In Supplementary Materials for
Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry
Herzog et al, Science 337, 1348 (2012)
the authors refer to the "ROSETTA nonlocal protocol" with a set of commandline flags:
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Box S5: Command-line flags for ROSETTA’s nonlocal application. User specific command-line flags are given in curly brackets.
-database {rosetta_DB_dir}
-in:file:fasta {protein.fasta}
-in:file:psipred_ss2 {protein.ss2}
-in:file:template_pdb {template.pdb}
-in:file:alignment {protein-template.aln}
-out:overwrite
-out:nstruct {n}
-cm:aln_format general
-frag3 {fragments3}
-frag9 {fragments9}
-abinitio::relax
-abinitio::no_write_failures
-abinitio:increase_cycles 1
-abinitio:rg_reweight 0.25
-nonlocal:builder star
-nonlocal:mode semirigid
-nonlocal:gap_sampling_extension 5
-jumps:ramp_chainbreaks
-jumps:overlap_chainbreak
-jumps:increase_chainbreak 0.5
-constraints:cst_fa_file {template.cst}
-constraints:cst_file {template.cst}
-bGDT
-evaluation:gdtmm
-----------------------------------------------------------------------
Is there a way to download this application? I don't see it as part of the Rosetta 3.5 bundle I downloaded
How different is this from just running abinitiorelax?
Some of these options don't appear to be available for abinitiorelax, but I'd like to know what value they add.
Thanks
I believe the application being referred to is the unreleased pilot application "nonlocal_abinitio". If I remember correctly, the concept behind this is that instead of treating the protein as a contiguous chain (as the regular abinitio protocol does), the nonlocal abinitio protocol broke the protein up into segments, roughly corresponding to secondary structural elements. This changed how fragment insertion and backbone alterations propagated and affected the structure.
However, it appears that the nonlocal_abinito application was never released, and was removed from even the developers' codebase about two years ago. I'm can't quite tell why, though I'm guessing it was because there wasn't any significant improvements seen over the regular abinito protocol. It's hard to say without knowing your exact use case, but it's likely that regular abinitio will work for your purposes, assuming you have the correct constraints set.