VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Jan 03 2010 - 02:23:41 CST

Hi,
  I believe the issue here is that the 3GBI structure contains only
one subunit, to get the other two displayed in VMD, you need to process
the BIOMT records that are found in the REMARKS fields of the PDB file,
and apply the required transformation matrices to generate the other two
instances. This is doable in an automated way using the "mono2poly"
VMD script posted here:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/mono2poly/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Dec 29, 2009 at 10:41:23PM +1100, Burak Cankurtaran wrote:
> 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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