On Mon, Nov 15, 2010 at 1:09 PM, Katarina Moravcevic
Hi all, I have only started using PHENIX and have made an interesting observation. If I run my model through PHENIX refine (individual sites, individual ADPs, occupancies, optimized X-ray/stereochemistry weight, optimized X-ray/ADP weight options selected) I obtain R/Rfree 0.15/0.18 and very nice geometry values (data is to 1.7A). However, if I now take this refined model and run it through Refmac (without any refinement) I obtain R/Rfree of 0.19/0.21. Can anyone explain why is there such a big difference? Will this be an issue during PDB submission?
Take a look at what phenix.refine reports for the number of reflections used for refinement in the logfile - I believe it will discard reflections that are flagged as suspicious (can't remember the reference, I think it's one of Randy Read's papers), and unless you're using a very recent version, it may also be ignoring reflections where F=0. There are probably a half-dozen other reasons why the programs disagree, but these are less obvious and potentially much harder to detect. If you're concerned about reproducibility, run phenix.model_vs_data with the reflections and PDB file, and make sure that the statistics it reports agree with what you're sending to the PDB. The program is well-documented and mostly open-source, and is a good sanity check for data in the PDB. The PDB is using a much more primitive method to check R-factors, and after they process your structure you'll get an email that includes something like this: Structure factor validation High_Res Low_Res Compl Num_Ref R_obs R_work R_free Corr(Fo-Fc) Reported PHENIX 2.500 20.005 81.28 15118 0.2183 0.2150 0.2884 N/A SFCHECK without TLS 2.50 19.64 87.9 8004 0.2850 0.2850 N/A 0.8546 REFMAC without TLS 2.500 67.386 87.609 8937 0.234 0.2336 0.0000 0.918 The lack of TLS in their validation means that they'll even overestimate the R-factors of most structures refined by REFMAC! (Although in this case I think I left the ANISOU records in the deposited PDB file, so I'm not sure what they're doing wrong.) They will never complain about this, in my experience, so it's not something you need to worry about. -Nat