## This takes a selection and fits that selection for every frame in the
## molecule (all atoms are moved, but the fit is based on the selection).
##
## For example:  fitframes top "protein"
##
## -Jim

puts "vmd -dispdev text < fit_frames.tcl -args psffile dcdfile temp_k"
set psffile [lindex $argv 0]
set dcdfile [lindex $argv 1]
set temp [lindex $argv 2]
set mol id top
set seltext protein
mol addfile     psf $psffile dcd $dcdfile
  set ref [atomselect $mol new id $seltext frame 0]
    set sel [atomselect $mol new id $seltext]
      set all [atomselect $mol new id all]
        set n [molinfo $mol new id get numframes]
          set fin [expr $n-1]

            for { set i 1 } { $i < $n } { incr i } {
                $sel frame $i
                    $all frame $i
                        $all move [measure fit $sel $ref]
                          }
                          animate write dcd fitted_$temp.dcd beg 1 end $fin waitfor all sel [atomselect top protein]