[MMTK] Using MMTK

Matias Saavedra matias_saavedra at yahoo.com
Mon Jul 18 22:31:59 CEST 2005






> No. A reduction, yes, but not a big one. The slowest
> part of  
> minimization for normal modes is the final one,
> which goes to high  
> precision. All of that is lost when you use PDB
> files.
Ok, i'm totally convinced of that now.

> However, it is possible to do whatever you do to PDB
> files to in-memory  
> configurations. There is some code for mutating
> residues (used  
> internally for cysteins), but there is also the
> possibility of building  
> a representation of the new chain and then copy over
> the positions from  
> the previous one atom by atom.
I have been looking in the mailing list and the
documentation, but i can't find a way to modify
(mutate) a residue. Could you tell me where can i find
that information?, Or give a short code example?

I want to transform every residue to alanin... so for
most of them, i just need to erase everything after
the Cb (beta-carbon)... but with glycin i need to
recalculate the coordinates of the newly added Cb...
and of course, add this atom to the system. Until now
i have been using a Biopython script to calculate the
new coordinates throug a rotation of N atom.

I need a little help  in the mutating code to start
working.

Thanks a lot Konrad.



		
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