[cctbxbb] map_to_asu - get the symop used to perform mapping

Nathaniel Echols nechols at lbl.gov
Mon Jun 24 15:55:18 PDT 2013


I'll leave this to your discretion; I don't really understand this
enough to have any strong opinions about how it should be done.  If
the inversion operation is always a binary choice, then I think your
idea of returning -j is sensible, in which case I guess it would be a
flex.int array.

-Nat

On Mon, Jun 24, 2013 at 2:56 AM,  <Graeme.Winter at diamond.ac.uk> wrote:
> Thanks Nat,
>
> I will code this up as a workaround (I can cache this for all hkl in a dictionary and look up later) - however it would be neat if map_to_asu() could return a flex array or something with this information it. I will have a play at adding this perhaps as map_to_asu_rtn_symops.
>
> Only tricky thing I see here is for spacegroups with inversion operations: guess I would need to return -j where j is symop number...
>
> I just wanted to check noone has done this, from responses this appears to be the case!
>
> Best wishes,
>
> Graeme
>
> ________________________________________
> From: cctbxbb-bounces at phenix-online.org [cctbxbb-bounces at phenix-online.org] on behalf of Nathaniel Echols [nechols at lbl.gov]
> Sent: 20 June 2013 18:59
> To: cctbx mailing list
> Subject: Re: [cctbxbb] map_to_asu - get the symop used to perform mapping
>
> On Thu, Jun 20, 2013 at 7:34 AM,  <Graeme.Winter at diamond.ac.uk> wrote:
>> In the progress of trying to (for reasons of my own) reproduce scale pack unmerged format files from flex arrays of Miller indices. map_to_asu is great, but it would be great to get the symop # used to perform the mapping as a result of this (it is computed somewhere in asu.h but not easily pushed out…)
>
> It looks like the point at which the actual symop is used is at least
> one layer of abstraction below the ASU mapping.  I think what happens
> is that it generates a list of *all* symmetry-equivalent indices, then
> picks the one that falls in the ASU.  In Python, this would look
> something like this:
>
> from cctbx import sgtbx
> hkl = (-10, 1, -8)
> sg = sgtbx.space_group_info("P6122").group()
> asu = sgtbx.reciprocal_space_asu(sg.type())
> for i_inv in range(sg.f_inv()) :
>   for j_smx in range(sg.n_smx()) :
>     rt_mx = sg(0, i_inv, j_smx)
>     hkl_ = hkl * rt_mx.r()
>     hkl_int = convert_to_integers(hkl_) # or fail if they're not integral
>     if asu.is_inside(hkl_int) :
>       save_this_symop()
>
> This is loosely derived from cctbx/miller/sym_equiv.cpp and
> cctbx/miller/asu.cpp; I'm probably butchering some of the details.
>
> -Nat
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