loop_closure.flags

-database Rosetta_master/main/database/
-beta
-in:file:fullatom
-multi_cool_annealer 10
-renumber_pdb 1
-overwrite
-out::file::pdb_comments
-run:preserve_header
-chemical:exclude_patches LowerDNA  UpperDNA Cterm_amidation VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated  tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated  lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm
-parser:protocol loop_closure.xml
-out:prefix closed_ 
-overwrite 
-no_nstruct_label 
-mute all 
-indexed_structure_store:fragment_store /gscratch/baker/brunette/DBs/hdf5/ss_grouped_vall_helix_shortLoop.h5