VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 19 2005 - 15:13:15 CDT

Hi,
  You can just type that command into the VMD text console.
Alternately, you can do that with the mouse by pressing 's' when the
mouse is in the graphics window, which changes the mouse to scaling mode.
When you're finished you can press 'r' again to return to rotation mode.
You can also do this from the Mouse menu. The next version of VMD will have a
nicer centering feature that will make it easier to recenter the view
on a particular structure of interest.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 19, 2005 at 04:08:15PM -0400, Margaret Shun Cheung wrote:
> On Mon, 19 Sep 2005, John Stone wrote:
>
> >
> >Hi,
> > If you've lost molecules to the far reaches of empty space and
> >the simulation isn't using periodic boundary conditions, then you're
> >just going to have to scale down the molecule and crank up the
> >far clip plane to something large. Try reducing the size by 10:
> > scale by 0.1
>
> Thank you, John. This was the case. Please tell me how to do "scale by
> 0.1". Thank you.
> Sincerely,
> Margaret
>
>
> >On Sun, Sep 18, 2005 at 04:11:45PM -0400, Margaret Shun Cheung wrote:
> >>Dear VMD wizards,
> >>
> >>I had a md simulations and molecules slowly drifted away, disappeard from
> >>the screen. I tried to adjust Near clip to 0 and far clip to 30, but
> >>still can't prevent such trajedy.... Please help. Thank you.
> >>
> >>
> >>Margaret S. Cheung,
> >>Ph. D. Postdoctoral Fellow,
> >>
> >>------------------------------------------------------------
> >>Room 2117 Tel: (301) 405-4892
> >>Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> >>University of Maryland http://glue.umd.edu/~mscheung
> >>College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> >>------------------------------------------------------------
> >
> >--
> >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
> >
>
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Room 2117 Tel: (301) 405-4892
> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> University of Maryland http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------ 

-- 
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