I tried Rosetta (mr_rosetta) to solve a difficult molecular replacement problem on my dataset, by following the demo inside released rosetta 3.2 software. I got questions about the README file:
In the 5th step, I generate 2000 models building all gaps up to length 8. According to the README, " The top 10% are selected by Rosetta energy; each of these structures are rescored with phaser; the best is relaxed again using the updated density". This means I need to use phaser to rescore 200 structures,which I can just write a shell script to do and is not a problem for me. The question is afterwards how many percentage of 200 structures I can define to "best". Maybe only top 10?
I appreciate if somebody, who have tried or know how to go through the whole process, can give me some valuable suggestions. Thanks.