Rosetta: Difference between revisions
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(New page: There is a locally installed version of Rosetta at our Linux cluster. My current way of doing things is: Go first to [http://robetta.bakerlab.org/fragmentsubmit.jsp] There you submit you...) |
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There you submit your sequence to create the fragments needed to run later locally the AbRelax protocol for ab initio folding. | There you submit your sequence to create the fragments needed to run later locally the AbRelax protocol for ab initio folding. | ||
I choose to that remotely since its too cumbersome to fully install it locally, and its pretty quick. | I choose to that remotely since its too cumbersome to fully install it locally, and its pretty quick. | ||
Then make a new directory with you sequence in FASTA format, eg: | Then make a new directory with you sequence in FASTA format, eg: | ||
<tt> | |||
<pre> | |||
>our lipase | >our lipase | ||
MRAPIPEPKPGDLIEIFRPFYRHWAIYVGDGYVVHLAPPSEVAGAGAASVMSALTDKAIV | MRAPIPEPKPGDLIEIFRPFYRHWAIYVGDGYVVHLAPPSEVAGAGAASVMSALTDKAIV | ||
KKELLYDVAGSDKYQVNNKHDDKYSPLPCSKIIQRAEELVGQEVLYKLTSENCEHFVNEL | KKELLYDVAGSDKYQVNNKHDDKYSPLPCSKIIQRAEELVGQEVLYKLTSENCEHFVNEL | ||
RYGVARSDQVRD | RYGVARSDQVRD | ||
</pre> | |||
</tt> | |||
The job gives two files, accessible after completion through the 'download' button. | The job gives two files, accessible after completion through the 'download' button. | ||
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And then you need something like this | And then you need something like this | ||
/Xsoftware/rosetta/rosetta_source/bin/AbinitioRelax.linuxgccrelease -in::file::fasta lip.fasta -database /Xsoftware/rosetta/rosetta_database | <tt> | ||
<pre> | |||
/Xsoftware/rosetta/rosetta_source/bin/AbinitioRelax.linuxgccrelease | |||
-abrelax -abinitio:relax | |||
-in::file::fasta lip.fasta | |||
-database /Xsoftware/rosetta/rosetta_database | |||
-in:file:frag3 aat000_03_05.200_v1_3 | |||
-in:file:frag9 aat000_09_05.200_v1_3 | |||
-out:pdb -out:path PDB_files_run1 -out:file:silent abrelax_silent | |||
</pre> | |||
</tt> | |||
Latest revision as of 09:05, 10 April 2010
There is a locally installed version of Rosetta at our Linux cluster.
My current way of doing things is:
Go first to [1] There you submit your sequence to create the fragments needed to run later locally the AbRelax protocol for ab initio folding. I choose to that remotely since its too cumbersome to fully install it locally, and its pretty quick.
Then make a new directory with you sequence in FASTA format, eg:
>our lipase MRAPIPEPKPGDLIEIFRPFYRHWAIYVGDGYVVHLAPPSEVAGAGAASVMSALTDKAIV KKELLYDVAGSDKYQVNNKHDDKYSPLPCSKIIQRAEELVGQEVLYKLTSENCEHFVNEL RYGVARSDQVRD
The job gives two files, accessible after completion through the 'download' button.
- _03_*
- _09_*
You need these files copied to your run directory for the big job ...
And then you need something like this
/Xsoftware/rosetta/rosetta_source/bin/AbinitioRelax.linuxgccrelease -abrelax -abinitio:relax -in::file::fasta lip.fasta -database /Xsoftware/rosetta/rosetta_database -in:file:frag3 aat000_03_05.200_v1_3 -in:file:frag9 aat000_09_05.200_v1_3 -out:pdb -out:path PDB_files_run1 -out:file:silent abrelax_silent