[cctbxbb] Reducing coordinates to asymmetric unit

[Graeme.Winter at Diamond.ac.uk]

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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