What have we proposed?

Over the course of the next 5 years (​timeline):

Fragment extension

ChimeraX requests Phenix to propose placement of the next several residues in a cryoEM map.

Ligand placement

ChimeraX requests Phenix to place a flexible ligand in a user selected region of a cryoEM map.

Restraints

ChimeraX will translate ISOLDE refinement restraints into Phenix format and hand off to Phenix. ChimeraX will display Phenix automatically generated restraints. An example restraint would be that a group of atoms is specified as rigid, or a metal position is held to nearby atoms.

Validation

ChimeraX will request validation problem lists from Phenix and allow user to fix problems, and request Phenix to run re-refinement.

REST communication

ChimeraX will utilize Phenix tools by making REST calls. Also Phenix will be able to send data to a ChimeraX REST server for visualization.