Hi David!
Dope is used to measures the quality of the model. (How PDB-like are some distributions).
Your last line should probably be: s0s1.energy() - (s0.energy() + s1.energy())
Best, Ajasja
PS: You can write '%s:A'%str(2) more elegantly as '%d:A'%2
On 28 October 2016 at 12:31, David De Sancho d.desancho@nanogune.eu wrote:
> Dear Ben > Thanks for the quick response. However I find something really puzzling > for a few tests. Mainly, that interface energy turns out to be unfavourable. > In the link below I include a gist with a self explanatory example of how > this turns out to be. It corresponds to the interface between two helices > in the designed a3D protein but I’ve tried with others too. > https://gist.github.com/daviddesancho/c854203311ec431d0c17fcfff5055e8c > Surely there is something about my selections that’s not right, but any > hints at what’s going on would be very helpful. > Thanks, > > David > > > On 26 Oct 2016, at 22:00, Modeller Caretaker modeller-care@salilab.org > wrote: > > On 10/26/2016 08:41 AM, David De Sancho wrote: > > I’m handling a problem where it is important to evaluate energies of > interfacial residues (e.g. interface residues between two helices in a > protein). In order to carry out this energy evaluation with Modeller, I > start by producing a model for the protein. Then I generate two > selections (e.g. one for each helix). Would it be possible to calculate > the energy for residues in the interface between both selections? > > > Calculating the energy of only the interactions between selections s1 and > s2 isn't possible to do directly in Modeller, but there's a simple > workaround: calculate the energy of the union s1+s2, then subtract the two > energies of s1 and s2 by themselves. You'll probably also want to set > nonbonded_sel_atoms to 2: > https://salilab.org/modeller/9.17/manual/node140.html > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >