VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 21 2005 - 13:22:07 CDT

Hi,
  The only way (in VMD 1.8.3) to clip an isosurface is to use the
6 user-defined clipping planes, either with the help of the clipping
plane tool found in:
  Extensions->Visualization->Clipping Plane Tool
or with the use of the 'mol clipplane' commands.

You could also cut down your density map using one of the many
map processing tools out there, as VMD 1.8.3 doesn't do that.
If I find a free afternoon to do the work, it shouldn't be too hard
to add a few more map processing features to VMD 1.8.4 before release.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 19, 2005 at 08:41:39PM -0400, Demetrios Braddock wrote:
> Hi John,
> I can now display my ccp4 map file. I simply changed the
> extension to .ccp4 and used the mol addfile command as you suggested,
> and it loaded in fine. I am trying to display a wireframe isosurface
> around a line representation of my model. I am able to get it up, but
> the boundry is too large for viewing clearly. Is there a handy way of
> reducing the boundry size of the isosurface view?
> Thanks,
> Demetrios
> --
> Demetrios Braddock MD, PhD
> Assistant Professor of Pathology, Yale University School of Medicine
> 404A Lauder Hall
> 310 Cedar Street
> New Haven, CT. 06510
> Office:203-737-1278
> Fax:203-785-6899
>
>
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-- 
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