<div>Thanks, this was exactly what I was looking for.</div><div>Shya<br><br></div><div class="gmail_quote">On Tue, Dec 6, 2011 at 8:20 PM, Thomas C. Terwilliger <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>></span> wrote:<br>
<blockquote style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left-color: rgb(204, 204, 204); border-left-width: 1px; border-left-style: solid;" class="gmail_quote">Hi Shya,<br>
<br>
Also you can get the alignment file with phenix.muscle (maybe that is what<br>
you were really looking for!):<br>
<br>
phenix.muscle -in my_two_sequences.dat -out my_alignment.ali<br>
where my_two_sequences.dat looks like:<br>
> title text for sequence of target (your structure) to follow<br>
LVLKWVMSTKYVEAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVEVPIIEKFT<br>
AQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPGAEVEVWQILDRYKIIRVKG<br>
<div class="im">> title text for sequence of template (supplied PDB) to follow<br>
</div>qlmdmrd AQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPGAEVEVWQILDRYKIIRVKG qlmdmrd<br>
and my_alignment.ali (your .ali file) looks like:<br>
> title text for sequence of target (your structure) to follow<br>
LVLKWVMSTKYVEAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGK<br>
RTLSLPVDAQVEVPIIEKFTAQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPG<br>
AEVEVWQILDRYKIIRVKG-------<br>
<div class="im">> title text for sequence of template (supplied PDB) to follow<br>
</div>------------------------------------------------------------<br>
-------------QLMDMRDAQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPG<br>
AEVEVWQILDRYKIIRVKGQLMDMRD<br>
<br>
<br>
I have added this to the documentation.<br>
<div class="HOEnZb"><div class="h5"><br>
All the best,<br>
Tom T<br>
<br>
>> Hi Shya,<br>
>> I'm sorry it is not very clear! The .ali file looks like this:<br>
>><br>
>> You can use an alignment file that sculptor can recognize. This file looks<br>
>> like this (there must be exactly the same number of characters for the<br>
>> target and the template sequences (including dashes for gaps):<br>
>>> title text for sequence of target to follow<br>
>> VDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDD<br>
>>> title text for sequence of template (supplied PDB) to follow<br>
>> -AFSGTWQVYAQENYEEFLRAISLPEEVIKLAKDVKPVTEIQQNGSDFTITSKTPGKTVTNSFTIGKEAEIT--TMDG<br>
>> You can create this with any alignment program, or by using a web server<br>
>> such as <a href="http://toolkit.tuebingen.mpg.de/hhpred" target="_blank">http://toolkit.tuebingen.mpg.de/hhpred</a> and this will generate<br>
>> alignments.<br>
>><br>
>> Let me know if that isn't what you need to know!<br>
>><br>
>> All the best,<br>
>> Tom T<br>
>><br>
>><br>
>> On Dec 6, 2011, at 2:36 PM, Shya Biswas wrote:<br>
>><br>
>>> Hi all,<br>
>>> I was wondering how to generate .ali file that I need to run rosetta MR.<br>
>>> I have most of the files for the run except this one. the documentation<br>
>>> did not help a lot.<br>
>>> thanks,<br>
>>> Shya<br>
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>><br>
>><br>
>> Thomas C. Terwilliger<br>
>> Mail Stop M888<br>
>> Los Alamos National Laboratory<br>
>> Los Alamos, NM 87545<br>
>><br>
>> Tel: <a href="tel:505-667-0072" value="+15056670072">505-667-0072</a> email: terwilliger@LANL.gov<br>
>> Fax: <a href="tel:505-665-3024" value="+15056653024">505-665-3024</a> SOLVE web site: <a href="http://solve.lanl.gov" target="_blank">http://solve.lanl.gov</a><br>
>> PHENIX web site: http:<a href="http://www.phenix-online.org" target="_blank">www.phenix-online.org</a><br>
>> ISFI Integrated Center for Structure and Function Innovation web site:<br>
>> <a href="http://techcenter.mbi.ucla.edu" target="_blank">http://techcenter.mbi.ucla.edu</a><br>
>> TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB" target="_blank">http://www.doe-mbi.ucla.edu/TB</a><br>
>> CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss" target="_blank">http://www.lanl.gov/cbss</a><br>
>><br>
>><br>
>><br>
>><br>
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>><br>
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</div></div></blockquote></div><br>