[Chimera-users] PB lines visualization

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 22 09:54:28 PDT 2015


Sorry, there is no feature to automatically show a trajectory’s periodic boundary box.

If it is a fixed-size box and you know the coordinates of the corners, you could create a simple input file describing the box and then open it in Chimera.   Possible file types include PDB (a fake molecule with “atoms” at the corners and “bonds” forming the edges) or BILD, a simple text format for geometric objects:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>
However, you’d have to do the work of creating the file yourself.

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 21, 2015, at 6:01 PM, Sana Saeed <bioinformatic.lady at yahoo.com> wrote:

> is it possible to visualize periodic boundary lines (solvated box) in chimera. 




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