trouble in floppytail modelling

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    • June 27, 2013 at 8:15 pm #1625
      Anonymous

        Hi,

        I’m using floppytail app (rosetta 3.5) to model my protein complex. The first chain in pdb file is a 353 residue protein and the second chain is a 138 residue protein. The “floppytail” region is N-terminal residues 1-37 in the second chain.

        In the generated structures I noticed that the N-term residue of second chain (beginning of “floppytail”) is not moving in space. All generated structures overlap in first chain(residue 1-353), and the first residue of second chain(residue 354 in pdb). I think the first chain is not supposed to move but I wanted N-term of second chain to move.

        I defined flexible region in flag file like this:
        -flexible_start_resnum 354
        -flexible_stop_resnum 390
        -flexible_chain B

        And I also tried to add these options, but they did not solve the issue.
        -FloppyTail::force_linear_fold_tree true
        -FloppyTail::C_root true

        Could someone give me some advice?

        Many thanks,
        Yisong

      • June 27, 2013 at 8:52 pm #8970
        Anonymous

          Update: I saw this in the new mannual page: “If you are modeling a complex, ensure that the flexible region has either the highest or lowest residue numbers possible: if it is a N-terminus, put its subcomponent first in the PDB file, or vice-versa if it is C-terminal. Use the C_root option if your flexible region is a lower residue number, and do not if it is higher. If you have more than two components in your complex, and are modeling a linker between them, then the linker’s chain must come between the groups of internally rigid parts in the input PDB file. “
          It looks like I’ll have to move the second chain to the beginning of pdb.
          The issue is solved after editing the pdb to put flexible region in beginning of the pdb and renumbering the fragments and constraint files accordingly.

          Yisong

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