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                             atom command
                        Leif Laaksonen CSC 1996
                        Timm Uhlmann       2003
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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



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LUL/2005
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