Hello,
I have been running some experiments attempting to combine two separate domains into a single chain model. To do this, I have the templates of the two domains I am interested in, and align the the sequence to the respective domains. I am then using restraints to bring the two domains together, attempting to replicate the native interface.
However, after initial runs of Modeller, it was clear that the starting domain orientations drastically impacted the resultant models, which appears to be in line with the starting orientation used: http://salilab.org/archives/modeller_usage/2007/msg00039.html , point 1.
After randomising the starting orientations of the two separate domains, in some instances the models can be minimised well, satisfying the added restraints, whereas for other models in unfavourable orientations, these models cannot be minimised and only a few restraints are being satisfied.
Do you have any suggestions for how to get Modeller to re-orientate the domains in these cases where they have unfavourable starting orientations?
Thank you.