Design

Dear caretakers/kind strangers,

I ran into an error that i do not understand when trying to do de-novo modelling of a helix linker using REMODEL. When i leave the blueprint file without any new residues it runs fine. But when i add new residues at the end (C Terminal) the program recognizes it is a C terminal extension, but throws this error. 

Hello there, Now I'm trying to optimize the protein sequence at binding interface for increased affinity to its target. A complex structure was previously solved by X-ray crystallography (PDB 3rh8). To make their affinity higher, I would like to design the protein sequence at both sides. Meiler Lab provides a step-by-step tutorial at his website (http://www.meilerlab.org/index.php/rosetta-tutorials). According to his tutorial, I tried, but I found something like error.

Hi, does anyone know how to do alanine scanning for just one protein?

I looked at different movers for RosettaScripts, like ddgScan, AlaScan, and ddg. Can any of these be used for a single protein with no interface? I want to see which protein residues are good targets for mutation.

I am in need of some major help. 

I am running the SEWING application because I am copying the secondary structures that fit onto a particular primer, and some key binding residues are located on the loop between two beta strsnds - so I need to generate a new segment file with a few beta strands.