Re: [modeller_usage] energy of interface between selections
To: Ajasja Ljubetič <>, David De Sancho <>
Subject: Re: [modeller_usage] energy of interface between selections
From: Modeller Caretaker <>
Date: Sat, 29 Oct 2016 18:48:02 -0700
Cc:
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