VMD-L Mailing List

From: Olaf Lenz (lenzo_at_mpip-mainz.mpg.de)
Date: Tue Dec 08 2009 - 13:07:39 CST

Jennifer Williams wrote:
> I have attached a word doc where I have tried using snapshots to explain
> what my problem is.

Yes, that is much more helpful, thanks.

> No the chain doesn't have an extension longer than the box size (it is
> in fact fairly short-its just that it crosses the pbc.

Ok, now I see the problem. In fact, your whole bonded structure
stretches the whole box. All atoms belong to one residue. There is no
way the pbc tools can do anything with this structure.
The problem is, that VMD does not support drawing bonds between atoms in
different images. So, the only thing you can do to visualize this
cleanly is to actually replicate the structure in the required directions.
I think a script that does this would be a useful extension to the
pbctools, so if you have problems doing this, I might be willing to put
some work into this tomorrow.

Olaf