VMD-L Mailing List

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Wed Aug 12 2009 - 15:11:00 CDT

Hello
Thanks for the response.
I am using the mouse. Basically I toggle "F" in the "VMD Main" menu and freeze one molecule and move the other with respect to the first using "translate, rotate". I guess this is not really moving the pdb coordinates. I am not sure how else to do it. I don't know how do use the "move" mode using the mouse or the move/moveby in the TKconsole. Is there a tutorial that would show me these tools? I looked on-line but could not find anything pertinent. Did I miss it? Can you direct me to it if it exist. I would be happy to learn by trial and error in the tutorial.

Thanks, Steve

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Wednesday, August 12, 2009 3:59 PM
To: Steve Seibold
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: positioning of a compound

Hi,
  Are you moving the atom coordinates manually using the
Mouse->Move->Molecule menu, or are you using atom selections for this
purpose?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 12, 2009 at 03:48:23PM -0400, 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
>
>
>
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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