Designating Fold Tree Edges as Flexible or Rigid

[Anonymous]

Hello Everyone,

Quick question: Is there a way to designate edges added to a fold tree as flexible or rigid? I have searched the documentation and tutorials for awhile but can’t find anything? I am referencing some of the fold tree diagrams in Protein-Protein Docking with Backbone Flexibility

Specifically, Figure 1 b. It looks like two doamins attached by a flexible linker. This would consist of 3 edges. But how does one designate that inner middle linker edge as flexible in the fold tree object?

OR, is the flexible region made up of many 1 residue edges to simulate a flexbile region?

Any help is appreciated,

Nathan

[Anonymous]

The MoveMap object controls whether residues are flexible or not (as granular as individual torsions, or bb/chi).  It also has settings for the Jumps in the FoldTree.

 

FoldTree itself has no concept of “what” can move.  MoveMap has no concept of kinematics, just what is flexible versus what is not.

[Anonymous]

Okay – this makes sense. So, really any docking/conformation sampling protocol must have both a MoveMap and a FoldTree?

[Anonymous]

All Poses have a FoldTree definitionally.  (A Pose contains a Conformation which contains a FoldTree and AtomTree).  Ultimately AtomTree determines the kinematics (“how” stuff moves, or how internal coordinate changes propagate as 3-D coordinate changes.)

 

If you are moving the backbone, the standard method for controlling what residues can move is MoveMap.

 

If you are repacking or designing, the standard method of determining which sidechains can do what are PackerTask and TaskFactory.

 

MoveMap and PackerTask overlap in that both can make statements about the mobility of sidechains; the packer takes PackerTask and most other things take MoveMap.

[Author]

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