CreatePredAlphaCost pred_alpha2k alpha11 T0372.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0372.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0372.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 30 dry6.5 20 dry8 15 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 40 backbone_clashes 2 \ break 300 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 80 \ 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 \ known_ssbond 0.5 \ // 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: # 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. SSBOND C176 C181 # include T0372.dssp-ehl2.constraints # include T0372.undertaker-align.sheets # include rr.constraints # try3 compared to try2... # from to # dry5 15 30 # break 50 100 # soft_clashes 20 40 # try3 was a polish on SAM_T06_server_TS1. # for try4, increased break from 100 to 200. # try4 will be a polish on T0372.try3-opt2.gromacs0.repack-nonPC.pdb.gz # attempting to heal breaks # for try5, add some helix constraints as follows: HelixConstraint S30 R38 1 HelixConstraint S98 I107 1 HelixConstraint G186 E202 1 # for try6, increasing breaks to 300 and constraints from 10 to 80. # for try8, just copied the try6.costfcn.