CreatePredAlphaCost pred_alpha2k alpha11 T0358.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0358.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0358.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 25 dry6.5 30 dry8 20 dry12 5 \ phobic_fit 3 \ sidechain 5 \ n_ca_c 7 bad_peptide 15 \ bystroff 5 \ soft_clashes 50 backbone_clashes 2 \ break 120 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 10 \ 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 0 // 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 T0358.dssp-ehl2.constraints //include T0358.undertaker-align.sheets //include rr.constraints Constraint F37.CB R42.CB -10. 7.0 14.0 0.5 //hopefully to bring the exposed regions on beta sheet closer together Constraint L63.CB V41.CB -10. 7.0 14.0 4 //Will bring the exposed region of the helix closer to the beta sheets. Constraint I67.CB I27.CB -10. 7.0 14.0 4 HelixConstraint (T0358)T2 (T0358)Y24 1.5 //from try11-opt2.helices HelixConstraint (T0358)E56 (T0358)G71 3 HelixConstraint (T0358)D75 (T0358)H87 3 constraint((T0358)F12.CA, (T0358)A52.CA) [> 5 = 10 < 17] w=1