Date: Tue Sep 23 2008 - 14:54:19 CDT

Thanks Anton


It sounds like a good Idea, I'll also take a look at the script you






From: Anton Arkhipov []
Sent: Tuesday, September 23, 2008 3:37 PM
To: Mark, Tom Z./Sloan-Kettering Institute
Subject: Re: vmd-l: viewing an embryo


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


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?



Tom Mark

Dr. Zhirong Bao Lab

Developmental Biology Dept.

Memorial Sloan-Kettering Cancer Center



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