RE: [PyMOL] Reconstructing selections

> i) Is there any guarantee that atoms are stored internally in 
> the same order that they appear in the PDB file?

set retain_order
sort

However, that's not really necessary:

> ii) If so, is there any way to directly construct a selection 
> containing e.g. atoms 1,3,8,10,11... of a given object?

select my_sel, my_object and id 1+3+8+10+11

> ... and of course any other comments or advice are most welcome!

In addition to "id" there is a new operator "rank" (0.98beta+) which gives
the literal order in the input source.  "id" actually uses the PDB atom
ids...which can be a problem with PDB files that don't have IDs.

Cheers,
Warren