Re: [cctbxbb] Asymmetric Unit with cctbx
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 ____________________________________________________________________________________ Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/
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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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
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/222to see what's on, when. ------------------------------------------------------------------------
_______________________________________________ cctbxbb mailing list [email protected] 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: [email protected] web: www.philipp-heuser.de
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participants (3)
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Peter Zwart -
Philipp Heuser -
Ralf W. Grosse-Kunstleve