Radius of Gyration

[JianyiYang]

Does anyone know how to get Rosetta3.0 to output the radius of gyration?

Thanks,
Christy

[Anonymous]

There are two RG methods for rosetta3’s energy function. You can find them at src/core/scoring/methods/RG_Energy.cc and RG_Energy_Fast.cc. The calculation differs slightly (I think “Fast” is the old ++ method, and the other is closer to the normal RG calculation; you should look at it yourself to choose which you want.

When you say “output”, what are you trying to do? If you want a report of the RG’s of a set of PDBs you already have, then just run the score executeable with a custom scorefunction which has one (only one) of the RG terms turned on.

https://www.rosettacommons.org/software/common/3.0/rosetta3_user_guide/app_scoring.html

For example, you can copy the standard scorefunction file /scoring/weights/standard.wts, add

rg = 1.0

to the bottom of it, and run the score app with that file passed in under the score::weights flag.

If you want RG as part of your energy function, and not just calculated at the end, then you can add it to the scorefunction at any time in the code (and sometimes from commandline). I’ll try to describe that if it’s what you wanted.

[JianyiYang]

Thanks! I think I have that working now!

Christy

> There are two RG methods for rosetta3’s energy function. You can find them at src/core/scoring/methods/RG_Energy.cc and RG_Energy_Fast.cc. The calculation differs slightly (I think “Fast” is the old ++ method, and the other is closer to the normal RG calculation; you should look at it yourself to choose which you want.
>
> When you say “output”, what are you trying to do? If you want a report of the RG’s of a set of PDBs you already have, then just run the score executeable with a custom scorefunction which has one (only one) of the RG terms turned on.
>
> https://www.rosettacommons.org/software/common/3.0/rosetta3_user_guide/app_scoring.html
>
> For example, you can copy the standard scorefunction file /scoring/weights/standard.wts, add
>
> rg = 1.0
>
> to the bottom of it, and run the score app with that file passed in under the score::weights flag.
>
> If you want RG as part of your energy function, and not just calculated at the end, then you can add it to the scorefunction at any time in the code (and sometimes from commandline). I’ll try to describe that if it’s what you wanted.
>
>

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