pep_flip [id two atoms] or [mol res1 res2]
This command allows the user to locate peptide conformations that are unusual. The technique has been described by Jones et al. [8] and will not be repeated here. If the database of structures has not been loaded, then it will be loaded before carrying out the calculation. It must, therefore, be properly defined in Lego_setup. The command makes a residue property called [mol]_residue_pepflip.
Example:
O > pep_flip a a1 a20 Util> Calculating zone A1 to A20 in molecule A , object C Util> The DB is now being loaded. Util> Loading data for protein:HCAC Util> Loading data for protein:PA Util> Loading data for protein:51C_3 Util> Loading data for protein:ACT_2 Util> Loading data for protein:APP_2 Util> Loading data for protein:AZA_1 Util> Loading data for protein:B5C_2 Util> Loading data for protein:BP2_1 Util> Loading data for protein:C2C_3 Util> Loading data for protein:CPA_5 Util> Loading data for protein:CPV_1 Util> Loading data for protein:CRN_1 Util> Loading data for protein:CYT_4 Util> Loading data for protein:DFR_3 Util> Loading data for protein:ECD_1 Util> Loading data for protein:FB4_1 Util> Loading data for protein:FDX_1 Util> Loading data for protein:FXN_3 Util> Loading data for protein:HIP_1 Util> Loading data for protein:INS_1 Util> Loading data for protein:LH1_1 Util> Loading data for protein:MBO_1 Util> Loading data for protein:NXB_1 Util> Loading data for protein:OVO_1 Util> Loading data for protein:PCY_1 Util> Loading data for protein:PPT_1 Util> Loading data for protein:PTI_4 Util> Loading data for protein:PTN_2 Util> Loading data for protein:REI_1 Util> Loading data for protein:RHD_1 Util> Loading data for protein:SGA_2 Util> Loading data for protein:SN3_1 Util> Loading data for protein:SNS_2 Util> Loading data for protein:TLN_3 Util> Residue A3 has a pep_flip r.m.s. value of 1.43 Util> Residue A4 has a pep_flip r.m.s. value of 0.41 Util> Residue A5 has a pep_flip r.m.s. value of 2.54 Util> Residue A6 has a pep_flip r.m.s. value of 1.56 Util> Residue A7 has a pep_flip r.m.s. value of 0.54 Util> Residue A8 has a pep_flip r.m.s. value of 0.69 Util> Residue A9 has a pep_flip r.m.s. value of 0.40 Util> Residue A10 has a pep_flip r.m.s. value of 0.70 Util> Residue A11 has a pep_flip r.m.s. value of 0.83 Util> Residue A12 has a pep_flip r.m.s. value of 0.50 Util> Residue A13 has a pep_flip r.m.s. value of 0.96 Util> Residue A14 has a pep_flip r.m.s. value of 0.97 Util> Residue A15 has a pep_flip r.m.s. value of 1.96 Util> Residue A16 has a pep_flip r.m.s. value of 1.53 Util> Residue A17 has a pep_flip r.m.s. value of 0.67 Util> Residue A18 has a pep_flip r.m.s. value of 0.33 Util> Residue A19 has a pep_flip r.m.s. value of 0.81 Util> Residue A20 has a pep_flip r.m.s. value of 0.23 O > dir a_*pep* Heap> A_RESIDUE_PEPFLIP R W 132 O >