!
! Example xprepare.inp file to select XPLOR force field, weighting factors,
! and describe unit cell, scattering factors, and diffraction data file.
! Not much different from the XPLOR tutorial.
! E A Merritt - Oct 1996

!
! the Engh & Huber parameters are taken from directory $TOPPAR
! probably you want a line in your .cshrc file something like
! setenv TOPPAR /usr/local/src/xplor/toppar
!

 parameter 
   @ TOPPAR:parhcsdx.pro
   @ TOPPAR:param1.cho
   @ TOPPAR:param.tips3p
 end

!
! Any extra parameter files to describe prosthetic groups, etc, go here
!
 parameter
   @ lactulose.par
 end

!
! The CHAINID_IS_SEGID option is a local mod to force XPLOR to use
! the PDB chain identifiers as the SEGID on both input and output
!
   eval ($CHAINID_IS_SEGID = 0)	! Force XPLOR to maintain Chain identifiers

! 
! Another local mod to XPLOR, this time an output format for print R-factor
! which is compatible with gnuplot rather than Mathematica
!
   eval ($PRRFAC_EAM = 0)	 

 set echo=false end

!
! Turn off charges on LYS GLU ASP and ARG residues
!
   vector do (charge=0.0) (resname LYS and ( name ce or name nz or name hz* ))
   vector do (charge=0.0) (resname GLU and ( name cg or name cd or name oe* ))
   vector do (charge=0.0) (resname ASP and ( name cb or name cg or name od* ))
   vector do (charge=0.0) (resname ARG and ( name cd or name *E or name cz 
					  or name NH* or name HH* ))

 flags
    include pele pvdw xref
 end

 xrefine

    ! unit cell
	a     = 70.48    b =  73.94      c = 163.64
	alpha = 90.0  beta =  90.0   gamma =  90.0

    ! Space group symmetry IT #19  P212121
	symmetry=(x,y,z)
	symmetry=(-x+1/2,-y,z+1/2)
	symmetry=(x+1/2,-y+1/2,-z)
	symmetry=(-x,y+1/2,-z+1/2)

!  These scattering factors are for Cu Kalpha
!  Include f' terms for S  (0.319 e)
!			O  (0.047 e)
!			N  (0.029 e)
!			C  (0.017 e)
!
!  but no f" terms in this setup because Friedel pairs have been averaged

   SCATter ( chemical C* ) 
   2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .217300

   SCATter ( chemical N* )
   12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -11.500

   SCATter ( chemical O* )
   3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .255500

   SCATter ( chemical S* )
   6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 1.18590

   SCATter ( chemical P* )
   6.43450 1.90670 4.17910 27.1570 1.78000 0.52600 1.49080 68.1645 1.11490

   nreflections = 50000

!
! It is NOT a good idea to ignore your low-resolution data.
! Resist any temptation to set the low resolution cutoff to 10A, or
! (bite your tongue!) even 6A, just to make your R factors look better.
! Include your low-resolution data, but fit it with a bulk solvent correction.
! Set mbins reasonably high so that the effect of the bulk solvent model can be
! evaluated graphically as a function of sin theta/lambda.
!
   resolution 50.0 2.65
   mbins = 15
                      
   reflection
     @ lactulose.xpl
   end

   method=FFT
   fft 
      memory=350000
   end
      
 end

 set echo=true end

!
! Cut on F > sigma(F)
!
    xrefine
        do amplitude ( fobs = fobs * heavy(fobs - 1.0*sigma))   ! sigma cutoff
        fwindow = 0.1 = 100000.0
    end
!
! This value is set either
! (a) by running the "check.inp" script 
! (b) making an empirical decision to up- or down-weight ideal geometry
!     as compared to the X-ray residual
!
    xrefine
	wa = 871000.
    end
!
! Parameters for bulk solvent correction 
! (see scripts ksolref.inp and bsolref.inp)
!
    eval ($KSOL = 0.65)
    eval ($BSOL = 40.)