[Biopython] Superpose structures...

[Christian Schäfer]

So, what you want to do is to superpose two structures by minimizing the 
RMSD between aligned residues and after that calculating the RMSD 
between two residues? Is that right? If so, ProFit is able to do that. 
Superimpostion is done by the ZONE command (which then returns the 
overall RMSD over the aligned regions after superimpostion); and 
calculating the RMSD between specific residues (after superimposition) 
is done via the RZONE command. You can even chose which kind of atoms to 
consider for RMSD calculation with the ATOMS and RATOMS commands.
I'm not sure if something that specific could be done with plain 
BioPython. But again, you can always write a wrapper for the ProFit part 
in Python.

Chris

On 12/24/2009 04:37 PM, Yasser Almeida Hernández wrote:
> I know i made that question already but this time is a quite different.
> I already superpose the structures (Profit isn't so suitable for my
> project), but now i want to compute the RMSD betweeen 2 residues in the
> superposed position. When i do that, the RMSD that i get is the same
> that if i superpose the structures according to that residue, and what i
> really want is the "deviation of 2 residues when its structures are
> superposed according to its binding sites residues", and i want to know
> how to do that in Biopython...
>
> Thanks
>