[cctbxbb] Fail to extend space-group with centring translations

Peter Zwart PHZwart at lbl.gov
Fri Dec 8 13:13:28 PST 2006

Hi Luc,

> with the latest cctbx release, the following Python snippet fails
> from cctbx.sgtbx import *
> info = space_group_info("P2/a")
> g = info.group()
> g.expand_ltr(tr_vec((1,1,1),2))

If you do it like this:

from cctbx import sgtbx
info = sgtbx.space_group_info("P2/a")
g = info.group()
t = sgtbx.tr_vec(  (1,1,1), 2 )
t = t.new_denominator( g.t_den() )
g.expand_ltr( t )
print sgtbx.space_group_info(group=g)

The trick lies in obtaining the translational denominator from the group 
it self and setting that value in your t vector. The same issue is there 
when multiplying in an extra rotation operator. In that case you need 
the g.r_den().

> from cctbx import sgtbx
> s = sgtbx.space_group_symbols("P21/c")
> g = sgtbx.space_group(s)
> g.expand_ltr(sgtbx.tr_vec((1,0,1),3))
> g.expand_ltr(sgtbx.tr_vec((2,0,2),3))

from cctbx import sgtbx
info = sgtbx.space_group_info("P2/a")
g = info.group()
g.expand_ltr(sgtbx.tr_vec((1,0,1),3).new_denominator( g.t_den() ) )
g.expand_ltr(sgtbx.tr_vec((2,0,2),3).new_denominator( g.t_den() ) )
print sgtbx.space_group_info( group=g )


> It seems like it is a deeply rooted limitation and that brings me to  
> the bigger picture. I am currently working on an EPSRC grant to write  
> the next generation of small molecule crystallographic software, a  
> joint collaboration between Judith Howard in Durham and David Watkin  
> in Oxford (all in UK, just in case…!). The CCTBX is obviously a  
> seducing foundation for such a project. Thus we have tried to push it  
> into corners which do actually matter to a significant minority of  
> small molecule crystallographers.
> So I would like to know how difficult it would be to lift the  
> limitation at hand. Would it trigger a cascade of changes throughout  
> the sgtbx?

The r_den, t_den thing is confusing and using an approach with rational 
numbers would make sense.

time time ...



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