[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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