Re: [modeller_usage] energy of interface between selections

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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