[cctbxbb] Finding neighbouring atoms using pair_asu_table

Lukas Reck reckl at tcd.ie
Fri Apr 19 06:37:57 PDT 2013


On Wed, Apr 17, 2013 at 8:44 PM, Nathaniel Echols <nechols at lbl.gov> wrote:
> To be honest I have never fully understood how this works, but for
> some reason it is necessary to perform an additional operation on the
> symmetry operator obtained by calling asu_mappings.get_rt_mx(j_seq,
> j_sym):
>
> ...
>
> Hopefully someone who actually understands symmetry (or our
> implementation of it, rather) can explain further.  At any rate, I've
> attached a script showing representative usage starting from your
> example, using a structure in the PDB.  (I'm displaying Cartesian
> coordinates because I'm a biologist, not a chemist, but all of the
> symmetry operations use fractional coordinates.)

Thanks, that seems to work! I'd still be interested in the rationale
behind this, though. Symmetry is difficult...

Best regards

Lukas Reck

--
School of Chemistry
Faculty of Engineering, Mathematics and Science
Trinity College Dublin
Dublin 2

Tel: (+353) 1 896 3452


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