Design

I have a 11aa long linker (known sequence) connecting two parts of a protein (NOT two independent domains). I want to model the linker before some downstream Rosetta analysis on the protein. It seems FloppyTail is often suggested for the modeling of linkers.

My question is: how is FloppyTail compared to Remodel + Fixbb? What if I just insert some 11aa long extension (of any sequence) between the two parts using Remodel, then I use fixbb to mutate this newly inserted extension to the sequence of my linker? How would this compare to FloppyTail?

Hello! I want to get the RMSD between the original ligand nd the one i designed. both the ligands are peptides of different lenght (the one i designed is smaller).
I tried to use calc_Lrmsd(pose1,pose2) but i got the following error:

Hello,

I am trying to run fixbb on a heterodimeric protein and explore different residues at 2 different positions in one chain. The program runs without error however all the structures output (100) have the native residues at those 2 positions. My .resfile and flags are below.

Resfile:

NATRO
EX 1 EX 2
USE_INPUT_SC
START
72 A NOTAA C
79 A NOTAA C

Flags

In the selection of binders from a library and their affinity maturation, a trade-off between affinity of the binder and its stability frequently can be observed. Starting from a binder library based on a very stable framework allows for high sequence diversity in the randomised positions of the putative binding site, and therefore stringent selection for high affinity, as very significant destabilisation would be needed to bring the stability of the binder down to a level where this stability significantly affects the fraction of folded molecules and therefore the outcome of selection.