(12) Helix addition :
# U08 -- A09
# -----> G07 -- C10
# |_ G11
# | G05 A12
# Add 2 BP helix TO --> A04 G13
# G03 U14
# C02 -- G15
# A01 -- U16
#
# Sample C10-G11 suite, No chain closure
# Missing U06 in structure. U06 is a bulge residue that is not yet built.
#
# Note : Had to manually remove "RES_NUM 1-5 7-16" line from silent_file, for
# rna_extract to run without error. Is this a new feature?
$ROSETTA_BIN/swa_rna_main.macosgccrelease \
-algorithm rna_sample \
-database $ROSETTA_DB \
-sample_res 10 \
-input_res 1 2 3 4 5 11 12 13 14 15 16 \
-tags S_000000 \
-in:file:silent in_region_6_3.out \
-in:file:silent_struct_type binary_rna \
-input_res2 7 8 9 10 \
-s upper_helix.pdb \
-out:file:silent region_5_3_sample.out \
-native rosetta_model.pdb \
-fixed_res 1 8 9 16 \
-rmsd_res 3 4 5 6 11 12 13 14 \
-jump_point_pairs 1-16 8-9 \
-alignment_res 1-16 8-9 \
-fasta fasta \
-global_sample_res_list 3 4 5 6 11 12 13 14 \
-cutpoint_open 8 \
-score:weights rna/rna_hires_07232011_with_intra_base_phosphate.wts \
-integration_test true \
-mute all \
-analytic_etable_evaluation 0