You are here

FastRelax results in bad structure

3 posts / 0 new
Last post
FastRelax results in bad structure
#1

I use FastRelax to do refinement for my pose. However, the structure becomes completely different and of bad quality after refinement. why did this happen? I added the original  and refined pdb file.


 

AttachmentSize
pose.pdb155.37 KB
pose_refined.pdb351.25 KB
Post Situation: 
Mon, 2021-04-26 08:39
Eden

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.

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

 

Tue, 2021-04-27 07:53
matteoferla

Thanks for your detailed explaination.

Sun, 2021-06-13 00:14
Eden