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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