[Biopython] Superimpose description error?

[Mark Livingstone]

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