{+ file: delete_atoms.inp +}
{+ directory: general +}
{+ description: Delete atoms from a structure +}
{+ comment: 
           Reads in a coordinate and structure file, deletes the
           selected atoms and writes out a new coordinate and 
           structure file +}
{+ authors: Axel T. Brunger, and Paul D. Adams +}
{+ copyright: Yale University +}

{- Guidelines for using this file:
   - all strings must be quoted by double-quotes
   - logical variables (true/false) are not quoted
   - do not remove any evaluate statements from the file -}

{- begin block parameter definition -} define(

{======================= molecular structure ==========================}

{* input molecular structure file *}
{===>} structure_infile="amy.mtf";

{* input coordinate file *}
{===>} coordinate_infile="amy.pdb";

{=========================== deleting atoms ==========================}

{* selection of atoms to be deleted *}
{* to delete all hydrogen atoms: (hydrogen) *}
{===>} atom_delete=(resid 71:74);

{=========================== output files ============================}

{* output molecular structure file *}
{===>} structure_outfile="delete_atoms.mtf";

{* output coordinate file *}
{===>} coordinate_outfile="delete_atoms.pdb";

{===========================================================================}
{        things below this line do not normally need to be changed          }
{===========================================================================}

 ) {- end block parameter definition -}

 checkversion 1.2

 evaluate ($log_level=quiet)

 structure @@&structure_infile end

 coordinate @@&coordinate_infile

 delete selection=(&atom_delete) end

 write structure output=&structure_outfile end

 write coordinate output=&coordinate_outfile end

 stop