CreatePredAlphaCost pred_alpha2k alpha11 T0351.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0351.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0351.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 20 backbone_clashes 2 \ break 50 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 15 \ hbond_geom 5 \ hbond_geom_backbone 10 \ hbond_geom_beta 50 \ hbond_geom_beta_pair 100 \ missing_atoms 1 \ maybe_metal 0.5 \ maybe_ssbond 1 // remove maybe_ssbond weight if protein known to be in reducing environment. // remove maybe_metal weight if protein known to have disulfides or // known not to bind metal ions. // Add the following for extra-cellular proteins: # known_ssbond 0.5 # and put ssbond command in constraints file // For comparative modeling, increase weight of break and hbond_geom... // put any constraints here, such as helix constraints, strand constraints, // sheet constraints, ssbonds, hbonds, or just arbitrary pairs of atoms. # include T0351.t06.str2.constraints HelixConstraint L3 K10 0.7 StrandConstraint F20 N24 0.684 StrandConstraint Y30 K33 0.643 # I used t06.o_notor2 to adjust this next line a bit HelixConstraint T42 W50 0.818 HelixConstraint D63 L72 0.659 # opening up this gap a bit HelixConstraint Q74 E84 0.627 HelixConstraint N91 L103 0.606 # this next is more likey than before (watching that H-tag!) HelixConstraint D106 E108 0.607 # sheet designed by: echo "20 25 33 38" | build_sheet.py -t T0351 -o down SheetConstraint F20 N24 K33 N27 hbond F20 5.0 include rr.0.1.constraints