Reply To: producing good idealized structures

[Anonymous]

there’s two idealize protocols in Rosetta++, one written using pose and one written before pose. In my experience the pose-idealize works much better. I believe you simply have to add ‘-pose’ along with ‘-idealize’.

I wouldn’t minimize the starting structure before idealizing. Keep in mind that, barring chain-breaks, idealizing is much more difficult at larger chain lengths and 700 is pretty large.