[cctbxbb] Asymmetric Unit with cctbx

Peter Zwart PHZwart at lbl.gov
Fri Jun 22 10:12:01 PDT 2007


Hi Philipp,

You could leave the map and tag map intact, and operate on the unique part only.

The bare volumes listed in the IT could pose problem: they define the
faces of the ASU, but do not specify which part of the faces them
selves lie in the ASU. I think the
miller_array.direct_space_asu().facets method provides more
information then what the IT gives. Check out
http://cci.lbl.gov/asu_gallery/ for more info.

Please note that an non-continuous ASU is not as weerd as one might
think: http://bones.swmed.edu/projects/crys_FFT.htm

HTH

Peter




2007/6/22, Philipp Heuser <philipp.heuser at embl-hamburg.de>:
> Hi Ralf, hi list,
>
> I am really sorry to bother you again with the same question, but after
> playing around with the tag_array, I think that was not really what I
> was looking for. On the one hand it identifies all  the points which are
> related to each other by symmetry, but it does not return the asymetric
> unit itself as listed in the crystallographic space group tables. E.g.
> if I copy all points where the tag_array is < 0 to a new grid, I end up
> with an uncontinuous grid.
>
> As far as I got it one possibility to get an continuous asymmetric unit
> would be to analyse the facets, which are given by
> miller_array.direct_space_asu().facets . Unfortunately I was not able
> yet to figure out if there is a methd included in the cctbx to apply
> these facets to my x,y,z real_map.
>
> If such an method is available it would be great to know how to use it!
>
> Thanks
> Philipp
>
>
>
>
>
>
> Ralf W. Grosse-Kunstleve schrieb:
> > Hi Phillip,
> >
> > sorry, that was an oversight. Replace
> >
> > -  real_map = fft_map.real_map()
> > +  real_map = fft_map.real_map_unpadded()
> >
> > and it should print identical values.
> >
> > > Is there any reason for the different sizes of the tag_array and the
> > > real_map? real_map.last() and tag_array.last() show different results.
> >
> > That was exactly the problem. The real_map is padded because of FFT
> > requirements. The tag_array is not.
> >
> > .real_map_unpadded() will make a copy. There will be another copy to
> > restore the padding in .structure_factors_from_map() call. The two
> > copies can be avoided in C++, but it is to cumbersome from Python.
> >
> > Ralf
> >
> >
> > ------------------------------------------------------------------------
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>
> --
>
> --------------------------------------------------
>
> Dr Philipp Heuser
> Postdoctoral fellow
>
> EMBL-Hamburg
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>
> phone:   +49 40 89902 188
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