Relax Refinement for complecated targets

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Relax Refinement for complecated targets
#1

Relax is good at refining alpha-helix structures, but it almost make all other kind of structures worse. Is there any way to help Relax do better on structures having beta-sheets? Any information is appreciated! Thanks

Post Situation:
Fri, 2012-01-20 09:57
jiongzhang

The algorithm is supposed to work the same, regardless of the secondary structure of the protein being relaxed. Is your beta protein larger (relax scales poorly beyond 100 residues or so)?

Fri, 2012-01-20 10:47
smlewis

You can use restraints/constraints with relax, and that's highly encouraged. If you can impose external information onto the relax procedure with constraints, you should do so.

For example, if you want to relax a PDB strucure into the Rosetta energy function, it's recommended to add in backbone and possibly sidechain constraints to keep the atoms from moving too far from the experimentally determined locations. Likewise, if you have NOE or contact information, you can impose that information with constraints. As you don't have to impose constraints on the whole structure, you can, for example, just constrain a particular loop that's giving you issues.

Fri, 2012-01-20 11:28
rmoretti

Besides constraints, is there any option that could fix some atoms during the refinement leaving Rosetta only refine the rest of the structure? Since "fix" and "constrained" are different. Thanks!

Wed, 2012-01-25 14:59
jiongzhang

I think you can run Relax through the RosettaScripts tool, which will let you custom-define a MoveMap. See the "relax a large structure" demo in the RosettaCON2011 demos (which you should be able to download from the same place you downloaded Rosetta3.3).

Thu, 2012-01-26 07:02
smlewis

You can also do this in PyRosetta if you know or are interested in learning Python. One caveat, and you may need to do this using RosettaScripts as well, is to set the chainbreak score to 100. In PyRosetta, this is: score.set_weight(chainbreak, 100). In Rosetta, I think you should be able to add a line in whatever scorefunction you will be using (score12, standard, etc.) that says:
chainbreak 100
There may be simple syntax to do this in RosetaScripts, but I don't have any experience using it.

Attached is a function for how I define the movemap in python for when I want to control the relax, if your interested in going that route...

Jared

Thu, 2012-01-26 16:16
Within RosettaScripts, you can change the weight of a given scoreterm using the <Reweight /> subtag of your scorefunction. e.g.
<SCOREFXNS>
<no_breaks weights=standard patch=score12 >
<Reweight scoretype=chainbreak weight=100 />
</no_breaks>
</SCOREFXNS>

(Hope the formatting on that isn't messed up.) See: http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/RosettaScripts_Documentation#SCOREFUNCTIONS
Thu, 2012-01-26 17:22
rmoretti

Thank you very much! I download the RosettaCON2011 demos, but there's no item in the folder "relax a large structure"?
I don't know what's wrong with it. Could you please check it? Or how I could get it in other way?

Fri, 2012-01-27 14:25
jiongzhang

Weird. I asked someone to fix it. In the meantime I attached the useful parts of it.

Fri, 2012-01-27 14:38
smlewis

Thank you!

Fri, 2012-01-27 20:46
jiongzhang

Could you also attach the xml script file please? Thank you very much!

Tue, 2012-03-06 13:00
jiongzhang