Xplor fit backbone.inp - Xplor script to overlay NMR structures by a specific atom selection

remarks based on file  nmr/average.inp
remarks original author: Axel T. Brunger
 
{== PUT PATH TO YOUR PSF FILE HERE ==>}
structure @../peptide.psf end                     {*Read the structure file.*}
 
{== MODIFY FITTED ATOM SELECTION TO YOUR NEEDS ==}
vector idend (store9) (
                        (name ca or name c or name n)
)
 
   {*============ The first stage consists of computing the mean structure.*}
 
eval ($nfile=0)
vector do (store1=0) (all)
vector do (store2=0) (all)
vector do (store3=0) (all)
vector do (store4=0) (all)
 
evaluate ($count = 0)
{== TYPE IN ACTUAL FILE NAMES ==}
for $1 in
(
"file1.pdb"
"file2.pdb"
)
loop main
 
evaluate ($count = $count + 1)
coor @@$1
 
   if ($count=1) then
      coor copy end              {*Store first structure in comparison set.*}
   end if
 
   coor sele=( recall9 ) fit end
 
                      {* swap equivalent groups to minimize rms difference *}
 
   vector do (store1=store1+x) (all)
   vector do (store2=store2+y) (all)
   vector do (store3=store3+z) (all)
   vector do (store4=store4+x*x+y*y+z*z) (all)
   eval ($nfile=$nfile+1)
end loop main
 
vector do (x = store1 / $nfile) (all)
vector do (y = store2 / $nfile) (all)
vector do (z = store3 / $nfile) (all)
vector do (bcomp=sqrt(max(0,store4/$nfile-(x**2+y**2+z**2)))) (all)
 
 
        {*The second stage consists of computing an overall rms difference.*}
 
evaluate ($ave_rmsd_all=0.)
evaluate ($ave_rmsd_back=0.)
 
coor copy end
 
evaluate ($count = 0)
{== TYPE IN ACTUAL FILE NAMES ==}
for $1 in
(
"file1.pdb"
"file2.pdb"
)
loop main
 
evaluate ($count = $count + 1)
coor @@$1
        coor fit sele=( recall9 ) end
        coor rms sele=( recall9 ) end
        eval ($out_file = "fitted_" + $1)
        write coor output=$out_file end
        eval ($ave_rmsd_back=$ave_rmsd_back + $result)
        coor rms select (not hydro and (recall9) ) end
   coor rms selection=( not hydrogen )end
   evaluate ($ave_rmsd_all =$ave_rmsd_all + $result)
end loop main
 
evaluate ($ave_rmsd_back=$ave_rmsd_back / $nfile)
evaluate ($ave_rmsd_all =$ave_rmsd_all  / $nfile)
display ave. rms diff. to the mean struct. for non-h atoms= $ave_rmsd_all
display ave. rms diff. to the mean struct. for the backbone= $ave_rmsd_back
 
   {*====== Finally, the average structure and RMSDs are written to a file.*}
coor swap end
vector do (b=bcomp) ( all )
 
remarks unminimized average over $nfile files
remarks ave. rms diff. to the mean struct. for non-h atoms= $ave_rmsd_all
remarks ave. rms diff. to the mean struct. for the backbone= $ave_rmsd_back
remarks b array (last column) is the rms difference from the mean
 
{====>}            {*Write average coordinates and RMSDs to specified file.*}
write coordinates output=average.pdb end
 
 
stop

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