Dear Everyone, Thank you to everyone for their thorough responses to my question. I do have one follow-up question, though. The majority of the references and discussion involves the influence of grid spacing on the generation of structure factors during refinement. Once the structure is fully refined, I will have the final set of structure factors, presumably to be deposited to the pdb. I am interested in the back-transformation from final structure factors to electron density maps. Does the grid spacing in this case have a general rule of thumb as well or, because the data has already been truncated, does it matter? Sincerely, Terry Ralf W. Grosse-Kunstleve wrote:
Probably, the original poster already got more than he bargained for, but for the records, a few more comments:
All FFT based structure factor programs require that the sampling rates along each axis be even.
I don't think this is true, unless I'm misunderstanding what "sampling rate" means. The FFT in phenix is based on FFTPACK (written in the 80s) which works for any number of grid points. FFTw also supports arbitrary gridding.
They may have other required factors depending on the space group, but they will be happy to inform you if you make a choice it doesn't like. They are also more efficient when the prime factors of the sampling rates are small numbers. Try to stick with multiples of 2,3, and 5 if possible.
That's good advice. FFTPACK is fastest for transform sizes that are multiples of 2,3,4 and 5. The map calculation algorithms in phenix automatically take this into account.
All FFT programs will fail if you sample your map courser than twice that frequency, as SFALL did for you.
This may be true for SFALL, but not for the FFT algorithms in the phenix libraries ($PHENIX/cctbx/include/cctbx/maptbx/structure_factors.h). The critical reference is:
David A. Langs (2002), J. Appl. Cryst. 35, 505.
As short as it is, this was an incredibly important paper. In retrospect, it is amazing that it took so long for someone to discover the trick.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- P. Therese Lang Post Doc Alber Lab, UC Berkeley