On 10/28/16 5:04 AM, Ajasja Ljubetič wrote: > Dope is used to measures the quality of the model. (How PDB-like are > some distributions).
DOPE is a pairwise atomistic statistical potential so it reports how PDB-like is each atom-atom interaction. So you can certainly use it to score a subset of a model. That said, I'm not sure that the difference between two DOPE scores necessarily makes sense, particularly if your proteins are not PDB-like.
*Normalized* DOPE, on the other hand, is a z score obtained by fitting DOPE scores for entire chains, so it doesn't make sense to use it for a subset.
> PS: > You can write'%s:A'%str(2) more elegantly as '%d:A'%2
Or even more elegantly as '2:A' ;) I assume the gist is a cut down version of a more flexible script. Residue numbers in Modeller include the insertion code, so are technically strings (e.g. '5B' is a perfectly valid residue number).
Note that you can also trivially calculate s0s1, the union of s0 and s1, with
s0s1 = s0 | s1
(no need to create a new selection).
Otherwise, the script looks fine to me.
Ben Webb, Modeller Caretaker