[Biopython] superimposing problem

[Peter]

On Tue, Dec 7, 2010 at 10:49 PM, George Devaniranjan
<devaniranjan at gmail.com> wrote:
> Thanks João for trying.
> I was also thinking that you would have to deform the 2nd coil to get
> exactly what I want.
>
> What I tried and not completly sussefully but  I will try that agian is as
> follows.
>
> 1) Superimpose 1st residue of coil1 with 1st residue of coil2, rot/tran
> coil2 and get the coordinates---lets call the rot/tran coil2   as mod_coil2
>
> 2) Superimpose last residue of coil1 with last residue of mod_coil2 and then
> rot/tran whole molecule---the result is not exactly what I want but it is
> the only solution I can think of for now.
> Thanks once agin João,
>
> George

Hi George,

Hopefully I have understood your aim, and the following makes
sense...

Have you thought about (in your head - no code needed) trying to
simultaneously try to superimpose the first residues AND the last
residues with a rigid body motion (rotation and translation)?

Assuming you are using just the C-alpha atoms for this. Lets
call these atoms S1, E1 and S2, E2 (start and end). Also
suppose that the distance S1 to E1 is bigger than S2 to E2.
The superposition will  give you S1, S2, E2, E1 on a line in space.
However, the relative rotation of the two loops is free.

So, if using C-alpha atoms,  I think you are going to have to include
at least one pair of atoms from the loop, e.g. M1 and M2 for the
C-alpha of the mid point residue.

However, if you are using more than just the C-alpha atoms, that
should give enough constraints for the superposition to be unique.
It may still not be what you want, in which case try adding more
constraints as above.

Peter