movie.xyz with vmd

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m.kalavera
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movie.xyz with vmd

Post by m.kalavera » Mon Apr 20, 2009 8:34 am

Hello everybody,
there is a new question about the visualization of the xyz format. If I try to view the movie.xyz in VMD I receive an error message about the first line of the file:

"read) ERROR: xyz file 'movie.xyz' should have the number of atoms in the first line."

I know, that the *.xyz file's should start with the number of atoms in the first row, but I can't look inside the file, because its binary.
How do you watch your movie.xyz files and how should I ?

Thx allot , your M.Kalavera

martin
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Re: movie.xyz with vmd

Post by martin » Mon Apr 20, 2009 8:58 am

Hi,

Sorry that's our fault. The hippo xyz file contains all the simulation data (i.e. the entire topology). It cannot currently be viewed with VMD, which just takes coordinates, but we're working on building an add-in for VMD. You can use analyse.exe to convert your xyz into a PDB movie, which you can use with VMD (or use the pdb movie that hippo creates). This can create somewhat large files, but you can tell it to skip frames.

There is an example on page 15 in the manual.

Hope this helps!
Best wishes,
Martin

m.kalavera
Posts: 29
Joined: Mon Feb 09, 2009 10:58 am
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Re: movie.xyz with vmd

Post by m.kalavera » Tue Apr 21, 2009 7:43 am

Hi Martin,
since yet I have been working with the movie.pdb, but I just got curious about the movie.xyz, because of the small file size and the fact, that your analysis tools use this input as default. So I just wanted to get an inside look for a better understanding of the analysis input.
Thx for your reply and I'm in anticipation of your plugin ,
your M.Kalavera

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