[phenixbb] Rosetta rebuilding...

Terwilliger, Thomas C terwilliger at lanl.gov
Mon Jan 16 08:40:28 PST 2012

Hi Francis,

[0] What is being rebuilt in rosetta? The whole model? Or is the model divided into chunks and each chunk sent to rosetta?

The model is being divided into chains, and each chain is rebuilt individually by rosetta (along with an electron density map as part of the rosetta target function).  If there is NCS present, then only one copy is rebuilt with Rosetta and it is copied to the positions of all the other copies.

[1] Can a specific region be chosen to be rebuilt? (In the case where most of the model is correct)

No, not at the moment (I know this would be useful!)

[2] How are the rosetta models  scored ? Specifically, "(d) refine Rosetta models, average density from top 20%, continue rebuilding each Rosetta model using averaged density".  What's the scoring function (mapCC, R-Free, LLG??) How's the top 20% obtained?

Rosetta models are scored by LLG in this process.

All the best,
Tom T

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