[phenixbb] rosetta mr

Shya Biswas shyabiswas at gmail.com
Tue Dec 6 19:37:08 PST 2011


Thanks, this was exactly what I was looking for.
Shya

On Tue, Dec 6, 2011 at 8:20 PM, Thomas C. Terwilliger
<terwilliger at lanl.gov>wrote:

> 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 at 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 at 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
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> phenixbb mailing list
> >> phenixbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20111206/80e283ac/attachment.htm>


More information about the phenixbb mailing list