[cctbxbb] Reducing coordinates to asymmetric unit

Thu Feb 11 07:34:55 PST 2010

The cctbx news article here gives a good introduction to the asu_mappings
(section 3.1):

http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf

<http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf>That, and
other IUCr Comp Comm newsletter articles on the cctbx, can be found on the
cctbx homepage:

http://cctbx.sourceforge.net/

I suspect the reason it spits out Cartesian coordinates is that they are
intended for use primarily in symmetry pair interactions, in which case
Cartesian coordinates are essential.

By the way, the function unit_cell.fractionalize() is overloaded to take a
flex array of sites, so the loop over all sites can occur in C++ rather than
Python:

fsites = cs.unit_cell().fractionalize(sites)

Of course, if sites is a python list you need to construct a flex array
first: flex.vec3_double(sites).

Thanks,

Richard

<http://cctbx.sourceforge.net/>

On 11 February 2010 14:14, <Graeme.Winter at diamond.ac.uk> wrote:

> Hi Richard,
>
> Many thanks for the pointers - I have managed to do exactly what I wanted
> (I think) with:
>
> ds = cs.direct_space_asu()
> sg = cs.space_group()
> am = crystal.direct_space_asu.asu_mappings(
>    space_group = cs.space_group(),
>    asu = ds.as_float_asu(),
>    buffer_thickness = 0.0)
>
> fsites = [cs.unit_cell().fractionalize(site) for site in sites]
>
> for fsite in fsites:
>    am.process(fsite)
>
> asu_sites = [cs.unit_cell().fractionalize(m[0].mapped_site()) \
>             for m in am.mappings()]
>
> for msite in asu_sites:
>    print '%.3f %.3f %.3f' % msite
>
> In case it is of any use to anyone! There are a couple of mysteries left
> here which don't make complete sense to me (why I can't process a list of
> coordinates, but have to pass them in one-at-a-time then gather them all
> together) - also why this takes frac coordinates and gives back cart.
> coordinates - though it's quite likely I am incorrect on both counts...!
>
> Thanks for your help though, and for all the great code in cctbx,
>
> Graeme
>
>
> -----Original Message-----
> From: cctbxbb-bounces at phenix-online.org on behalf of Richard Gildea
> Sent: Thu 2/11/2010 12:59 PM
> To: cctbx mailing list
> Subject: Re: [cctbxbb] Reducing coordinates to asymmetric unit
>
> Hi Graeme,
>
> I think what you need are the direct space asu mappings tools - see
> cctbx/crystal/tst_ext.py or cctbx/regression/tst_direct_space_asu.py if you
> want to look at more of the tools that are available there.
>
> If I understand correctly, something along the lines of this should do what
> you want:
>
>    asu_mappings = xs.asu_mappings(buffer_thickness=0)
>    xs_asu = xs.deep_copy_scatterers()
>    frac = xs.unit_cell().fractionalize
>    for i, mappings in enumerate(asu_mappings.mappings()):
>      xs_asu.scatterers()[i].site = frac(mappings[0].mapped_site())
>    for sc in xs_asu.scatterers():
>      assert asu_mappings.asu().is_inside(sc.site)
>
> Hope that helps,
>
> Richard
>
> On 11 February 2010 11:45, <Graeme.Winter at diamond.ac.uk> wrote:
>
> >  Hi Folks,
> >
> > Does anyone have a handy bit of CCTBX Python code which will take a
> > spacegroup and unit cell, and a list of coordinates, and return the list
> of
> > coordinates reduced to the asymmetric unit? I tried the "dumb" approach
> of:
> >
> > use unit cell and sites -> fractional sites
> >
> > for site in fractional sites:
> >   for smx in sg.smx()
> >     for ltr in sg.ltr()
> >       apply smx, ltr
> >       is in asu? return
> >
> > and it did not always return an answer, so there's clearly somthing I
> don't
> > understand. Fractional coordinates are all in [0,1).
> >
> > I'm sure someone must have done this!
> >
> > Thanks in advance,
> >
> > Graeme
> >
> > Graeme Winter
> > Software and MX Support Scientist
> > Diamond Light Source
> >
> > +44 1235 778091 (work)
> > +44 7786 662784 (work mobile)
> >
> >
> >
> >
> >
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