First of all thanks both for the advice. I have been trying the use of mdl.energy() to see whether I was able to obtain a more sensible result for the energy of the interface. However, I found out that for using energy more tricky bits seem to be required, starting by an alignment between two sequences. I have tried using bits and pieces from Modeller scripts (importantly , the mutate_model.py script) and produced the following:

https://gist.github.com/daviddesancho/da9dd057cf14cceac1e7e6b8dd0b56e4

Does this seem a reasonable way of calculating interface energies for you? To me it looks unnecessarily complicated considering I am trying to run single point energy calculations for different selections of a structure, so maybe there is a simple route to take.

When it comes to the results, I am confused because it again suggests unfavourable (positive) values for everyone, and particularly for the interface energy of interest.

Really grateful of any advice that you may provide.

David

On 30 Oct 2016, at 02:48, Modeller Caretaker <modeller-care@salilab.org> wrote:

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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