KEYWORDS: For commands longer than four letters, only the first four letters 
  are necessary. '!' will comment out rest of the line. 'stop' will
  terminate input.
  absf_rms <real value>: absolute rmsF for placing data at absolute scale.
    example: absf_rms 205 (obtained from absolute)
  anocut <real value>: cutoff for large anomalous differences.
    reflections with abs(F+-F-)>anocut*rmsdel are rejected.
    example: anocut 5.0 
    default: 4.0
  atom <real value> <real value> <real value> <real value> <real value>:
    fractional atomic coordinates, b factors, occupancies of 
    anomalous scatters.
    example: atom .51329 .07269 .32309  31.80000 .90000
  batch_group <integer> <integer>: 
    lower and higher batch limits of this group. Sequential group
    numbers (starting from 1) are assigned to each batch_group
    definition.
    example: batch_group 101 200 !group 1
             batch_group 201 300 !group 2  
  bover <real value>: overall B factor of your structure factors.
    example: boverall 30.0 
    default: 20.0
  cell <real value> <real value> <real value> <real value> 
    <real value> <real value>: unit cell constants. 
    example: cell 120.0 120.0 200.0 90.0 90.0 120.0 
  comment <anything>: put any comment here.
    example: comment MAD experiment of hCG
  copy_per_au <integer>: number of copies per assymetric unit
    example: copy_per_au 2 
    default: 1
  cycle <integer>: number of cycles of refinement in ASLSQ.
    example: cycle 5
    default: 4
  dffcut <real value>: reflections with abs(F+-F-)/F>dffcut are not included 
    in statistics of anoscl.
    example: dffcut 5.0
    default: 10.0
  difference_Fourier <real value> <integer>: Do Fa difference Fourier
    in aslsq with peak height cut and number of peaks to output.
    example: diff_F 5.0 10
    default:
  dispcut <real value>: difference between two wavelengths 
    |F(l1)-F(l2)|>dispcut*rmsdel are rejected from wvlscl.
    example: dispcut 5.0
    default: 4.0
  error intensity/amplitude
    example: error intensity
    default: amplitude 
  facut <real value>: fa sigma cutoff
    example: facut 2.0
    default: 1.0
  faflag <real value1> <real value2>: reflections with 
    fa > <real value1>*exp(-<real value2>*s**2) are flaged.
    example: faflag 600.0 20.0
    default: 100000, 20; if famax is defined, <real value1>=famax
  famax <real vaule>: maximum fa cutoff. 
    example: famax 600
    default: 100000
  famin <real vaule>: minimum fa cutoff used in statisics of MADFAZ.
    example: famin 0
    default: 0
  fcscale <real vaule>: scale applied to calculated fa
    example: fcscale 1.10
    default: 1.0
  fdeviation <real vaule>: |f-fave|>fdeviation*sigma will not be used 
    in madlsq fitting or madabcd.
    example: fdeviation 6.0
    default: 10.0
  fit scale/fp/fpp <integers>: 0/1 for each wavelength (0: fix, 1: refine)
    example: fit scale 0 1 1 1
               (refine relative scale of wavelengths 2, 3, and 4)
             fit fpp 0 0 1 1
               (refine f" of wavelengths 3 and 4)
             fit fp 0 1 1 0
               (refine f' of wavelengths 2 and 3)
  format scalepack/ccp4 or <fortran format statement>: any Fortran format 
    statement specifying h,k,l,batch,i,sigi,or
    example: format scalepack 
               (take NO MERGE ORIGINAL INDEX scaling output from scalepack)
             format ccp4
               (take a modified output from AGROVATA, the agravata.f is
                distributed along with madsys which output a formatted
                file named AGRO_OUT)
             format 4i4,2f8.3
    default: scalepack
  fp <real values>: anomalous scattering factor f' of each wavelength.
    example: fp -4.1 -10.0 -8.5 -3.2
  fpp <real values>: anomalous scattering factor f" of each wavelength.
    example: fpp 0.51 4.0 5.5 3.7
  frange <integer>: number of amplitude/intensity ranges for estimating
    lack of closure errors in madabcd.
    example: frange 10
    default: 5
  fzcut <real value>: fz sigma cut.
    example: fzcut 1.0
    default: 2
  fzmax <real value>: maximum fz.
    example: fzmax 6000
    default: 100000
  groups_include <integers>: groups to include.
    example: group 1 2 3 4
  infile <function keyword> <file names>: input file name for a specific
    function. For f2ano, anoscl, anomerge, anores, wvlscl and fa, the 
    program expects same number of files as the number of wavelengths. 
