[Biopython] aligning a bound ligand from one PDB complex to a reference structure?

[R. K. Belew]

thanks so much João!  and of course: i can apply the transform
to ALL the mobile structure's atoms, THEN filter for the ligand's atoms.
thanks again for this hint.  - Rik

On 6/4/16 3:39 PM, João Rodrigues wrote:
> Hi Rik,
>
> From what I understand, you just want to align the structures (including
> the ligand) based on the protein only. The align command in Pymol is
> deceptively simple. To replicate this in Biopython you need a sequence
> alignment, to find the matching pairs between the two structures,
> followed by a superimposition based on this matching.
>
> I wrote a small script that does what I think you
> want: https://gist.github.com/JoaoRodrigues/e3a4f2139d10888c679eb1657a4d7080
>
> The trick is basically to get the rotation matrix (from Superimpose)
> based only the CAs and then apply that transformation on every atom of
> the second (mobile) structure. In you case, apply the transformation
> necessary to align all the CAs of 4DMN onto those of 3AO1 to all atoms
> of 3AO1.
>
> Let me know if you have questions.
>
> Cheers,
>
> João
>