Reply To: Using rosetta 3 to make a fragment library and then use it to model loop of a protein structure

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January 24, 2011 at 3:31 pm #4849
Anonymous

    Hi,

    A) The Rosetta fragment stuff is getting overhauled between 3.1 and 3.2, I think. I’ve emailed the new fragment guy to see if he has useful comments.

    B) Check out src/core/fragment/ConstantLengthFragmentSet.cc, function read_fragment_file. It looks like the columns are:

    pdb chain aa_index aa ss phi psi omega

    and the rest of the columns are unused. They’re probably legacy stuff left over from Rosetta2 that wasn’t ported.

    C) Rosetta3.1 has an internal fragment picker. It is sort-of documented, there’s a README in src/core/fragment. I think 3.2 will have a new and completely different one (which I think will be fully documented.)