[cctbxbb] coordinates -> space group + matrices

[Kris Andersen]

Jon, thanks for your reply.

I'm familiar with findsym, but it doesn't (to my knowledge) give the  
space group operations. What I'd like is something to find the space  
group and then give the symmetry operations in the basis of my  
coordinates (or a way to transform my coordinates into the basis of  
the symmetry matrices). I was hoping it may be possible to put  
together elements of the ccbtx library to do this easily?

P.S. In my haste to come up with an example that wasn't totally  
trivial, I forgot to mention I was thinking in terms of the atoms  
being different, hence the R3m symmetry. The example was suppose to  
be for a perosvikite.


On Sep 17, 2007, at 11:33 PM, Jon Wright wrote:

> Kris Andersen wrote:
>> This is probably a simple (maybe stupid) question, but that never
>> stopped me before:
>>
>> I want to give cctbx a set of primitive vectors and coordinates
>> (cartesian or fractional), and have it return (1) the space group and
>> (2) all the symmetry matrices.
>>
>> For example, given
>>
>> R = [4 0 0    % primitive vectors
>>       0 4 0
>>       0 0 4]
>>
>> x = [0.00  0.0   0.00   % fractional coordinates
>>       0.51  0.51  0.51
>>       0.50  0.50  0.00
>>       0.00  0.50  0.50
>>       0.50  0.00  0.50]
>>
>> I want cctbx to tell me this is space group #160 R3m, that there are
>> 6 symmetry operations, and give me the corresponding matrices.
>
> Hello,
>
> Looks like the "F3m" setting, assuming all atoms are the same?  
> Would you
> want to keep that or would you prefer it on the trigonal or hexagonal
> axes? Not sure if cctbx whether has a find symmetry algorithm, but  
> there
> are a couple of other possibilities. Ton Spek's Platon software will
> read a structure in a cif file in space group P1 and then try to find
> the correct space group for you. Also there is Harold Stokes findsym
> program (http://stokes.byu.edu/findsym.html).
>
> Good luck,
>
> Jon
>
>> This sounds easy, given everything cctbx can do, so it must be
>> possible. Is there a simple example anywhere?
>>
>> Thanks.
>>
>> --
>> Kristopher E. Andersen         http://www.physics.nau.edu/~andersen/
>> Northern Arizona University                    kris.andersen at nau.edu
>> Department of Physics and Astronomy                   (928) 523-7202
>>
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