[cctbxbb] cctbxbb Digest, Vol 92, Issue 17

[Gabor Bunkoczi]

Hi Bert,

actually, my "first" thought solves this problem. If you turn all your
points into an xray_structure, and get the asu_mappings, this gives you the
coordinates of the equivalent site in the asu (returned by the
"mapped_site" method). However, it won't make a list of equivalent sites
unique, i.e. if you have site1 = ( 0.1, 0.1, 0.1 ) and site2 = ( 1.1, 0.1,
0.1 ) (in fractional coordinates), you get a mapping for the same site
twice, so perhaps the most efficient method is just to transform your
scalar field into the unit cell, and then discard points that are outside
the asu. If the grid is not congruent with the unit cell, you are probably
better off using asu_mappings, since you will be able to interpolate on a
finer grid.

BW, Gabor


On Mon, Nov 21, 2016 at 2:02 PM, Tijskens Engelbert <
Engelbert.Tijskens at uantwerpen.be> wrote:

> > Message: 3
> > Date: Mon, 21 Nov 2016 13:38:21 +0000
> > From: Gabor Bunkoczi <gabor.bunkoczi at googlemail.com>
> > To: cctbx mailing list <cctbxbb at phenix-online.org>
> > Subject: Re: [cctbxbb] convert an arbitrary point to one inside the
> >       asymmetric unit
> > Message-ID:
> >       <CABYxhoUxqFsc0f_TjWwn4oC4hKFk8AEbzwx5=9=_+gwW3
> xmkpg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > On second thought, the simplest solution is to use the direct_space_asu
> > object. This is available for all space groups:
> >
> >>>> from cctbx import sgtbx
> >>>> sgi = sgtbx.space_group_info( "P2" )
> >>>> asu = sgi.direct_space_asu()
> >>>> asu.is_inside( ( 0, 0, 0 ) )
> > True
> >>>> asu.is_inside( (0, 0, 0.51 ) )
> > False
> >
> > BW, Gabor
> >
> Thanks for your quick reply, Gabor.
> Unfortunately, it does not solve my question. For the example you give
> above, the second point is not inside the asu, and my question is how i can
> the corresponding point inside the asu, For a simple space group as P2 the
> answer is easily figured out by hand. For a space group such as I m -3 m,
> it becomes complicated. I would like to have a (computationally efficient)
> method for finding the point inside the asu given an arbitrary point which
> works for every space group.
> Any “third” thoughts?
>
> kindest regards, bert
>
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