resulting model?  (Please include the program version.)  As a
general rule, reciprocal-space refinement without phases should work
regardless of the origin or ASU, so it could just be a weighting
problem.  If you are running real-space refinement that is potentially
more problematic, but I doubt that's the problem in this case.


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