- This topic has 4 replies, 2 voices, and was last updated 11 years, 9 months ago by Anonymous.
February 24, 2012 at 9:44 am #1173Anonymous
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.
February 24, 2012 at 2:43 pm #6692Anonymous
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 #6704Anonymous
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?
February 27, 2012 at 10:51 am #6705Anonymous
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”)
February 27, 2012 at 2:38 pm #6707Anonymous
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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