[phenixbb] calculate Fc for the whole unit cell from a Fc of a single symmetric unit.
Dale Tronrud
det102 at uoxray.uoregon.edu
Mon Jul 11 16:00:40 PDT 2011
On 07/11/11 15:35, Edward A. Berry wrote:
> It seems to me there are two things that could be meant by "expand to P1"
>
> One is when data has been reduced to the Reciprocal Space
> asymmetric unit (or otherwise one asymmetric unit of a
> symmetric dataset has been obtained) and you want to expand
> it to P1 by using symmetry to generate all the
> symmetry -equivalent reflections.
>
> The other is where a full P1 dataset has been calculated from just
> one asymmetric unit of the crystal (and hence does not exhibit the
> crystallographic symmetry) and you want to generate the transform
> of the entire crystal. (I think this is how all the space-group -
> specific fft programs used to work before computers got so fast it
> was less bother to just do everything in P1 with the whole cell)
> Presumably this involves applying the real space symmetry
> operators to get n rotated (or phase-shifted for translational
> symmetry) P1 datasets and adding them vectorially.
If I recall, that is how XPLOR calculated structure factors but
that is not how a Ten Eyck space group specific FFT works. First
it expands the atoms into the largest subgroup composed only of
symmetry elements that can be optimized (e.g. three-folds are
out). Then the electron density of the asymmetric unit of that
space group is calculated. Finally the structure factors are
calculated by a combination of line group optimized 1-D FFTs and
clever rearrangements that move data from useless positions in
memory to places where the final 1-D FFTs can use them.
Both the calculation of the map (the slowest step) and the
FFT itself are sped up by a factor of the number of usable
symmetry operators. In addition the amount of RAM required was
greatly reduced. Back in the day the latter was often more
important because memory was so limited.
Dale Tronrud
>
> It would be important to decide which of these is required, and which
> each of the suggested methods provides
>
> eab
>
> Ralf Grosse-Kunstleve wrote:
>> We can expand reciprocal-space arrays, too, with the
>> cctbx.miller.array.expand_to_p1() method. You can use it from the
>> command line via
>>
>> phenix.reflection_file_converter --expand-to-p1 ...
>>
>> See also:
>> http://www.phenix-online.org/documentation/reflection_file_tools.htm
>>
>> Ralf
>>
>>
>> On Mon, Jul 11, 2011 at 10:56 AM, <zhangh1 at umbc.edu
>> <mailto:zhangh1 at umbc.edu>> wrote:
>>
>> Sorry I haven't got a chance to check my email recently.
>>
>> Yes, I meant expansion to P1. The thing is cctbx relies on the atomic
>> model I think, but I only have model Fc available.
>>
>> Hailiang
>>
>> > I suspect what Hailang means is expansion into P1.
>> >
>> > I am sure this can be accomplished through some either existing or
>> > easily coded cctbx tool. However, when I looked into a different
>> task
>> > recently that included P1 expansion as a step, I learned that
>> SFTOOLs
>> > can do this, albeit there was a bug there which caused trouble in
>> > certain space groups (may be fixed by now so check if there is an
>> > update).
>> >
>> > Hailang - if P1 expansion is what you need, I could share my own
>> code as
>> > well, let me know if that is something you want to try.
>> >
>> > Cheers,
>> >
>> > Ed.
>> >
>> > On Fri, 2011-07-08 at 14:44 -0700, Ralf Grosse-Kunstleve wrote:
>> >> Did you get responses already?
>> >> If not, could you explain your situation some more?
>> >> We have algorithms that do the symmetry summation in reciprocal
>> space.
>> >> The input is a list of Fc in P1, based on the unit cell of the
>> >> crystal. Is that what you have?
>> >> Ralf
>> >>
>> >> On Wed, Jul 6, 2011 at 1:38 PM, <zhangh1 at umbc.edu
>> <mailto:zhangh1 at umbc.edu>> wrote:
>> >> Hi,
>> >>
>> >> I am wondering if I only have structure factors
>> calculated
>> >> from a single
>> >> symmetric unit, is there any phenix utility which can
>> >> calculate the
>> >> structure factor for the whole unit cell given the
>> symmetric
>> >> operation or
>> >> space group and crystal parameters? Note I don't have an
>> >> atomic model and
>> >> only have Fc.
>> >>
>> >> Thanks!
>> >>
>> >> Hailiang
>> >>
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