From: Anton Arkhipov (
Date: Tue Sep 23 2008 - 14:37:15 CDT

Hi Tom,

Just a few days ago I helped another person to write a simple script
that does something that can be of use in your case. Basically, you
need to prepare a file that contains frames of your "trajectory", and
for each frame it has the same number of "particles" - 300 in your
case. Then, for those particles (cells) that do not exist at a given
frame yet, you just set their coordinates to something very far away,
so that when you look closely at your embryo those cells cannot be
seen. This is a simple hack that can work well for visualization and
for many types of analysis.

Maybe someone on the list knows a better solution...

If you are interested, please let me know, I will send you the script
then and tell how to use it.



On 23 Sep 2008, at 14:04, 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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