[MMTK] atom index in normal modes

khinsen at cea.fr khinsen at cea.fr
Thu Jul 21 09:16:17 CEST 2005

On 21.07.2005, at 01:26, OMAR NABEEL ALY DEMERDASH wrote:

> Hello,
> What is the easiest way to determine the C-alpha to which each ordered
> triple of a normal mode corresponds, using the pdb residue indices for
> the C-alphas?

There is no way at all in general, because there are so many ways to  
construct a system using zero, one, or several PDB files.

However, if your system contains all the C-alphas from a single PDB  
file, and nothing else, then you can rely on the order of the C-alphas  
being the same as in the PDB file.  You could then use an in-memory  
representation of the PDB file (MMTK.PDB.PDBConfiguration) to identify  
the PDB atom numbers corresponding to each residue.

However, please be sure that this is really what you need. I have  
worked with C-alpha normal modes for eight years and I have never  
needed any such tricks. The only reason I see for referring to PDB atom  
or residue indices is to exchange data with other programs that are  
very PDB-centric. In the context of normal modes analysis, it is  
usually easier to reproduce the functionality of such programs in a few  
lines of Python code than to work on elaborate interfaces.

Konrad Hinsen
Laboratoire Leon 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: khinsen at cea.fr

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