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

[João Rodrigues]

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


2016-06-04 12:13 GMT-07:00 R. K. Belew <rbelew at ucsd.edu>:

> Sorry, this is a [repost from BioStars](https://www.biostars.org/p/195014/);
> no response there(:
>
> 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?
>
> PS:  poking at PyMOL,  i seem to be able to do what i want using its
> `matrix_copy` command:
>
>     extract 4dmn_0L9, 4dmn and organic
>     align 4dmn////CA, 3ao1////CA
>     matrix_copy 4dmn, 4dmn_0L9
>
> but i want to do it in bioPython!
>
> thanks for any hints, Rik
>
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