VMD-L Mailing List

From: Devanand T (devanand.t.1986_at_gmail.com)
Date: Wed Nov 21 2018 - 00:19:11 CST

On Wed, Nov 21, 2018 at 11:44 AM Monika Madhavi <monikamadhavi_at_gmail.com>
wrote:

> Dear all,
>
> I have a pdb of a parallelepiped unit cell of a solid. I want to create a
> slab of this solid by repeating the unit cell along x,y and z directions.
>
See replicatemol command from topotools. Link:
https://www.ks.uiuc.edu/Research/vmd/plugins/topotools/#TOC-replicatemol-mol-nx-ny-nz-
If your aim is to "create a slab of this solid by repeating", then you
might want to use "addbond" command to covalently bond between atoms at the
interface of cells.

> I can add images of the unit cell in the x,y and z directions by using the
> "Graphics -> Representations -> Periodic" in vmd and by enabling periodic
> images to draw. Is there any method to save the visualization as a pdb? or
> what is the easiest method to create such a pdb from the pdb of the unit
> cell I have?
>
> Thank you.
> Best regards,
> Monika
> --
> W.A.Monika Madhavi
> Lecturer (Probation),
> Department of Physics,
> University of Colombo.
> 

-- 
regards,
*Devanand T*
*SRF (Computational Biology) @ IMSc, Chennai*
*Phone (off) : 91-44-22543108*
*Mobile : 91-9791479561*
*Home Page : www.imsc.res.in/~devanandt/
<http://www.imsc.res.in/~devanandt/>*