VMD-L Mailing List

From: Burak Cankurtaran (Burak.O.Cankurtaran_at_alumni.uts.edu.au)
Date: Tue Dec 29 2009 - 05:41:23 CST

Hi,

I'm trying to visualise the dna structure 3GBI from the protein databank.
VMD shows only one of the dna strands, while there are three all together.
When I view the strucutre using the jmol viewer on the protein databank site,
there is an option to show each model separately or all 3 models at once.
I have no experience with the PDB file format, but the 3 models seem to correspond
to the three dna strands within the one pdb file.

How can VMD show the full structure?

Also, I have no experience with biological molecules either. I'll will want to
relax the geometry at a later stage. So, VMD has an option to add water
molecules surrounding the structure. Are the water molecules placed
in a random fashion or are there smarts built into the method? If
I did relax the geometry, will the water molecules and the structure
be close to a minimum?

Thanks
Burak

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