Hi Shya,
I'm sorry it is not very clear!  The .ali file looks like this:

You can use an alignment file that sculptor can recognize. This file looks like this (there must be exactly the same number of characters for the target and the template sequences (including dashes for gaps): 
> title text for sequence of target to follow
VDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDD
> title text for sequence of template (supplied PDB) to follow
-AFSGTWQVYAQENYEEFLRAISLPEEVIKLAKDVKPVTEIQQNGSDFTITSKTPGKTVTNSFTIGKEAEIT--TMDG
You can create this with any alignment program, or by using a web server such as http://toolkit.tuebingen.mpg.de/hhpred and this will generate alignments. 

Let me know if that isn't what you need to know!

All the best,
Tom T


On Dec 6, 2011, at 2:36 PM, Shya Biswas wrote:

Hi all,
I was wondering how to generate .ali file that I need to run rosetta MR. I have most of the files for the run except this one. the documentation did not help a lot.
thanks,
Shya
_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb


Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: [email protected]
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss