Bounding box around xyz data?

[bart...@gmail.com]

Hi everyone,

I've generated some XYZ files of the silicon unit cell and would like to visualize them with the bounding box but not sure how.  I've attached an image from VICS-II, VESTA's forerunner.  Unfortunately, it isn't quite correct: the corners of the box should be located in the center of the 8 outer-most atoms.  Interestingly, JMol does it automatically but because I am generating a document that uses other images from VICS/VESTA, I would prefer to render these consistently.

The xyz file is:

19

SiHex

Si  2.036625  2.036625  3.394375

Si  0.000000  0.000000  0.000000

Si  2.715500  2.715500  0.000000

Si  2.715500  0.000000  2.715500

Si  0.000000  2.715500  2.715500

Si  1.357750  1.357750  1.357750

Si  4.073250  4.073250  1.357750

Si  4.073250  1.357750  4.073250

Si  1.357750  4.073250  4.073250

Si  0.000000  0.000000  5.431000

Si  2.715500  2.715500  5.431000

Si  0.000000  5.431000  0.000000

Si  2.715500  5.431000  2.715500

Si  0.000000  5.431000  5.431000

Si  5.431000  0.000000  0.000000

Si  5.431000  2.715500  2.715500

Si  5.431000  0.000000  5.431000

Si  5.431000  5.431000  0.000000

Si  5.431000  5.431000  5.431000

Thank you!

[Koichi Momma]

There is no concept of "unit cell" in the XYZ file format, and VESTA
treat these data without any conversion.
So, VESTA cannot draw unit cell (bounding box) for XYZ files any more.

To draw bounding box for these data, convert the data by exporting them
to a file format (e.g. CIF) having a concept of "unit cell," and then
open the exported file again.

Best regards,
Koichi

--
Koichi Momma
National Museum of Nature and Science
4-1-1, Amakubo, Tsukuba, Ibaraki 305-0005, Japan
TEL: +81-(0)29-853-8163
FAX: +81-(0)29-853-8998
k-m...@kahaku.go.jp
vest...@gmail.com

[bart...@gmail.com]

Thanks! That's exactly what I needed.