[phenixbb] strange MR problem

intekhab alam faisaldbg at gmail.com
Mon Dec 12 20:58:33 PST 2011


i want to make one clarification here that clashes appear when i used the
mtz file generated by CCP4 along with the MR solution from Phaser in Refmac
5. Refinemnet is fine in Phenix with R and Rfree of 25/30.
i am using Phenix
On Tue, Dec 13, 2011 at 1:38 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> 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.
> -Nat
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