[Molvis-list] How to superpose two molecules in a molecular viewer?

[Elmar Krieger]

Julio Cesar da Silva wrote:
> I have a doubt about how to superpose two molecules in a molecular viewer. 
> I need to superpose two protein structure in a spacefill representation. I 
> would like to show one of them with semi-transparency. I have tried to do 
> this in the softwares Rasmol and Pymol, but I could not. I would like to 
> show both of them at same time and can see both. So, I would like to show 
> one semi-transparent and the other one normal. Please, does someone know 
> how to do this? Could you help me? Thanks.

You could download the freeware 'YASARA View' from http://www.yasara.org

Here is what the result would look like:
http://yasara3.cmbi.ru.nl/service/transsup.jpg

The steps are:
- Show the first molecule in spacefill representation
- Create a transparent VdW surface for the second molecule
- Hide the atoms of the second molecule
- Raytrace the result, choosing a 'ball zoom factor' of 1.5 (this makes 
sure the size of the spacefill representation matches the VdW radii).

Good luck,
Elmar

-- 
Elmar Krieger, PhD
YASARA Biosciences & CMBI Outstation Austria
Neue-Welt-Hoehe 13/b
A-8042 Graz
Austria/Europe

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