fragment generation – local vs server

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    • July 25, 2008 at 9:09 am #343
      estrauch
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        Dear all

        Can anyone clarify the advantages and disadvantages of these two ways of generating fragment libraries? I note that the FAQ now strongly recommends the server. Two advantages of the server might be

        – access to secondary structure prediction methods not otherwise distributed (only Psipred seems available in a form that can be plugged into rosetta_fragments/nnmake/make_fragments.pl)

        – automatic updating of nr etc

        In general, though, it would be handy to be independent of server load and obtain fragments locally. My general experience is that make_fragments.pl does a good job.

        Am I missing something? What method to other people prefer and why?

        Cheers

        Dan

      • July 28, 2008 at 1:05 am #4000
        Anonymous

          Hi Dan,

          We recommend the server because some users does not familiar with modifying the paths specified in perl scripts and the installations of other programs on linux, such as PSI_BLAST.

          Generate fragments locally is more convenient if you know Perl scripts and familier with shell configurations.

          Yi
          > Dear all
          >
          > Can anyone clarify the advantages and disadvantages of these two ways of generating fragment libraries? I note that the FAQ now strongly recommends the server. Two advantages of the server might be
          >
          > – access to secondary structure prediction methods not otherwise distributed (only Psipred seems available in a form that can be plugged into rosetta_fragments/nnmake/make_fragments.pl)
          >
          > – automatic updating of nr etc
          >
          > In general, though, it would be handy to be independent of server load and obtain fragments locally. My general experience is that make_fragments.pl does a good job.
          >
          > Am I missing something? What method to other people prefer and why?
          >
          > Cheers
          >
          > Dan

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