Hi 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 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 > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage