VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 29 2004 - 13:52:17 CDT

I forgot to mention that in order to try the PBCWrap script,
you'll have to make a fake "xst" file since that script was
originally written for use with NAMD. If that isn't convenient,
you might have a look and see if Thomas Cheatham's 'ptraj' utility
can wrap coordinates for you before you load up the structure into VMD.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 29, 2004 at 01:49:52PM -0500, John Stone wrote:
>
> 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 

-- 
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