[cctbxbb] Asymmetric Unit with cctbx

[Philipp Heuser]

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
>
>
> ------------------------------------------------------------------------
> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge 
> <http://us.rd.yahoo.com/evt=47093/*http://tv.yahoo.com/collections/222>to 
> see what's on, when.
> ------------------------------------------------------------------------
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/cctbxbb
>   


-- 

--------------------------------------------------

Dr Philipp Heuser
Postdoctoral fellow

EMBL-Hamburg 
c/o Building 25A, DESY
Notkestrasse 85
22603 Hamburg

phone:   +49 40 89902 188
fax:     +49 40 89902 149
mail:    philipp.heuser at embl-hamburg.de
web:     www.philipp-heuser.de

--------------------------------------------------