VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 29 2004 - 13:49:52 CDT

Jim,
  From your followup email, it sounds like you want to force your
structure to be wrapped around the periodic cell boundary. There's a
Tcl script in the script library that Jan Saam wrote for this purpose.
It might meet your needs, give it a try:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcwrap/

Another option would be to pre-wrap your coordinates using other external
tools before loading your structure into VMD.

  John

On Thu, Apr 29, 2004 at 02:41:23PM -0400, Jim Shepherd wrote:
> I think either you are misunderstanding the original question or that I
> am misunderstanding your answer. When importing a polymer molecule that
> extends beyond the periodic boundary, the molecule is displayed
> extending outside the cell. This leaves its corresponding location on
> the other side of the same cell vacant. This behavior can make it
> difficult to see the interactions of the molecule with its neighbors in
> the primary cell. Is there a way to have VMD display the portions of a
> molecule that extend over a boundary in the other side of that cell so
> that primary cell will be completely filled and no molecules will be
> displayed outside of this cell? My interpretation of your answer is
> that it states how to display multiple cells. While this would fill in
> all of the vacancies of the middle cell, that middle cell would then be
> difficult to visualize because of the surrounding cells. Maybe multiple
> cells could be displayed per your suggestion and then clipping planes
> could be set up to "remove" the neighboring cells from the display?
>
> Thanks for your suggestions.
> -Jim
>
> On Thu, 2004-04-29 at 10:56 -0500, John Stone wrote:
>
> > Hi,
> > If you load the Amber files with the "crdbox" version of the crd
> > reader plugin, it should correctly load your file. Once loaded,
> > you should be able to use the controls in the "periodic" tab to
> > see additional periodic cell images. The main issue is correctly
> > loading your Parm/CRD files. You didn't specify which version of
> > Amber you're using, just make sure to use the "parm7" for Amber 7.x
> > and "parm" for the older versions.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Apr 28, 2004 at 11:25:09AM -0400, Xiang, Tian-Xiang wrote:
> > > Dear Sir:
> > >
> > >
> > >
> > > I have an Amber coordinate .crd file with box conditions. How can I
> > > display the molecules in the center box
> > >
> > > along with those in the neighboring image cells. Since my system is a
> > > polymer, many polymer segments extend
> > >
> > > beyond the center box such that the system displayed contains many
> > > artificial holes. If I can also display the image cells, maybe
> > >
> > > the holes can be filled this way. In all, I want to display an image
> > > fully filled with the molecules without artificial holes.
> > >
> > >
> > >
> > > Any suggestions are appreciated.
> > >
> > >
> > >
> > > Xiang
> > >
> > >
> > >
> >
> > --
> > 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 

-- 
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