VMD-L Mailing List

From: Heather Mayes (hmayes_at_hmayes.com)
Date: Mon Feb 11 2013 - 16:40:22 CST

Dan,

The following xyz format will load in VMD:

3
comment line here
8 2.465768 2.166862 -2.698484
1 2.365184 3.049708 -3.066592
1 3.400463 1.963461 -2.797846

That is, the first line should tell VMD the total number of atoms in
the file, the second line is a comment line, and the remaining lines
have 4 columns: atomic number, then xyz coordinates. It is not picky
about spacing, so if you just add the missing data and lines, your xyz
coordinates will load.

Happy computing,
-Heather

On Mon, Feb 11, 2013 at 9:46 AM, DanLiu <Dan.Liu_at_simap.grenoble-inp.fr> wrote:
> Dear All,
> I'm wondering if it's possible to plot a 3-D structure with only xyz
> coordinates. Or I have to change the file into some other supported format?
> My data is list as follows:
> ⋯⋯
> -2.57811 0 -4.17147
> 0 -4.17147 -2.57811
> 0 -4.17147 2.57811
> -2.57811 0 4.17147
> -4.17147 2.57811 0
> 2.57811 0 -4.17147
> 4.17147 -2.57811 0
> 2.57811 0 4.17147
> 0 4.17147 2.57811
> 0 4.17147 -2.57811
> 4.17147 2.57811 0
> -4.17147 -2.57811 0
> 4.33744 6.91555 2.74408
> 6.91555 2.74408 4.33744
> ⋯⋯
> Thank you in advance.
> Best wishes
> Dan