[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] initial model



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
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage