VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 09 2013 - 15:55:12 CDT

Chris,
  If you already know the direction you want to to apply the
clipping plane in from a vector, you can also use VMD the
"mol clipplane" text commands to define the clipping planes
yourself, or with your own small script rather than doing it
in the GUI using the clipping plane tool plugin. Have a look
at that and let us know if that's what you need or if you still
have questions.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 09, 2013 at 03:44:53PM -0500, Chris Knorowski wrote:
> Thanks Axel,
> The problem is I am rotating the screen, the planes that I would like to
> cut are not necessarily in the x,y,z direction. Using the clipping tool
> you can set it so that the normal to view is clipped but it is just not
> very easy to line up correctly. Its much easier to line it up so that the
> plane I want to clip is perpendicular to the view (in orthographic). I can
> calculate the vector to clip but it isn't straightforward to do,
> especially when I want to do it on a lot of differently oriented crystals.
> I guess I'm asking if there is a command that outputs what the current
> north, south or east vector in the display window is.
> Thanks,
> Chris
>
> On Wed, Oct 9, 2013 at 3:19 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> On Wed, Oct 9, 2013 at 9:25 PM, Chris Knorowski <cdknorow_at_iastate.edu>
> wrote:
> > Dear all,
> >
> > I have a quick question about vmd. I am using the clip tool to aid in
> > visualizations of crystal structures. I'm wondering if there is a
> quick way
> > to figure out what direction in vmd the image is oriented so I can
> plug that
> > into the clip tool. For example, I'd like to be able to clip the
> plane
> > whose normal is straight up (not the normal to the view).
>
> Display->Axes
>
> if you don't rotate. x is to the right, y is up and z is toward you.
>
> axel.
> >
> > Thanks,
> > Chris
> >
> >
> > --
> > Christopher Knorowski
> >
> > Iowa State Physics Department
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>
> --
> Christopher Knorowski
>
> Iowa State Physics Department 

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