VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 11 2011 - 11:02:12 CDT

Hi,
  Besides what Axel already mentioned, if you're wanting to clip away
geometry rather than just selecting a subset of atoms, you may want to
try using the clipping plane tool in the Extensions->Visualization menu.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 11, 2011 at 02:16:25PM +0100, Jennifer Williams wrote:
>
> Hi,
>
> I have a cubic molecule (.xyz file) and I simply want to take a slice
> through it. i.e as if to cut it in half and display the face of the
> cut-edge.
>
> Reading through the documentaion I thought the "mol volume" tool might
> do the trick but I can't seem to get the command right. I thought the
> command was the following...
>
> mol volume top {0 0 0} {1 0 0}
>
> with the first set of brackets denoting whether I would be cutting
> parallel to the x, y or z axis and the second denoting how far along
> the cartesian axis of the molecule I would be cutting (or vice versa
> -I can't tell at the moment).
>
> so for example if I wanted to slice the molecule at the midpoint
> parallel to the x axis, I supposed the command would be:
>
> mol volume top {1 0 0} {0 0.5 0}
>
> Am I missing something? Could someone please give the correct command
> to do this?
>
> Thanks
>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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