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frelax relaxation with constrains

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frelax relaxation with constrains

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.

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Fri, 2012-02-24 01:44

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?

Fri, 2012-02-24 06:43

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?

Mon, 2012-02-27 01:08

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

Mon, 2012-02-27 02:51

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.

Mon, 2012-02-27 06:38