[modeller_usage] Automatically find gaps in the alignment

[Edelmiro Moman <moman AT prosciens.com>]

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,

--
Edelmiro Moman, PhD
ProSciens, computer-aided drug design
2-4 rue du Palais de Justice
L-1841 Luxembourg

Phone  : +352 2728-2588
E-mail : moman AT prosciens.com
http://prosciens.com