    For others, one file is expected. You can split the files on
    several lines for those that expect the same number of files as the
    number of wavelengths. 
    absolute: protein sequence in 1- or 3-letter code.
    anomerge, wvlscl: output from f2ano or anoscl.
    anores: output from f2ano or anoscl.
    anoscl: output from f2ano.
    aslsq: output from mergit.
    f2ano: scaling program output.
    fa: scaling program output.
    madabcd: output from madlsq and wvlscl.
    madfaz: output from mergit.
    madlsq: output from wvlscl.
    mergit: output from madlsq.
    phase: output from madlsq and wvlscl. Same as madabcd.
    wvlscl: output from f2ano or anoscl.
    example: infile f2ano l1.hkl l2.hkl
             infile f2ano l3.hkl l4.hkl
             infile f2ano l1.hkl l2.hkl l3.hkl l4.hkl
             infile madabcd wvlscl.dat madlsq.dat          
  inflate_error <real value>: inflate lack of errors by <real value> fold.  
    example: inflate 2.0
    default: 1.0
  inverse <integer> <integer> <integer> <integer>: inverse beam geometry with 
    starting batch # and end batch # for the direct sweep, batch difference 
    between direct and inverse data sweep, batch tolerance in pairing.
    example: inverse 1 40 40 4 (this inverse beam data contain batches 1-40 
               as direct sweep, 41-80 as inverse sweep, pair any hkl/-h-k-l 
               that are separated by 40+/-4 batches)
  iterations <integer>: number of iteractions of madlsq phasing.
    example: iteractions 5
    default: 2
  list <integer>: list every <real value>-th reflection.
    example: list 1000 
    default: 10000
  local_scaling all/centrics/acentrics, group <integers> reso <real vaule>
    <real value>: define local scaling group.
    example: local all group 1 2 3 reso 30 3.0 (This scaling group uses both 
               centrics and acentrics of group 1, 2, and 3 and at resolution 
               30-3.0A)
             local centrics group 3 4 5 resol 20 4.0 (This scaling group uses
               only centric reflections for determing scale factors)
  mirror <integer> <integer> <integer> <integer> <integer> <integer>: mirror
    geometry with starting batch #, end batch #, batch tolerance in pairing, 
    and spindle axis direction specified by three numbers along the a*,b*
    and c*.
    example: mirror 1 82 4 1 1 0 (this mirror geometry data contains batches 
               1-82, pair any reflections related by the mirror plane at 
               +/- 4 batches, spindle is along a*+b*)
  name <character> <integer> <integer>: atom name, atomic number and number 
    of sites per asy_unit.
    example: name se 34 4
  number_wavelength <integer>: number of wavelengths.
    example: number_wavelength 3 
    defaults: 4
  nstep <integer>: number of steps to search at either side of Fz in a
    2-D phase probability distribution to obtain a best Fz and best
    phase probability distribution.
    example: nstep 10
    default: 0
  observations <integer>: minimum number of total observations for each
    reflection in wvlscl before merging into other reflections.
    example: observation 6
    default: 1
  outfile <function keyword> <file names>: output file names for a 
    specific function. You can either write out output from every function, 
    or if you run several functions sequentially as outlined in the flow
    chart, you can just save the output from your final function.
