Loop modelling,

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    • June 8, 2013 at 3:29 pm #1605
      Anonymous

        Hi,

        I preform using loop modelling base of fragment database to remodel the loops of a protein,
        But when it generates several models (e.g., 10000), it changes the other part of the protein (e.g., helix conformer) too.
        But I expect , only remodels the loops site not other sites.

        Thanks

      • June 10, 2013 at 3:18 pm #8882
        Anonymous

          Hi Berk,

          Only thing I can think of is that something is strange with your loop file or input flags. Can you post both?

        • June 11, 2013 at 10:52 am #8886
          Anonymous

            Hi,
            Thanks,
            Now my problem is solved , as I used this commands,
            -loops:input_pdb inputs/Inactive_min_ph.pdb
            -loops:loop_file inputs/Inactive.loop_file
            -loops:frag_sizes 9 3 1
            -loops:frag_files inputs/aat000_09_05.200_v1_3.gz inputs/aat000_09_05.200_v1_3.gz none
            -loops:remodel quick_ccd
            -loops:remodel perturb_kic
            -loops:refine refine_kic
            -loops:fix_natsc true
            -loops:neighbor_dist 0.0
            -loops:extended
            -ex1
            -ex2
            -out:pdb
            -out:prefix Inactive_H
            -out:file:fullatom
            -nstruct 1000

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