VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 05 2004 - 14:12:41 CDT

Dear Jacqueline,
  The 'mol clipplane' command is a new feature that has been undergoing
various changes, so we've been reticent to put much effort into documenting
it. As yet, it is only a text command and has no GUI counterpart.
The implementation in VMD 1.8.2 is simple and basically allows you to:
 - enable up to 6 user-defined clip planes
 - each clip plane has a status of '0' for off, '1' for on
 - each clip plane has an origin, and a normal direction which together
   completely specify its orientation.

We have changed some things in VMD 1.8.3 which alter the behavior
of clipping planes, even with the same parameters. If you just want
to use the implementation in 1.8.2 for the short-term, I can help you
use it.

Essentially, you enable a clipping plane like this:
  mol new 1e79
  mol clipplane center 0 0 0 {0 0 0}
  mol clipplane normal 0 0 0 {1 0 0}
  mol clipplane status 0 0 0 1

That'll get you started for now.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 02, 2004 at 01:48:26PM -0600, Jiancong Xu wrote:
> Hi, folks,
>
> This may be a stupid question, but I hope somebody can help me with this.
>
> I really don't know how the 'mol clipplane' works though I checked out the
> manual page on 'mol' where only the formats of this command are given. I
> woner somebody can explain a bit to me.
>
> Thanks so much,
>
> Jacqueline
>
> ============================
> Henry Eyring Center for
> Theoretical Chemistry
> University of Utah 

-- 
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