Design

Hello All

I want to design the interface of a two-chain complex( actually design only one of the partner)  using raf / rac design script which I have attached it here.

Is it better and more accurate to change this script in order to get and use resfile ? 

I prefer to design interface automatically without resfile (just script defines interface residues)  because I have no idea about which residues in interface should be designed or not. or what types of mutations are allowable

Hi there,

I would like to know if somebody could share the binary file format specification of the silent file. I try to read the PDB section without any luck. Before digging through the code of extract_pdb I thought it would be faster to quickly ask how to read the binary section.

Thank you very much.

Cheers,

Max 

I  want to graft a coenzyme binding sites to a scaffold,  so the first thing is to define a theozyme. However, the exsiting .PDB structures  binding the coenzyme are not accessible, what I can download is only protein crystal structure without ligand. I that way, what should i do？ Should i DOCK the ligand to the protein at first? could anyone explain me the procedure? Thanks a lot!

Hi, I need your help on your experience of the number of structures generated from Rosetta by specifying nstruct:

Have you ever met a situation, for example, you specify nstruct = 100, and Rosetta generates less than 100 structures at the end of the run?

More information:

1)  I am using RosettaScripts to design a protein interface. I have specified a cutoff of SASA but I don't think it would affect the final number of structures.