VMD-L Mailing List

From: markt_at_mskcc.org
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
have.

 

Regards,

Tom

 

 

From: Anton Arkhipov [mailto:anton_at_ks.uiuc.edu]
Sent: Tuesday, September 23, 2008 3:37 PM
To: Mark, Tom Z./Sloan-Kettering Institute
Cc: vmd-l_at_ks.uiuc.edu
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
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.

 

Best,

 

Anton.

 

 

On 23 Sep 2008, at 14:04, 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

 

 

 
 
=====================================================================
     
     Please note that this e-mail and any files transmitted with it may
be
     privileged, confidential, and protected from disclosure under
     applicable law. If the reader of this message is not the intended
     recipient, or an employee or agent responsible for delivering this
     message to the intended recipient, you are hereby notified that any

     reading, dissemination, distribution, copying, or other use of this

     communication or any of its attachments is strictly prohibited. If

     you have received this communication in error, please notify the
     sender immediately by replying to this message and deleting this
     message, any attachments, and all copies and backups from your
     computer.