Re: [cctbxbb] Reducing coordinates to asymmetric unit

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.pdfThat, 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, 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: [email protected] 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, 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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