Hi 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 1.7.1.743. On Tue, Dec 13, 2011 at 1:38 PM, Nathaniel Echols 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

...

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

On Mon, Dec 12, 2011 at 8:26 PM, intekhab alam wrote: the 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

Thanks for the reply and suggestions. regards intekhab Alam On Tue, Dec 13, 2011 at 2:07 PM, Nathaniel Echols wrote:

On Mon, Dec 12, 2011 at 8:58 PM, intekhab alam wrote:

...

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.

Sorry, I'm not sure what would cause the clashes - hopefully someone on ccp4bb will have an answer. (It could simply be a result of the X-ray/geometry weighting not being correct - a sure sign of this, regardless of program used, is excessively high RMS(bonds) and RMS(angles).) I'm glad Phenix is working though!

...

i am using Phenix 1.7.1.743.

FYI, you should update to 1.7.3 - the geometry may be significantly improved at this resolution.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL