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

Re: [modeller_usage] clockwise pentamer to anticlockwise model

>        I want to model a pentamer. I have two templates. One of the
> templates is arranged anti-clockwise in the order ABCDE. The other
> template runs clockwise (AEDCB) and has identical chains. Thus if I
> overlap the two templates, subunit B overlaps with subunit E and so on.

Probably the easiest way to do this is to manually edit your clockwise
template to put the chains in the same order as in the desired
anti-clockwise model. It will be essentially impossible to align the two
sequences correctly otherwise. You imply that you tried this already,
but I can't tell why it didn't work for you without more information.

(I'm assuming that your alignment between the two templates is
C-terminus to C-terminus, N-terminus to N-terminus for each chain. If
the sequence in the template is reversed, i.e. C-terminus in template
aligns with N-terminus in model, you would have to manually edit the PDB
to reverse the sequence.)

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage