## 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 molid   top
set seltext protein

# load files
mol new     $psffile waitfor all
mol addfile $dcdfile waitfor all

# create atom selections
set ref [atomselect $molid $seltext frame 0]
set sel [atomselect $molid $seltext]
set all [atomselect $molid all]

# count frames
set n   [molinfo $molid get numframes]
set fin [expr $n-1]

# loop over all frames and perform fit
for { set i 1 } { $i < $n } { incr i } {
  $sel frame $i
  $all frame $i
  $all move [measure fit $sel $ref]
}

# write resulting trajectory to a new DCD file
animate write dcd fitted_$temp.dcd beg 0 end $fin waitfor all sel $ref