forgot to also send to the list.

---------- Forwarded message ----------
From: Nicolas Bock <>
Date: Thu, Apr 15, 2010 at 15:46
Subject: Re: [PyMOL] feature request: supercell construction
To: Thomas Holder <>

Hi Thomas,

On Thu, Apr 15, 2010 at 03:42, Thomas Holder <> wrote:
Hi Nick,

> I noticed a few things:
> - when I run "supercell 2, 1, 1" I get another cell outline along the
> a axis, but no atoms are shown in the second cell. Do I have to run
> another command for them to show up?

the script does not create symmetry mates. The "symexp" command can
create symmetry mates within a given radius (it will not just fill up
the cell).

Maybe I just don't understand the symexp command, but how would it help me in constructing a 2x2x2 supercell from a unit cell with atom positions? Isn't the radius meaningless in this context since it implies a radial cutoff, whereas a simple cubic unit cell has a cubic cutoff? When I look at a crystal I would want the supercell construction to get a better idea of how the bulk crystal looks like. With small unit cells this is sometimes tricky without explicitly constructing a supercell. Also, in the case of a triclinic unit cell, for example, finding the correct symmetry operation for the "symexp" command might be rather tricky.

> - when I run the command again with other values for a, b, or c,
> nothing changes. I would expect that running the sequence "supercell
> 2, 1, 1" and then "supercell 2, 2, 1" would show me a 2x2x1 supercell
> at the end, but I see only the 2x1x1 supercell.

the second call will create a new state for the same object. This is not
convenient, so I changed it to replace the first state again. I put the
modified script to the PyMOLWiki: