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Re: [modeller_usage] Getting alignment positions fixed



Paul Wilhelm Elsinghorst wrote:
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.

I'm not sure I get it - if you already know what your alignment is, why are you asking Modeller to produce a new alignment? You can just provide the existing alignment file to Modeller as an input.

If you're trying to use the salign_fix_positions example, you should use negative rather than positive values for fix_offsets - the defaults are inappropriate for most applications.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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