[phenixbb] crystal packing pattern

Nathaniel Echols nechols at lbl.gov
Thu Mar 15 08:05:22 PDT 2012

On Thu, Mar 15, 2012 at 7:59 AM,  <bsubedi at btk.fi> wrote:
> Could someone help me with a program/tool to see the pattern of protein packing
> in the crystal. I would like to make comparative study between regions of the
> protein in two different chains and if crystal packing has some effect on
> conformational alteration.

I always found PyMOL most useful for this - if you have a PDB file
with symmetry records loaded, this command will generate all symmetry
copies within 20 Angstroms:

symexp s = my_object, my_object, 20

Increase the radius to view more of the lattice.

I believe Coot does something smarter where it only draws molecules in
range (Draw menu->Cell and Symmetry, then click "Symmetry by
molecule").  This is probably better for interactive visualization -
the only drawback is that you can't easily save the symmetry copies to
a file, or make pretty pictures.


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