[Biopython] superimposing problem

[George Devaniranjan]

Hello Peter,
Thank you for your suggestion.
I am using CA/C/N/O  for superimposition of S1/S2 and E1/E2.

Not sure I got exactly what you meant but I am going to think about it
tonight  and see if that makes sense.

The idea that I am trying to see is ---if 2 coils from diff protein have
approximately the same length (S1-E1  = S2-E2 distance) and have the same
number of residues what is the "floppiness" or (no of conformations) that
you can see.

So as in my figure I sent (reattached) it does not matter where the
intermediate residues are they can flop about.
Thanks I will think about this more in the next few days.
Regards,
George



On Tue, Dec 7, 2010 at 6:00 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> 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
>
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