Hi, I need some help here. I've been reading the document for fixbb protocol in this page: http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/app_...
In the box listing flags for rotamers, I found one called preserve_input_cb which is supposed to keep unidealized ca_cb bond parameters from input file. However, I cannot find which layers this flag belongs to. What's the key word should I put before the flag in the option file?
The option is called -packing:preserve_c_beta; the documentation is wrong. I'm not sure it actually works; casual inspection of the code suggests it does, but I have a nagging feeling it doesn't. Let me know if it does!
Also, for options with unique names, the namespacing is irrelevant. Just -preserve_c_beta ought to work.