VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Tue Jul 29 2003 - 11:38:15 CDT

Hi,

On Tue, Jul 29, 2003 at 04:43:23PM +0000, J. Rui Rodrigues wrote:
> Dear vmd-l
> In the last few days I've been trying to display some periodic images
> and a couple of questions came up...
>
> After setting a,b,c for every frame, when I pick an atom in the "self"
> cell or in an image cell, VMD always reports the coordinates from the
> self cell.
> However, when I set a bond label between atoms in diferent cells, VMD
> reports a distance.
> Is this distance correct? I mean, am I really getting the distance
> between atoms in diferent cells?

Yes, VMD is taking into account the transformation vector between the
two images.

>
> Apparently it doesn't seem possible to select atoms in an image cell
> within a given distance from an atom in the self cell... but maybe I am
> missing something.

No, that's not possible yet, but certainly a desirable feature.

>
> How can I calculate the minimum distance between my protein and its
> images along a MD trajectory?

At present, I can't offer any concrete suggestions besides creating some
bond labels between possible contacts and monitoring those distances over
the course of the trajectory.

> Displaying periodic images seemed very promising at first glance, but
> unfortunatly it's not taking me to anywhere.
> Can you give me any idea of how this could be done?

This is still a brand new feature in VMD, and we'll definitely be adding
to it as things progress, but developer time only goes so far. We'll
let you and the other vmd-l-ers know when something along these lines
becomes available.

Cheers,
Justin

>
> Thanks,
> Rui Rodrigues
>
> --
> J. Rui Rodrigues
> Departamento de Qu?mica
> Faculdade de Ci?ncias e Tecnologia
> Universidade de Coimbra
> 3004-535 Coimbra
> Portugal
>
> 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys