[MMTK] Missing positions

[Konrad Hinsen]

On Mar 15, 2006, at 15:45, vanitha at cs.wisc.edu wrote:

> Just wondering... how does one deal with missing positions in a PDB? I
> viewed a PDB that had missing positions in Swiss PDB Viewer that
> automatically filled them in. I then did a "Save Layer" but that  
> didn't
> help. I'm currently looking at the file 1AVX.pdb that has two  
> chains. Any
> thoughts will be greatly appreciated!

I don't think there is a single optimal way to deal with missing  
positions. It all depends on why the positions are missing and what  
your criteria for a good reconstruction are. MMTK does not try to  
fill in anything except for hydrogen positions.

For the next most common case of incomplete sidechains, you could try  
to take the coordinates of a fully defined sidechain of the same type  
(even from another protein) and superpose its backbone part to the  
backbone section in your destination protein. You could then copy  
over the sidechain atom positions. However, this will likely produce   
rotamers that are energetically unfavourable. If the sidechain is not  
that important for your purposes, you might prefer to "amputate" the  
missing part and thus convert the residue to a different one. But  
that's a decision that no program can take for you.

Konrad.
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Konrad Hinsen
Laboratoire Léon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: konrad.hinsen at cea.fr
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