Re: [phenixbb] calculate Fc for the whole unit cell from a Fc of a single symmetric unit.

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. 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, mailto:[email protected]> 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, mailto:[email protected]> 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 >> >> _______________________________________________ >> phenixbb mailing list >> [email protected] mailto:[email protected] >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> >> _______________________________________________ >> phenixbb mailing list >> [email protected] mailto:[email protected] >> http://phenix-online.org/mailman/listinfo/phenixbb > > > _______________________________________________ > phenixbb mailing list > [email protected] mailto:[email protected] > http://phenix-online.org/mailman/listinfo/phenixbb > >

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