{+ file: bfactor_plot.inp +}
{+ directory: general +}
{+ description: Calculate B-factor distribution for a structure +}
{+ comment: 
           the average B-factor is calculated for each residue 
           and also for the mainchain atoms and sidechain atoms in
           each residue +}
{+ 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 =========================}

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

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

{========================== atom selection ===========================}

{* select atoms to be included in calculation *}
{===>} atom_select=(known and not(hydrogen));

{* select main chain atoms *}
{* note: atoms outside this selection will be considered to be
         side chain atoms *}
{===>} atom_main=(name ca or name n or name c or name o or name ot+);

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

{* output listing file *}
{===>} list_outfile="bfactor_plot.list";

{===========================================================================}
{        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

 coordinates @&coordinate_infile

 set display=&list_outfile end

 display >>>> B-factor plot for:
 display >>>>   structure file= &STRIP%structure_infile
 display >>>>   coordinate set= &STRIP%coordinate_infile
 display
 display  segid  resid  resname     B-factor   B-factor-main   B-factor-side
 display

 set display=OUTPUT end

 for $id in id ( &atom_select and tag ) loop bfac

   show (segid) (id $id)
   evaluate ($segid=$result)
   show (resid) (id $id)
   evaluate ($resid=$result)
   show (resname) (id $id)
   evaluate ($resname=$result)

   show ave(b) (segid $segid and resid $resid)
   evaluate ($bfactor=$result)

   show ave(b) (segid $segid and resid $resid and &atom_main)
   evaluate ($bfactor_main=$result)

   show ave(b) (segid $segid and resid $resid and not(&atom_main))
   evaluate ($bfactor_side=$result)

   set display=&list_outfile end
   display  $segid[a4]    $resid[a4]    $resname[a4]   $bfactor[f10.4] \
   $bfactor_main[f10.4]      $bfactor_side[f10.4]
   set display=OUTPUT end
   
 end loop bfac

 stop