ROSETTA_EM_REFINEMENT
Scripts for EM Refinement in Rosetta
launch_rosetta_local.py - defines an area for intensive sampling (in script, probably should move to arguments) launch_rosetta_global.py - is essentially the tutorial commands for a global refinement
Thanks to Gabe Lander and Mark Herzik (esp for density weighting) and Ray Wang (for other advice)
Dealing with Lys acetylation
(adapted from https://www.rosettacommons.org/demos/latest/public/patched_residue_types_in_centroid-fullatom_protocols/README)
move lys_acetylated.txt to database/chemical/residue_type_sets/centroid/patches/lys_acetylated.txt
add the line: patches/lys_acetylated.txt into database/chemical/residue_type_sets/centroid/patches.txt
Edit Residue Name from ALY to LYS
Other notes:
make sure chains are A not 1A remove Mg and GTP (there are tutorials for dealing with this on DiMaio website)
-ignore_unrecognized_res flag has been removed from rosetta_scripts command
#more local sampling notes Here are two useful arguments you can pass to "CartesianSampler":
residues_to_exclude="" residues_to_include=""
In this way you can tell Rosetta which residues you would like to in/exclude in the "auto" refinement setup.
eg: