************************************************************************** find command Leif Laaksonen CSC 2001 Eero Häkkinen CSC 2002 ************************************************************************** # # Find S-S bonds in a structure # Apply the search on all structures available or just to the structure # with number "StructureNumber". It is also possible to give a distance # Fbond inside which the S-S must be. # find ssbo$nds all [Fbond] StructureNumber [Fbond] # # Find hydrogen bonds (equivalent to calculate hydrogen bonds). # Array "gomHydrogenBondingParams" can be used to customize hbond criteria. # Following array elements are recognized: # Maximum distances: # d-a Distance between donor and acceptor # d-a_nohydrogens Distance between donor and acceptor # (used then "nohy$drogens" is applied) # h-a Distance between hydrogen and acceptor # d-h Distance between donor and hydrogen # Minimum angles: # d-h-a donor-hydrogen-acceptor # d-a-aa donor-acceptor-<atom bonded to acceptor> # h-a-aa hydrogen-acceptor-<atom bonded to acceptor> # Maximum angles: # aromatic Angle between aromatic plane and vector donor-hydrogen # hbon$ds Seg Res Atm hbon$ds Seg Res Atm nohy$drogens -hbo$nds # # Find protein chains in a structure. # Returns a list of two items lists. First item is segment name and the # second item is a residue number ranges in form # ResN11[-ResN12][,ResN21[-ResN22][,...]] # chain$s Seg Res IStruct all sele$cted # # Find atoms around other atoms or around coordinate point. # Return atom or residue number ranges in form # Num11[-Num12][,Num21[-Num22][,...]] # Return segment names as comma separated list. # Return selection list as list of segment names, residue number ranges and # atom number ranges. # Structure index "IStruct" can also be "all" or "sele$cted". # atom$s around Seg1 Res1 Atm1 FRad Seg2 Res2 Atm2 IStruct FRad FXc FYc FZc IStruct resi$due around Seg1 Res1 Atm1 FRad Seg2 Res2 Atm2 IStruct FRad FXc FYc FZc IStruct segm$ent around Seg1 Res1 Atm1 FRad Seg2 Res2 Atm2 IStruct FRad FXc FYc FZc IStruct sel$list around Seg1 Res1 Atm1 FRad Seg2 Res2 Atm2 IStruct FRad FXc FYc FZc IStruct # # Search for atoms using multiple selection lists. # Return atom or residue number ranges in form # Num11[-Num12][,Num21[-Num22][,...]] # Return segment names as comma separated list. # Return selection list as list of segment names, residue number ranges and # atom number ranges. # Structure index "IStruct" can also be "all" or "sele$cted". # atom$s join Seg1 Res1 Atm1 IStruct Seg1 Res1 Atm1 Seg2 Res2 Atm2 IStruct Seg1 Res1 Atm1 Seg2 Res2 Atm2 Seg3 Res3 Atm3 IStruct ... resi$due join Seg1 Res1 Atm1 IStruct Seg1 Res1 Atm1 Seg2 Res2 Atm2 IStruct Seg1 Res1 Atm1 Seg2 Res2 Atm2 Seg3 Res3 Atm3 IStruct ... segm$ent join Seg1 Res1 Atm1 IStruct Seg1 Res1 Atm1 Seg2 Res2 Atm2 IStruct Seg1 Res1 Atm1 Seg2 Res2 Atm2 Seg3 Res3 Atm3 IStruct ... sel$list join Seg1 Res1 Atm1 IStruct Seg1 Res1 Atm1 Seg2 Res2 Atm2 IStruct Seg1 Res1 Atm1 Seg2 Res2 Atm2 Seg3 Res3 Atm3 IStruct ... ************************************************************************** LUL/2002 **************************************************************************