Unsolved

I used fixbb in Rosetta 3.4 to perform fixed BB design using damped LJ potential (by specifying parameter -soft_rep_design). But I noticed that the final score reported by fixbb seemed to be calculated using default weights. (I got to know this by using score_jd2 to recalc the score for deboys using default weights and damped weights and compare them to the score reported by fixbb.) Does this mean my design was really done using damped LJ?

I'm trying to use the docking .xml scipts mentioned in the paper "RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite" under the heading "Ligand docking and design". It is also mentioned in a book chapter "Rosetta Ligand docking with flexible XML protocols."

I modified it for my purposes (chain name, start from other coordinates). I can produce docked structures, but only if I don't include the rotate mover by removing it from the low_res_dock mover:

Hi. I am trying to fix atoms (or residues) in place during the relax application. After searching through the forum, I saw that MoveMap could be used to accomplish this for the FastRelax application. I assume this is the same thing as the "fast" option for relax in the newest version of Rosetta. The old post I am referring to can be found here http://www.rosettacommons.org/content/frelax-relaxation-constrains. However, I am unsure how the commands listed at the end of the post can be applied.

Hi all,

I'm new to PyRosetta and just had a quick question. Is there a way to make mutations to an existing protein structure using PyRosetta? I'm currently doing all the mutations in PyMOL then saving the mutants as new pdb's and calling them into PyRosetta for analysis. If I could just write a short script to mutate the structure using PyRosetta, it would save me a lot of time. Thanks!