Modar internal command:

 calc

To delete/remove atoms, connections, angle, dihedrals, improper dihedrals from current structure.

  • Syntax
    delete <subcommand>  <select expr> ...

  • Subcommands and examples:
    • atom

      #to remove atoms and also all connections involved

      delete atom select=”residue PROA 10”


    • bond/connect

      #to remove connection between two atoms

      # all relevant angles, dihedrals, impropers, cmaps will be removed also

      delete bond select=”residue PROA 10” select=”residue PROA 11”


    • angle

      #to remove angle among three atoms

      delete angle select=”atom PROA 10 C” \

                   select=”atom PROA 11 N” \

                   select=”atom PROA 11 CA”



    • dihe/dihedral

      #to remove dihedral involving two atoms, i.e. *--j--k--*

      delete dihe  select=”atom PROA 11 N” \

                     select=”atom PROA 11 CA”



    • dihe4

      #to remove dihedral among four atoms, i.e. i--j--k--l

      delete dihe4  select=”atom PROA 10 C” \

                    select=”atom PROA 11 N” \

                    select=”atom PROA 11 CA” \

                    select=”atom PROA 11 C”


    • impr4

      #to remove improper dihedral among four atoms, i.e. i--j--k--l

      delete impr4  select=”atom PROA 11 N” \

                    select=”atom PROA 10 C” \

                    select=”atom PROA 11 CA” \

                    select=”atom PROA 11 HN”



    • impr

      #to remove improper dihedral for center atoms involved,

      # i.e. i--*--*--*, i is the center atom

      delete impr   select=”atom PROA 11 N”


  • Variables exported:
    none

 

 

 

 

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