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

zhangh1 at umbc.edu zhangh1 at umbc.edu
Mon Jul 11 15:01:49 PDT 2011


Thanks a lot!
> 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> 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> 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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