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PostPosted: Fri Mar 01, 2013 12:43 am 
Millimolar User
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Joined: Fri Mar 01, 2013 12:30 am
Posts: 1

Has anyone managed to run animation from .xtc trajectory data from MD simulations?
I am using ePMV (v0.5.145) in Blender 2.62 and I loaded the 1BTA.pdb file from the Tutorials section
( and loaded the accompanying 1BTA.xtc trajectory
data into the Data player tab; the protein states corresponding to simulation frames are ok and scroll-able in
the step/value panel, but I had no luck with actually seeing the simulation/animation happening... :cry:
Anybody could help me with that please?
I would be immensely grateful, as I could really use it for my scientific visualizations.

Thanks in advance!!


I made a small progress - I managed to export my simulation data into .pdb format and load it into Blender
with ePMV and then in Data Player I can now select .model in Data tab; I can now see the different protein
confromation states in the viewport. BUT - I can only see the PointCloud representation being affected, which is
still a bummer, since I cannot render it, nor I can animate it (actually I can, but the atom vertices just fall down
and behave like particle system of some kind).

Also, when I change the protein state/frame the protein PointCloud representation position has now a different
location to its backbone mesh which stays in the centre. Anybody could give me a hint how to link
the two so I can animate it/render its states?

Again - many thanks for help!

PostPosted: Mon Mar 11, 2013 6:05 pm 
Picomolar User
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Joined: Wed Apr 22, 2009 2:08 am
Posts: 235
Hi there,

First of all when dealing with conformation either PDB or xtc, first thing to do is to uncheck the center molecule option in the preferences.
You are right for the xtc, I just find out that this seems to not work in Blender. I will fix that and prepare an update. I think that while I was working on 3dsMax or softimage, I probably change something that blender didnt like. I will let you know once it is fix.


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