VMD-L Mailing List

From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Tue Sep 23 2008 - 14:48:30 CDT

As I understand, VMD cannot deal with trajectories
with varying number of atoms. What you can do
is to create "fake" coordinates for the cell centers in each
frame, choosing them in such a way that they do no appear
in your system (for example, put very large coordinates).
When the coordinates become reasonable, as they are
substituted by the true ones, the "cells" will appear in
your visualization.
Another way would be to use a pdb file with B-factors,
for example, 0.00 for existing cells and 1.00 for non-existing
ones. Then your selection (updated every frame) could
be beta < 1.0. This would show at each frame only
the existing cells. But you need to create "fake" coordinates
for the non-existing cells anyway.
Leandro.

On Tue, Sep 23, 2008 at 4:04 PM, <markt_at_mskcc.org> wrote:

> Hi, I want to use VMD to view an embryo of c elegans as it develops from
> 4 to 300 cells.
>
> I have the xyz coordinate for each cell center each minute. Cells divide
> so my system has a non-constant
>
> Number of particles.
>
> Is it possible to do it , if so how?
>
> Thanks
>
> Tom Mark
>
> Dr. Zhirong Bao Lab
>
> Developmental Biology Dept.
>
> Memorial Sloan-Kettering Cancer Center
>
>
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