Re: [cctbxbb] Introducing arbitrary translations in symmetry operations

Hi Emre, This turns out to be a very long-standing oversight. Could you try again with the next cctbx build? http://cci.lbl.gov/cctbx_build/all.html Wait for build tag 2011_06_03_XXXX or higher. It should give you 2*a,2*b,2*c. The oversight was in cctbx/sgtbx/space_group_type.cpp, in the cmp_change_of_basis_mx class. I was only evaluating "is one the unit matrix but not the other". I had to add "is one a diagonal matrix and not the other". Ralf P.S.: If you want to try the new version straightaway, you can use the command libtbx/development/cctbx_svn_getting_started.csh Then manually build from sources as described here: http://cctbx.sourceforge.net/current/installation.html

________________________________ From: Emre S. Tasci To: cctbx mailing list Sent: Friday, June 3, 2011 3:49 AM Subject: Re: [cctbxbb] Introducing arbitrary translations in symmetry operations

Dear Ralf,

Thank you very much for your answer. What we are actually trying to do is to refer to the tables of ITA (2006) 15.2.1.* where you have your space group & additional generators and voila! It's not the normalizers defined as a group but the group+normalizers defined as a new group.. 8)

Here is yet another question-- I might be missing something obvious here so you got my apologies beforehand if it proves that I do:

Take for instance SG #16, P222. I add the 3 translation operators x+1/2,y,z x,y+1/2,z x,y,z+1/2 plus the inversion: -x,-y,-z

then I get  SG #47, Pmmm with (2*b,2*c,2*a) -- but why not (2*a,2*b,2*c)? As I said, I'm highly suspecting that I'm missing something very very obvious but at this moment I'm baffled.

With my best regards, Emre

On 06/02/2011 07:32 AM, Ralf W. Grosse-Kunstleve wrote:

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But we couldn't find a way to introduce "x,y,z+t" while we are "expand_smx"ing the space group with these operators.

The space_group class only supports finite groups (and only in settings that can be represented with integral rotation parts and rational translation parts). We have the class cctbx.sgtbx.search_symmetry, which multiplies the discrete origin shifts into the space group and keeps track of the continuous allowed origin shifts separately.

It would need new code to determine a full description of affine normalizers. (Are they considered space groups?)

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