FastRelax results in bad structure

Gromacs has a comedy page describing the term “blowing up”. Your protein, to use this highly technical term, blew up.

In FastRelax, there are two ways to combat this if the starting pose is bad —such as one downloaded from Swiss-Model. This is because the starting sidechains are all unhappy.

• Relax with fixed backbone, followed by regular relax
• Relax with CA constraints (see https://www.rosettacommons.org/node/10951)

scorefxn = pyrosetta.create_score_function('ref2015')

# fixed bb

movemap = pyrosetta.MoveMap()

movemap.set_bb(allow_bb=False)

movemap.set_chi(allow_chi=True)

relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn, 5)

relax.set_movemap(movemap)

relax.apply(pose)

# free BB

relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn, 15)

relax.apply(pose)

However, structures can blow up if a cartesian method is used with a non-cartesian one. For example:

scorefxn = pyrosetta.create_score_function('ref2015')

relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn, 5)

relax.cartesian(True)  # Boom

relax.minimize_bond_angles(True)   # Super boom

relax.minimize_bond_lengths(True)   # Hyper boom

relax.apply(pose)



scorefxn_cart = pyrosetta.create_score_function('ref2015_cart')

relax.set_scorefxn(scorefxn_cart)

relax.apply(pose) # no boom