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[modeller_usage] Getting alignment positions fixed



Hi folks,


I have a problem getting the alignment of two sequences the way I want
it to be. Please have a look at this picture to see what I'm looking
for:

http://pwe.no-ip.org/other/modeller.jpg

I'd like to set up my alignment file in a way that the alignment done by
modeller gives exactly this result. I fiddeled with fixed_pos things but
couldn't get it to work, actually I didn't figure out how it really
works. This is the file I have for now:

http://pwe.no-ip.org/other/modeller.txt

If anyone could assist me a little or point me to the right direction
I'd be glad.


Thanks so far,


Paul

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