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

[Edward A. Berry]

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, <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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