On Fri, Dec 2, 2011 at 3:36 PM, Dialing Pretty
After coot rebuid,Igot a protein 3-D structure, and Phenix comprehensive validation demonstrated it is almost acceptable.Then I did the Phenix refinement , and I select all the strategies which suitable for my resolution, all the restraints and weights (default choice) suitable for my resolution, all the other options suitable for me. I optimized it 10 rounds.However after I got the PDB output file and the mtz output file after refinment, analysis by Phenix comprehensive validation demonstrated the quality of the quality of the protein 3-D structure has been lowered significantly, which makes it unacceptable.
What are the RMS(bonds) and RMS(angles), and which version are you using? You probably just need to optimize the X-ray/stereochemistry weight - there is an option for this in the second tab in the GUI (or on the command line, optimize_xyz_weight=True).
Will you please tell me how to process my refinement? In Phenix refine, which kinds of combination of strategy combination are allowable, which are not allowable, which kinds of combination of restraints and weight combination are allowable, which are not allowable, which kinds of combinations of option are allowable, which are not allowable, and why?
For strategies, the main restriction is on overlapping atom selections for group_adp and individual_adp, plus if you are refining individual anisotropic ADPs for any atoms, these may not be part of any TLS group. Several of the other methods (such as rotamer correction) may not be compatible with twinned refinement (it's a bug, sorry). You probably shouldn't use both types of simulated annealing at once. There are many other empirical rules that are dependent on resolution and structure quality, which we don't have a good summary for yet. There is also an incomplete list of frequently asked refinement questions here: https://www.phenix-online.org/version_docs/1.7.3-924/refine_faq.htm If you email the log file to [email protected], we may have suggestions more tailored to your particular situation. (You should send it to that address, not the phenixbb, since it may contain revealing information about your structure.) -Nat