forgot to also send to the list.
---------- Forwarded message ----------
From: Nicolas Bock <nicolasb...@gmail.com>
Date: Thu, Apr 15, 2010 at 15:46
Subject: Re: [PyMOL] feature request: supercell construction
To: Thomas Holder <spel...@users.sourceforge.net>
Hi Thomas,
On Thu, Apr 15, 2010 at 03:42, Thomas Holder
<spel...@users.sourceforge.net>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:
>
> http://www.pymolwiki.org/index.php/Supercell
>
>
Thanks!
> Cheers,
> Thomas
>
>
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