VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 24 2004 - 10:13:25 CDT

Axel,
  To my knowledge there is nothing wrong with the periodic image
display feature in regards to non-orthogonal unit cells, but it is
correct that VMD doesn't handle unit cells that require symmetry
operations to be applied. The PBC display feature works with simple
unit cells that are packed along the x/y/z axes, via simple translations.
If non-translational symmetry is required, VMD cannot display that sort of
periodic cell. Looking at Kieth's image, I do not immediately see what's
wrong, perhaps he's getting a different result than I am, or I've misunderstood
what he expects the structure to look like. On my machine, I see what seems
to match his description of what he expects, so I'd like to find out
exactly what the problem is that he's having.

As well, if you're aware of any non-orthogonal periodic cell that does
not display as you'd expect (which consists of only translational
symmetry operations) I'd like to see examples. If you have periodic cells
that require more complex symmetry operations, that will have to wait until
we can parse spacegroup operators and the like.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 24, 2004 at 04:56:02PM +0200, Axel Kohlmeyer wrote:
>
> On Tue, 24 Aug 2004, Keith Refson wrote:
>
> KF> Dear VMD developers,
>
> hello keith,
>
> KF>
> KF> I am seeing a problem displaying periodic images of the
> KF> attached PDB file. The spatial relationship between the
> KF> periodic images is clearly not correct for repeats in the
> KF> Y and Z directions, but appears OK only for X. This is most
> KF> clearly seen by choosing a "dynamicbonds" representation for
> KF> "name Mg00 O00" and CPK for "all". The MgO layer should
> KF> be an infinite periodic solid.
> KF>
> KF> I guess that the periodic image generation is not able to
> KF> cope with the non-orthogonal axes of the cell.
>
> exactly. IIRC, this has been discussed on VMD-L and
> i occasionally get (painfully) reminded myself.
>
> KF>
> KF> A couple of supplementary questions:
> KF>
> KF> 1) Is there any way of adding bonds between periodic images
> KF> - for a layer structure this would be the correct display mode.
>
> not directly. the best suggestion so far, was to write a small
> program that adds copies (of parts) of the unit cell to the
> file and then have the periodic images overlap.
>
> KF> 2) Is there any way of actually drawing the unit cell box?
>
> if you create a faked gaussian cube file, you can use the
> isosurface representation.
>
> alternatively, you can draw directly with vmd graphics commands,
> see, e.g.
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part2.html#chap4_sect6
>
> for an example (using a cubic cell). this can probably be easily
> adapted to your needs.
>
> hope that helps,
> axel.
>
>
>
> KF> Thanks
> KF>
> KF> Keith Refson
> KF>
>
> --
>
>
> =======================================================================
> Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer_at_rub.de
> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> =======================================================================
> 

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