On Thu, Jul 12, 2012 at 12:38 AM, 周文昌
I had one problem using phaser-MR to solve my structure. Phaser-MR gives me one solution with TFZ=15.4 and LLG=165 which seems to be promising but phenix.refine does not give me a low R values (0.4884/0.5424). I went back and checked the solution from phaser-MR, I found RFZ=18.8, higher than TFZ. Does anyone think this is a problem to solve my structure?
The space group is C121, I believe there are 4 copies of my search model in ASU.
What is the resolution, and what is the sequence identity of the search model? I don't know whether the high RFZ means anything, but the first thing I would check is whether the packing of the MR solution makes sense; Phaser will do a good job preventing molecules from overlapping (unless you changed it to use much less conservative criteria), but it won't guarantee that the molecules pack into a nice continuous lattice. If there are big gaps, it may not be a real solution. I think we need to add an entire FAQ page for high R-factors. However, there are an increasing number of tools and/or tricks in Phenix to deal with problems like this - in approximate order of runtime: - run phenix.refine for more cycles - at least 20. See this paper for an example of why this can be important: http://journals.iucr.org/d/issues/2012/07/00/kw5044/index.html - use phenix.morph_model (refer to previously mentioned paper) - use phenix.den_refine (or DEN in CNS) - use MR-Rosetta Also, if you're willing to share your data with us, we're collecting difficult-to-refine structures for benchmarking new methods. (It will of course be kept confidential.) -Nat