VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Sep 23 2008 - 15:10:02 CDT

On Tue, 23 Sep 2008, Anton Arkhipov wrote:

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

not necessarily better, but different:
just create single pdb files for each frame
and then load them into individual molecules
and use the multi-mol animation plugin to
animate them (and clone reps to copy the visualization
of one to all).

http://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/

cheers,
   axel.

AA>
AA> If you are interested, please let me know, I will send you the script then
AA> and tell how to use it.
AA>
AA> Best,
AA>
AA> Anton.
AA>
AA>
AA> On 23 Sep 2008, at 14:04, markt_at_mskcc.org wrote:
AA>
AA> >Hi, I want to use VMD to view an embryo of c elegans as it develops from 4
AA> >to 300 cells.
AA> >
AA> >I have the xyz coordinate for each cell center each minute. Cells divide
AA> >so my system has a non-constant
AA> >
AA> >Number of particles.
AA> >
AA> >Is it possible to do it , if so how?
AA> >
AA> >
AA> >Thanks
AA> >
AA> >Tom Mark
AA> >
AA> >Dr. Zhirong Bao Lab
AA> >
AA> >Developmental Biology Dept.
AA> >
AA> >Memorial Sloan-Kettering Cancer Center
AA> >
AA> >
AA> >
AA> >
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AA> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.