[phenixbb] lower limits on grid spacing/binning
terry at lego.berkeley.edu
Tue Oct 30 18:57:21 PDT 2007
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?
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
> 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.
> phenixbb mailing list
> phenixbb at phenix-online.org
P. Therese Lang
Alber Lab, UC Berkeley
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