VMD-L Mailing List

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Tue Sep 23 2008 - 15:03:01 CDT

OK, I'll send it to you off the list....

Anton.

On 23 Sep 2008, at 14:54, markt_at_mskcc.org wrote:

> 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.
>
>