On 08/14/2010 05:38 AM, sdh wrote: > I want to model a multi-domain protein. Thus, I aligned manually all > templates (corresponding to the individual domains) and used them as an > input for Modeller. (Note that the templates overlap only over few > residues.) > > However, when I compared the initial model (.ini) to the aligned > templates, I saw that Modeller did something more than just transferring > the coordinates from the templates. Namely, the relative orientation of > domains is not as in my structural alignment. Is thee any way to force > Modeller to use exactly the input coordinates?
Modeller simply transfers the coordinates from templates to the target in regions where there is only a single aligned template. Note that before it does this, however, it checks the alignment for sanity. In so doing, it does a pairwise structural alignment of the templates: http://salilab.org/modeller/9v8/manual/node275.html
If you don't want it to do this, override the automodel.check_alignment() method, e.g.
class MyModel(automodel): def check_alignment(self, aln): pass
a = MyModel(...)
Alternatively, you can supply your own initial model in whatever orientation you prefer: http://salilab.org/modeller/9v8/manual/node26.html
Note that unless you have sufficient overlap between your domains, you won't generate accurate inter-domain restraints, and so you won't necessarily get a good final model even if your initial one looks OK.
Ben Webb, Modeller Caretaker