VMD-L Mailing List

From: Jim Shepherd (jimshep_at_mindspring.com)
Date: Thu Apr 29 2004 - 13:41:23 CDT

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