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
>>> phenixbb@phenix-online.org
>>> 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: terwilliger@LANL.gov
>> 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
>>
>>
>>
>>
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>>

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