generating emap and hkl file from structure

[Jack Tanner]

!calculate structure factors for model

!----------------------------------------------------
!You need to change this stuff

 eval ($pfile ="protein.psf")   {input protein structure file}
 eval ($xfile ="protein.x")     {input coordinate file}
 eval ($rfile ="protein.fob")   {xplor fobs output file}
 eval ($f_cut=0.0)           {amplitude sigma cutoff}
 eval ($f_win1=0.1)          {amplitude window}
 eval ($f_win2=100000.0)     {amplitude window}
 eval ($lres=99.0)           {low resolution limit of data set}
 eval ($hres=2.66)           {high resolution limit of data set}

!End of stuff you need to change
!----------------------------------------------------

 struc           @$pfile end
 coor            @$xfile

!read scattering factors and parameter file
 @scatfact.inp
 parameter @parhcsdx.pro end

 xrefine
   a=73.400   b=109.200   c=33.600  alpha=90.00  beta=95.10  gamma=90.00
   symm=( X,Y,Z       )
   symm=( -X,Y+1/2,-Z )
   nreflections=35000
   fwind $f_win1 $f_win2
   resolution  $lres $hres
   mbins=10
   method=FFT
   fft  memory=2000000 end
   generate
   update
   do amplitude (fobs=fcalc)
   write refl fobs  output=$rfile end
   ?
 end

stop


>Hello,
>
>I'm a complete newbie to xplor, and I haven't been able to figure out
>how
>to get xplor to do what I want.  I'd like to be able to take a PDB file
>and work "backwards" as it were to generate an emap and a reflections
>file
>which have the density and reflections which would be calculated based
>on
>the given structure.  I'm sure it's possible to generate an Fcalc map,
>and
>it ought to be possible to generate an hkl file with theoretical
>intensities and phases.
>
>I've found the map.imp tutorial, and this seems a likely starting
>canidate, but I can't figure out how to get it to give me Fcalc instead
>of
>2Fo-Fc, (I've got an idea, but I'm not sure its right), and I can't
>figure
>out at all how to get xplor to calculate the expected reflections.
>
>I'd appreciate any help anyone can provide here.
>
>Thanks,
>Jon Christopher
>
>P.S. Please CC any replies to jac8792 at tamu.edu.
>
>--
>Dr. Jon A. Christopher           / jac8792 at tamu.edu | Project URLs:
>Department of Biochem./Biophys. /  spock: http://quorum.tamu.edu/spock
>Texas A&M University MS-2128   / lesstif: http://www.lesstif.org/
>College Station, TX, 77843    / personal: http://quorum.tamu.edu/jon


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Dr. John J. Tanner
University of Missouri - Columbia
Chemistry Dept.
125 Chemistry Bldg.
Columbia, MO 65211
USA

phone:  573-884-1280
fax:    573-882-2754
tannerjj at missouri.edu
http://www.chem.missouri.edu/TannerGroup/tanner.html
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