frelax relaxation with constrains

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    • February 24, 2012 at 9:44 am #1173
      Anonymous

        Hi.
        Is there experience with using frelax with constrains, like “frelax.constrain_relax_to_native_coords” or “frelax.constrain_relax_to_start_coords”. The first uses a defined pose I guess (frelax.set_native_pose), while the latter tries to keep the situation at the begin of relax? Is there any possibility to restrict this constrains to a subset of amino acids… that is: keep a motive more or less fixed while relaxing the rest? Like in the packmovers using the .res file with NATRO.
        Thanks
        ast

      • February 24, 2012 at 2:43 pm #6692
        Anonymous

          I believe what you are looking for exists, but I’m not sure. If it exists, it will be through supplying a user-defined MoveMap object. The MoveMap is like the resfile/PackerTask except for backbone movement rather than sidechains (I am oversimplifying a bit here…). See if your frelax object takes a MoveMap?

        • February 27, 2012 at 9:08 am #6704
          Anonymous

            Hi,
            FastRelax has a function called “.set_movemap” (and “.get:movemap”). How do I define the movemap? The class “MoveMap” has “MoveMap.import” but also a bunch of stuff like “MoveMap.set_chi”, “…set_jump”, “…torsion_id_begins” which looks to me like a way to stitch together a movemap internally, though I would prefer some sort of file format (like the .res) to feed into MoveMap. Nonetheless, one funtion in “Move.Map” got my attention: “MoveMap.set_ranges_unmodifiable”, is this maybe a way to fix some residues and let the rest move freely?
            Thanks

          • February 27, 2012 at 10:51 am #6705
            Anonymous

              Ok, it seems to work, here is what I did:
              -write a move map file, basically like the .res file: setting all residues to relax free = “BBCHI” and the ones I want to fix = “NO”
              -setting up an instance of MoveMap
              -loading the movemap file with: .init_from_file(“….”)
              -checking the movemap with .show(“total residue number”)
              -connecting FastRelax with the movemap via: FreeRelax.set_movemap(“instance of movemap”)
              -use FreeRelax
              Thanks…

            • February 27, 2012 at 2:38 pm #6707
              Anonymous

                If init_from_file works, great!

                The simple MoveMap setup interface is the functions set_chi, set_bb, and set_jump. Each takes a residue/jump identifier and a boolean for mobile/immobile.

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