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
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
Hi Shya, Also you can get the alignment file with phenix.muscle (maybe that is what you were really looking for!): phenix.muscle -in my_two_sequences.dat -out my_alignment.ali where my_two_sequences.dat looks like:
title text for sequence of target (your structure) to follow LVLKWVMSTKYVEAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVEVPIIEKFT AQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPGAEVEVWQILDRYKIIRVKG title text for sequence of template (supplied PDB) to follow qlmdmrd AQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPGAEVEVWQILDRYKIIRVKG qlmdmrd and my_alignment.ali (your .ali file) looks like: title text for sequence of target (your structure) to follow LVLKWVMSTKYVEAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGK RTLSLPVDAQVEVPIIEKFTAQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPG AEVEVWQILDRYKIIRVKG------- title text for sequence of template (supplied PDB) to follow
-------------QLMDMRDAQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPG AEVEVWQILDRYKIIRVKGQLMDMRD I have added this to the documentation. All the best, Tom T
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thanks, this was exactly what I was looking for.
Shya
On Tue, Dec 6, 2011 at 8:20 PM, Thomas C. Terwilliger
Hi Shya,
Also you can get the alignment file with phenix.muscle (maybe that is what you were really looking for!):
phenix.muscle -in my_two_sequences.dat -out my_alignment.ali where my_two_sequences.dat looks like:
title text for sequence of target (your structure) to follow
LVLKWVMSTKYVEAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVEVPIIEKFT AQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPGAEVEVWQILDRYKIIRVKG
title text for sequence of template (supplied PDB) to follow qlmdmrd AQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPGAEVEVWQILDRYKIIRVKG qlmdmrd and my_alignment.ali (your .ali file) looks like: title text for sequence of target (your structure) to follow LVLKWVMSTKYVEAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGK RTLSLPVDAQVEVPIIEKFTAQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPG AEVEVWQILDRYKIIRVKG------- title text for sequence of template (supplied PDB) to follow
-------------QLMDMRDAQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPG AEVEVWQILDRYKIIRVKGQLMDMRD
I have added this to the documentation.
All the best, Tom T
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
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Shya Biswas -
Thomas C. Terwilliger -
Tom Terwilliger