[Molvis-list] loading dimers
Dr. Christoph Gille
christoph.gille at charite.de
Mon Dec 6 10:30:10 EST 2010
The protein file 1M4U has a record of chain A and chain L.
These are the 2 chains of the asymmetrical unit that you described.
When you apply the symmetry operation given in the pdb file then you will see the
four chains of the biological molecule.
Some 3D-programs allow to switch between the biological and the asymmetrical molecule on the fly.
For example in the STRAP multiple sequence alignment program
You will find a pull down menu in the left upper corner of the 3D view.
It offers "Asymmetric unit" and "Biological molecule".
The switch can not only be done interactively but can also be performed by a command in a script
encoded in a HTML-page.
That means the user may click a HTML-element and the view changes between asymmetrical unit and biological molecule.
What 3D viewer are you using?
> I am putting together a tutorial on the Noggin BMP-7 complex (1M4U.pdb). I
> cannot figure out how to load the dimer form of the molecule, when I use
> load 1M4U.pdb; one monomer of each protein shows up. What is the command to
> load the entire molecule? is it possible to switch between the monomer and
> dimer without reloading the file every time?
> Hannah Regan
> Kenyon College '12
> Gambier, OH
> Molvis-list mailing list
> Molvis-list at bioinformatics.org
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