VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Dec 21 2018 - 21:45:16 CST

Only have time to give an idea.

Use rotations and translation matrices to transform the coordinates of your
system by 60 degrees and some translation.
If I were you I would move my system to the origin, orientate in the x-y
plane and then create rotations of 60 degrees to create the other units.

First one will be rotation of the principle molecule by 60 degree
Second one will be rotation of the principle molecule by 120 degree
..
Last one will be rotation of the principle molecule by 300 degree

In this case you will not have to translate

The orientation part in any plane is important to ensure the correct side
of the monomer forms interactions in the dimer.

Another method could be to find a hexameric beta barrel structure and use
it as a guide. There might be other other methods, but none come to mind at
the moment.

Hope this helps.

On Sat, Dec 22, 2018 at 7:17 AM Prabir Khatua <prabir07chem_at_gmail.com>
wrote:

> Dear VMD users,
>
> I have a monomer protein with antiparallel beta sheets. I want to generate
> a hexamer beta barrel structure using this monomer. Can anyone please
> suggest me how to do it using VMD? It would be really helpful if anyone
> provides me an idea or a script file in doing so.
>
> Thanks,
>
> Prabir
>
> --
>
> *Prabir Khatua*
> *Postdoctoral Research Associate*
> *Department of Chemistry & Biochemistry*
> *University of Oklahoma*
> *Norman, Oklahoma 73019*
> *U. S. A.*
>
>
>
>
>
>
>
>
>
> 

-- 
Best,
/A