************************************************************************** atom command Leif Laaksonen CSC 1996 Timm Uhlmann 2003 ************************************************************************** The 'atom' command controls the display and the display style of the atoms. One can choose between the atom/style on or off using the "-" sign in front of the command. # # display the atoms with name segment name Seg # residue name Res # atom name Atm # atom display Seg Res Atm # # display all atoms with a radius of Float around Seg1 Res Atm1 # display Seg1 Res1 Atm1 around Float # # display all atoms of name Seg2 Res2 Atm2 with a radius Float around # Seg2 Res2 Atm2 # # this function returns also the number of atoms selected # around Float Seg2 Res2 Atm2 # # display all atoms of name Seg2 Res2 Atm2 with a radius Float around # Seg2 Res2 Atm2 with colour Colour_name # # this function returns also the number of atoms selected # around Float Seg2 Res2 Atm2 Color_name # # display all atoms of name Seg2 Res2 Atm2 with a radius Float around # Seg2 Res2 Atm2 with colour Int Int Int (RGB colour indexes, 0-255) # # this function returns also the number of atoms selected # "Int Int Int" # # display all atoms of name Seg2 Res2 Atm2 with a radius Float around # Seg2 Res2 Atm2 with colour Float Float Float (RGB colour, 0.0 - 1.0) # # this function returns also the number of atoms selected # "Float Float Float" # # turn the display off for Seg Res Atm # atom -display Seg Res Atm # # turn the display off for atoms within radius Float around Seg1 Res Atm1 # -display Seg1 Res1 Atm1 around Float # # turn the Seg2 Res2 Atm2 atom display off for atoms within a radius Float # around Seg1 Seg2 Atm2 # around Float Seg2 Res2 Atm2 around Float Seg2 Res2 Atm2 Color_name "Int Int Int" "Float Float Float" # # change the atom colour for Seg Res Atm to Colour_name/RGB index # atom coulor Seg Res Atm Color_name "Int Int Int" "Float Float Float" # # colour atoms Seg Res Atm according to the vector array value # from Fmin to Fmax # byvector Seg Res Atm Fmin Fmax # # colour atoms Seg Res Atm according to their atomic partial charge value # from Fmin to Fmax # bycharge Seg Res Atm Fmin Fmax # # display atoms Seg Res Atm as CPK spheres # atom cpk Seg Res Atm # # turn the CPK display off for atoms Seg Res Atm # atom -cpk Seg Res Atm # # display atom labels (full, atom, residue) # full includes segment, residue and atom names (numbers) # by default only the atom label (name) is shown # atom label Seg Res Atm full atom residue -label Seg Res Atm # # display atoms Seg Res Atm in the licorice display style # atom licorice Seg Res Atm # # turn the licorice display style off for atoms Seg Res Atm # atom -licorice Seg Res Atm # # scale the CPK sphere(s) for Seg Res Atm with a value of Float # atom scale cpk Float Seg Res Atm # # when executing a command to include atoms according to a radius # the atoms included will be selected either by atom or by whole residue # this command selects either the atom based or whole residue base selection # default: atom atom selection atom residue # # Create (replace or append) a new atom structure # Rename a structure # Delete all or a single structure # Merge all or a single structure # structure append Name NumberOfAtoms new Name NumberOfAtoms rename FileName delete delete Istructure merge merge Istructure Idestination ************************************************************************** LUL/2005 **************************************************************************