Dear Almudena, I promise not to make a habit of advertising other programs on the Phenix mailing list, but just once I would like to encourage you (and the community) to try all the tools at your disposal. Different refinement programs have different strength and weaknesses. Secondary-structure restraints in Phenix are great for low-resolution data, but so is jelly-body refinement in Refmac. A dodgy 3.2 Å structure I'm currently working on was improved dramatically by Buster-TNT. The Ramachandran plot tightened, and R free plunged by four percentage points. Andreas On 05/02/2015 10:44, Almudena Ponce Salvatierra wrote:
Dear all,
I am refining my structure (data at 3 A), with a model that is complete. However the Rs values are: R work= 0.25 and Rfree= 0.32. I have read "Improved target weight optimization in phenix.refine" (In the computational crystallographic newsletter 2011) and what I understand is that just by marking the boxes "improve xray/stereochemistry weight" and "improve xray/adp weight" it should work... giving me the best possible Rfree.
I'm refining individual coordinates, occupancies, b-factors (isotropic for all atoms), TLS, and using secondary structure restraints, automatic ligand linking and experimental phases restraints. Also, I chose this strategy because I have finished building the structure and according to some of the suggestions in "towards automated crystallographic structure refinement with phenix.refine".
I am actually quite confused and don't know what to think... is it a matter of the weights? is it only that this is as good as it gets?
Any suggestions and comments are welcome.
Thanks a lot in advance,
Best,
Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
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