[cctbxbb] Best way to compare two structures using cctbx?

[Luc Bourhis]

On 12 Mar 2013, at 18:19, Jan Marten Simons wrote:

> Seems I praised emma a little bit too soon, as this example leads to an 
> exception:
> 
> [...]
> m = emma.model_matches(
>    xs1.as_emma_model(),
>    xs2.as_emma_model(),
>    tolerance=0.5,
>    break_if_match_with_no_singles=False
>    ).refined_matches[0] <<<<<<<<<<<<<<<<<<<<<<<<

You get an "list index out of range" at the point I marked, don't you? That means emma has not found any match. You should always assert that .refined_matches is not empty in production code.

> I've got no idea as to why those two (random) structures cannot be compared. 
> Have I found a bug in emma?

In one of the structure the distance between the 2 scatterers is 1.75 whereas it is 0.06 in the other one. There is therefore no isometry that can map xs1 onto xs2 and emma behaves correctly here.

Best wishes,

Luc