[Biopython] Superimpose description error?

[João Rodrigues]

Hey Mark,

Indeed it is wrong the other way.

Well, Id say it depends what you are looking at. You can trim all
selections to bb + cb/h (gly) so that you always have the same number of
atoms. That is what we do here for mutant analysis.
you can also code to iteratively add side chain carbons until the wt and
mutant no longer match. This would give you a better description of the
side chain orientation.
No dia 2 de Ago de 2012 06:42, "Mark Livingstone" <livingstonemark at gmail.com>
escreveu:

> Hi Guys,
>
> In Bio.PDB.Superimpose,  it says:
>
> set_atoms(self, fixed, moving)
> Put (translate/rotate) the atoms in fixed on the atoms in moving, in
> such a way that the RMSD is minimized.
>
> Aren't the words fixed & moving in that description round the wrong way?
>
> In my research at present I am using a curanted set of 2,141 pairs of
> PDB files curated because they have only 1 mutation. Unfortunately,
> because Superimpose counts atoms before alignment, only 9 / 2,141 PDB
> pairs will align using the example shown in Superimpose.py source
> code.
>
> The way I have gotten around this is for each of the two PDBs to make
> a List of the CA atoms and the align these lists. Not optimal, but
> seems to work.
>
> The only other way I can see would be to get a full list of atoms then
> snip out the mutation side chain atoms allowing Superimpose to work as
> per the source code example - also not optimal but close.
>
> I am doing this because I am experimenting with different ways of
> using RMSD, so the better I get the alignment, the better my results -
> even if it is only different in decimal place differences. Are there
> any better approaches?
>
> Thanks in advance,
>
> MArkL
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>