From: Norman Geist (
Date: Fri Jun 10 2016 - 01:55:01 CDT

For visualizytion purpose you want to wrap by using the "-compound" option, eg:

pbc wrap -compound res

Which will keep residues together. Instead of "res" you can also use "fragment" which will keep together everything that has a bond.

Most likely to prevent long bond inside the solute, you can additionally center some part of your system, eg:

pbc wrap -all -compound res -center com -centersel protein

If all that doesn help, you could easily hide atoms outside the unit cell when using coordinate range selections in representations, eg:

protein and x > 0 and x < 40 and y > 0 and y < 40 ...

where 0 and 40 would represent the box bounds.

Norman Geist

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von Irem Altan
> Gesendet: Donnerstag, 9. Juni 2016 17:16
> An:
> Betreff: vmd-l: hiding atoms outside the unit cell
> Hi,
> Is there any way to hide anything outside the unit cell? I have a protein that
> I want to view as “lines,” which means that if I do “pbc wrap,” I get a lot of
> lines resulting from atoms that are placed to the other side of the cell. I
> would like to create periodic images of the protein and hide whatever is
> outside the unit cell. Is this possible?
> Best,
> Irem