VMD-L Mailing List

From: Lutz Maibaum (lutz.maibaum_at_gmail.com)
Date: Wed Jun 20 2007 - 23:19:01 CDT

On Wednesday 20 June 2007 19:56, Jordi Cohen wrote:
> There might indeed be an error in the volmap docs, I'll go fix it.

Great, thanks.

> To get a minmax, volmap takes your selection's size and pads it by a
> certain amount that is selection- and maptype-dependent (e.g., 3-
> sigmas for density maps). This is absolutely necessary to always get
> properly-looking maps.

Just out of curiosity, why would that be? And this brings me to a related
question: does the volmap computation take into account periodic boundary
conditions? In other words, does the Gaussian weight of each atom "wrap
around" periodic boundaries?

> To accomplish what you want, you may wish to try something like this
> (i don't have VMD in front of me, so I'm hoping it will work as-is):
>
> set sel [atomselect top all]
> volmap density $sel -minmax [measure minmax $sel]
>
> or something of that order...

Thank you for the suggestion, I will give it a try.

  Lutz