VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 24 2004 - 09:29:15 CDT

Keith,
  Which version of VMD are you using? I seem to remember that there
was a bug in one of the early versions that supported periodic image
display. When I load your structure, I don't see anything obviously
wrong, so it is making me wonder what results you're getting, and thus
which version you're using, etc. There isn't presently a method of
displaying bonds between periodic images, nor a built-in unit cell
display feature though that is easy to add. Let's sort out your main
problem first and address the other two once that's taken care of.

  John

On Tue, Aug 24, 2004 at 11:34:31AM +0100, Keith Refson wrote:
> Dear VMD developers,
>
> I am seeing a problem displaying periodic images of the
> attached PDB file. The spatial relationship between the
> periodic images is clearly not correct for repeats in the
> Y and Z directions, but appears OK only for X. This is most
> clearly seen by choosing a "dynamicbonds" representation for
> "name Mg00 O00" and CPK for "all". The MgO layer should
> be an infinite periodic solid.
>
> I guess that the periodic image generation is not able to
> cope with the non-orthogonal axes of the cell.
>
> A couple of supplementary questions:
>
> 1) Is there any way of adding bonds between periodic images
> - for a layer structure this would be the correct display mode.
>
> 2) Is there any way of actually drawing the unit cell box?
>
> Thanks
>
> Keith Refson
> --
> Dr Keith Refson,
> Building R3
> Rutherford Appleton Laboratory
> Chilton
> Didcot kr AT isise
> Oxfordshire OX11 0QX DOT nd DOT rl DOT ac DOT uk 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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