xray <xray-statement> end

<xray-statement> :==

  reset
  --{Erases xray database.}
  nreflections=<integer>
  --{Allocates space for reflections.}
  reflection {<xray-reflection-statement>} end
  --{Read reflections.}
  a=<real> b=<real> c=<real> alpha=<real> beta=<real> gamma=<real>
  --{Unit cell specifications.}
  symmetry=?|reset|<symmetry-operator>
  --{Add a symmetry operator to symmetry database.
     Operators are from the International tables e.g. (-x,y+1/2,-z)
     and must include parenthesis. Reset removes all operators
     except identity.}
  scatter <atom-selection> <real> <real> <real> <real> <real>
          <real> <real> <real> <real> [fp <real>] [fdp <real>]
  --{Scattering factor parameters a1, b1, a2, b2, a3, b3, a4, b4, c, i
     The atomic form factor for selected atoms is:
        f(real)=sum(i=1,4) a[i] exp(-b[i] s**2/4) + c + f' + if''}
  scatter reset
  --{Remove current atomic form factors.}
  scatter ?
  --{Print info about current atomic form factors.}
  associate <xray-object> <atom-selection>
  --{Associate a reciprocal space object with the specified atoms.
     Default: associate fcalc ( not hydrogen ).
     Multiple associate statements are permitted.}
  associate reset
  --{Remove all associate definitions.}
  aselection=<atom-selection>
  --{Selected atoms with f' enabled.}
  method=direct|fft
  --{Use direct summation or fast Fourier transform. Default=fft}
  target=( <xray-expression> )
  --{Crystallographic target specification.}
  dtarget(<xray-object>)=( <xray-expression> )
  --{Define derivative of target with respect to object.}
  monitor=( <xray-expression> )
  --{Refinement monitor expression.}
  tselection=( <xray-expression> )
  --{Target selection expression.}
  cvselection=( <xray-expression> )
  --{cross-validation selection expression.}
  lookup=<logical>
  --{Use lookup tables for cos, sin, exp.}
  fft {<xray-fft-statement>} end
  --{Set parameters for fft method.}
  tolerance=<real>
  --{Tolerance (in Angstroms) for recalculating structure factors used
     in target calculation. If tolerance is exceeded, structure factors
     are re-calculated during calls to energy.
     Recommended: 0.0 for minimization and 0.2 for dynamics.}
  wa=<real>
  --{Overall weight for target function.}
  do <xray-do-statement>
  --{Manipulates crystallographic objects.}
  show <xray-show-statement>
  --{Show properties of crystallographic objects.}
  flip
  --{Flip all friedel mates.}
  declare <xray-declare-statement> end
  --{Declare crystallographic objects.}
  undeclare <xray-undeclare-statement> end
  --{Undeclare crystallographic objects.}
  rename <xray-rename-statement> end
  --{Rename crystallographic objects.}
  query <xray-query-statement> end
  --{Query crystallographic objects.}
  group <xray-group-statement> end
  --{Groups crystallographic objects.}
  ungroup <xray-ungroup-statement> end
  --{Ungroups crystallographic objects.}
  generate <real> <real>
  --{Generate additional reflections to produce a full asymmetric unit
     of reflections for the specified resolution range.}
  delete <xray-delete-statement> end
  --{Delete reflections.}
  expand
  --{Expand all reflections and symmetry operations to P1.}
  unexpand
  --{Un-does the expand statement. This is only possible if 
     reflections and/or symmetry operations were not altered since
     the last expand statement.}
  anomalous=<logical>
  --{Non-anomalous / anomalous data.}
  friedel_average
  --{Performs averaging of all friedel mates.}
  mapresolution <real>
  --{High resolution limit for maps and FFT method.}
  bins=<integer>
  --{Number of reciprocal space bins. Default=8
     Declares a symbol $bin_number.}
  binresolution <real> <real>
  --{Resolution limits of reciprocal space binning.
     declares symbols $bin_resolution_low and $bin_resolution_high.}
  print target
  --{Print the current value of the crystallographic target.
     Also defines symbols: $target, $test_target, $monitor and $test_monitor.}
  predict <xray-predict-statement> end
  --{Predict crystallographic data.}
  write reflection {<xray-write-reflection-statement>} end
  --{Write reflection data.}
  write map {<xray-write-map-statement>} end
  --{Write map.}
  write mask {<xray-write-mask-statement>} end
  --{Write mask.}
  read map {<xray-read-map-statement>} end
  --{Read map.}
  read mask {<xray-read-mask-statement>} end
  --{Read mask.}
  mask {<xray-mask-statement>} end
  --{Compute a mask.}
  optimize overall {<xray-optimize-overall-statement>} end
  --{Optimize an overall B-factor.}
  optimize group {<xray-optimize-group-statement>} end
  --{Optimize group B-factors or group occupancies.}
  optimize bfactor {<xray-optimize-bfactor-statement>} end
  --{Optimize individual (restrained) isotropic B-factors.}
  special {<xray-special-statement>} end
  --{Obtain information about special positions.}
  fmap {<xray-fmap-statement>} end
  --{Preparation of flagmap for smf, imf, search tsmap, psearch and lidens.}
  smf {<xray-smf-statement>} end
  --{Compute Symmetry Minimum Function.}
  imf {<xray-imf-statement>} end
  --{Compute Image-seeking Minimum Function.}
  mapyard {<xray-mapyard-statement>} end
  --{Stores and restores real-space objects in P1.}
  search {<xray-search-statement>} end
  --{Rotation and translation searches for molecular replacement.}
  psearch {<xray-psearch-statement>} end
  --{Peak search in P1 map with symmetry relations as defined with fmap.}
  lidens {<xray-lidens-statement>} end
  --{Determine density values in P1 map by linear interpolation.}
  histogram {<xray-histogram-statement>} end
  --{Histogram matching.}
  peakpick {<xray-peakpick-statement>} end
  --{Pick peaks from a map.}
  average {<xray-average-statement>} end
  --{Average real-space object using mask and non-crystallographic symmetry.}
  multiscale {<xray-multiscale-statement>} end
  --{Scaling of structure factors to one another.}
  statistics {<xray-statistics-statement>} end
  --{Print resolution-wise statistics about reciprocal space objects.}
  skeletonize {<xray-skeletonize-statement>} end
  --{Skeletonization of real space object.}
  proximity {<xray-proximity-statement>} end
  --{Calculate real space objects containing atom object information.}