VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 08 2008 - 11:25:47 CDT

Hi,
  After you've modified the atom coordinates with "$sel move $M1",
VMD does not reposition the center of rotation for the interactive display.
If you want to reset the center of rotation for the interactive display,
you would either use the command "display resetview" or press the "="
key both of which have the same effect of causing VMD to auto center
the displayed structure based on computing a new bounding box for the
atoms in the molecule.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 08, 2008 at 01:22:40PM +0300, Anneta Tzampazi wrote:
> Hello again and thank you for your immediate support. I am writing because I
> have encountered a problem concerning the rotation of my protein. I want to
> study the albumin adsorption onto a graphite surface and my Professor and I
> came up with the following idea: we will calculate the hydrophobicity of the
> surface of my molecule and select the part of this surface which is more
> hydrophobic, which will probably be the right conformation for my protein
> and will interact with the graphite surface. In order to do so, we thought
> that rotating the molecule round each axis and estimating the Van der Waals
> forces will provide me with the information I need. But I have not succeeded
> yet in rotating the molecule with exactly the way I want it. I need the
> molecule to rotate round its geometrical centre and I tried via VMD to do
> this. So, I followed these steps:
>
> 1) set sel1 [atomselect top all] , to select the whole molecule
> 2) set gc [measure center $sel1] , to get the {x y z} of the geometrical
> centre
> 3) set M1 [trans offset $gc] , to set both the offset and centering matrices
> to the coordinates of my geometrical centre
>
> After these, when I use the command $sel1 move $M1 my protein shows up
> somewhere in the screen and its rotational behaviour is not the behaviour I
> want. I could use all the help you can give. I need my molecule to rotate
> round its geometrical centre and round each one of the three axes. Thank you
> in advance once again.
>
> Yours,
> Anneta 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078