VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Oct 09 2013 - 17:08:15 CDT

Hi Chris,

There isn't, to my knowledge, one command that will do it. There are
however a set of them that should work just fine:

North
coordtrans [measure inverse [lindex [molinfo top get rotate_matrix] 0]]
[list 0 1 0]
East
coordtrans [measure inverse [lindex [molinfo top get rotate_matrix] 0]]
[list 1 0 0]

The way to unpack the meaning behind these is to work outwards. molinfo
top get rotate_matrix gets the current rotation matrix, measure inverse
will invert that matrix. Then we use coordtrans to multiply this matrix
inverse by the cardinal directions in vector form. In playing with the
results in the clip-plane tool, the command for north will pick up the
top half of the loaded structure in clip-plane, and east will pick up
the right half of the loaded structure (with distance 0). South and west
are just inversions away.

-Josh Vermaas

On 10/09/2013 03:44 PM, 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
> <mailto:akohlmey_at_gmail.com>> wrote:
>
> On Wed, Oct 9, 2013 at 9:25 PM, Chris Knorowski
> <cdknorow_at_iastate.edu <mailto: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 <mailto:akohlmey_at_gmail.com>
> http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
>
> --
> Christopher Knorowski
>
> Iowa State Physics Department