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Dear Rosetta people,

I have been installed rosetta3.9 on our local cluster. To do that, I have used the following command to compile the Rosetta and enable mpi ability after I copy the $ROSETTA_PATH/main/source/tools/build/site.settings.topsail file to the $ROSETTA_PATH/main/source/tools/build/site.settings:

./scons.py mode=release extras=mpi bin -j 20

I'm refining tubulin based on this tutorial here: https://www.rosettacommons.org/demos/latest/public/electron_density_structure_refinement/structure_refinement

I save the nucleotides and separate pdb files, convert them into mol2 and generate params file that I pass to Rosetta.

It seems, however, that Rosetta completely flips the orientation of the nucleotides. 

Hey all! I just have a couple of questions:

01. In FlexPepDock, what does the interface score (I_sc) correspond to? The interface between the receptor and peptide? Or is it something else?

02. Can the interface score be used to evaluate the strength of binding between the receptor and peptide? If not, how can I evaluate the said parameter?

Thank you very much! Cheers!

Hello,

I was using Rosetta 2016.02 "local  refinement" to calculate the interface scores of known protein complexes (in a bound form).

Now, I tried docking the same protein complexes, with exactly the same flags with Rosetta 2018.21. I realized that the content of the score file has changed and it gives totally different I_sc and total_score.  Almost any protein complex that I tried gives favorable results now (i.e. I_sc < -5).  Why is this the case? 

I couldn't find what has changed since 2016.02 version.