VMD-L Mailing List

From: jen hsin (jhsin_at_ks.uiuc.edu)
Date: Wed Aug 12 2009 - 15:02:15 CDT

Hi Steve,

Are you using the mouse modes to move your proteins? If you use the
"Translation/Rotation/Scale" modes, you only move the camera view of
the protein and not its atomic coordinates, so once you reset the view
everything goes back to the same view. To actually change the
position of your protein, one uses the "Move" mode of the mouse (Main
Window -> Mouse -> Move -> 8 Molecule), or the "move/moveby" commands
in TkConsole.

Cheers,
Jen

On Aug 12, 2009, at 2:48 PM, Steve Seibold wrote:

> I have constructed a pdb model of a compound and am trying to place
> it in my protein. When I do this I open up both protein pdb and my
> compound pdb simultaneous in VMD. The problem is when I try to
> position the compound into the pocket of the protein. I cannot seem
> to move it closer in the sense that no matter how long I freeze the
> protein and move the compound it never appears to get closer. Is
> this just because it is VERY difficult or is there some barrier to
> doing this. I attempted it for quite some time and could never get
> the compound positioned correctly. Is there a way to do this with
> VMD. I am using the WINDOW version.
>
> Thanks, Steve
>
>
>