PDB:4DMN is a HIV-1 integrase structure with a bound ligand (PDB:0L9).  i want to bring this ligand into alignment with another, reference structure PDB:3AO1.

i can do alignments of the two structures, and i can identify the ligand's heteroatoms by checking the residue.get_full_id() tags.  but there are obviously no CA atoms to associated with the ligand to use as references for `Superimposer` to use for alignment.  So i figure i need to do it in two steps: first align the two structures, then use the transform found by `Superimposer` on the ligand. 

but i don't know how to do the second bit?  thanks for any hints,

  Rik

Hi there,

Cross-posting from the Biopython mailing lists. 

Superimposer() will give you the rotation/translation matrix you need to superimpose the two structures. Then you just need to apply them selectively to the atoms you want (with Superimposer.apply). 

This script posted on [github][1] will do this and an additional sequence alignment step necessary when the two proteins are not exactly the same, in order to get matching atoms to perform the superimposition on. 

  [1]: https://gist.github.com/JoaoRodrigues/e3a4f2139d10888c679eb1657a4d7080