[modeller_usage] Automatically find gaps in the alignment

Hello,

I am in this situation (last script in the page):

http://salilab.org/modeller/wiki/Missing%20residues

In summary: I have PDB files with short gaps and want to produce gap-less models just from one template each. The models should be identical to the templates except, obviously in the missing regions. I do not care much about the accuracy of the predictions for those regions.

The aforementioned script does exactly that. The problem is that I need to define all the gaps manually.

The question is: can Modeller identify and/or report those gaps (position and length) in order to help us to automatise the task?

If not, are you aware or another tool that does that or should I write an ad hoc script?

Best regards,