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

Graeme.Winter at diamond.ac.uk Graeme.Winter at diamond.ac.uk
Mon Jun 24 02:56:21 PDT 2013


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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