    For f2ano and anoscl, there will be same number of output files as the 
    number of wavelengths. For others, one file is output.
    absolute: no output. 
    anomerge: in xplor format, containing h,k,l,delta(F) and sigma. unit 41.
    anores: no output.
    anoscl: output after anisotropic parameterized local scaling. 
      unit 31-30+n for n wavelengths.
    aslsq: containing refined fcscale and site, b and occupancy of anomalous 
      scatters. unit 65.
    f2ano: paired reflections. unit 21-20+n for n wavelengths.
    fa: merged reflections containing fz, fa, delta(phi). unit 55.
    madabcd: containing phased reflections and a,b,c,d coefficients. unit 60.
    madfaz: phased reflections containing fz, phi, etc. unit 55.
    madlsq: unmerged reflections containg fz, fa, delta(phi). unit 45.
    mergit: merged reflections containing fz, delta(phi), etc. unit 55.
    phase: containing phased reflections and a,b,c,d coefficients. unit 60.
    wvlscl: reflections after scaling among wavelengths. unit 40. 
    example: outfile fa mergit.dat
  output Ft/Fn Facalc/Faobs (Facalc/Faobs required for Fn only)
    example: output Ft (Ft containg the normal scattering component of the
      entire unit cell content) 
    example: output Fn, facalc (Fn containing only the normal scattering 
      component of non-anomalous scatters alone)
    defaults: Ft
  pmax <real value>: maximum sigma(phi).
    example: pmax 60
    default: 50
  print verbose
    example: print verbose
    default: not verbose
  qmax <real value>: maximum quart (a value representing goodness of madlsq
    fitting).
    example: qmax 30.0
    default: 20.0
  random <3 integers>: random pairing based only on batch separation is
    applied with low batch limit, high batch limit and batch difference
    allowed in pairing.
    example: random 1 30 20
  refine scale/b/occupancy: define what to refine, position always refine.
    example: refine scale
             refine scale b (you can do this, but will be very unstable,
               refine scale first, then input refined scale, refine b or 
               occupancy)
    default: not to refine scale, b or occupancy 
  resolution <real value> <real value>: upper and lower resolution range 
    in angstrom.
    example: reso 30 2.0 
    default: infinity to zero angstrom, i.e. the entire possible range
  rmsdeltaF <real value>: rms(F+-F-) obtained from a previous run.
    example: rmsdel 118
    default: calculate within the program
  scale <real values>: relative scale between the wavelengths as obtained
    from ABSOLUTE.
    example scale 1.00 0.996 0.992 1.003 (relative scale between the four 
      wavelegths)
    defaults: 1.00 1.00 1.00 1.00
  scattering_factor <9 real values>: scattering factor exponentials 
    (a(i),b(i),i=1,4),c as in International table Vol IV.
  sc_cycle <integer>: number of cycles of scattering_factor_refinement in
    madlsq. 
    example: sc_cycle 5
    default: 4
  sequence <integer>: letter code of your input amino acid or nucleic
    acid or sugar sequence (one or three letter code). One letter code only
    works for amino acid sequence, for which a list of one letter codes
    is formatted as '72i1'. For three letter code, the format is 
    '18(i3,1x)' for each line, e.g. part of a line can look like 
    'GLY ARG THR ' or 'dT  dA  U   '. Supported sugars are: SIA, FUC, MAN, 
    GAL, GLC, NAG.
    example: sequence 3 (three letter code)
    default: 1
  shell <integer>: number of resolution shells. 
    example: shell 10
    default: 5
  skcut famax/fzmax/facut/fzcut/pmax/qmax <real value> reso <real values>
    alternative way of defining cuts in scattering factor refinement 
    in madlsq. 
    example: skcut famax 600 facut 1.0 reso 20 3.5
    example: skcut famax 600 fzcut 2.0 facut 1.0 qmax 20.0 
    default: same as defined under each individual cutoff.
  step <real value>: step size in sigma of searching the best Fz in 
    MADABCD.
    example: step 1.0
    default: 0.5
  stop: stop input stream.
    example: stop
  symmetry <character>: space group name as appears in International table
    except: 
    p2c: c unique p2
    p21c: c unique p21
    b2: c unique c2
    r3r: r3 of rhombohedren setting
    r32r: r32 of rhombohedren setting.
    PLEASE: Always check the symmetry printout to make sure that they
      are correct since not all space groups have been extensively
      tested.
    example: symm P212121 
  wave_scaling group <integers> resolution <2 real values>: scaling group
    in WVLSCL.
    example: wave_scaling group 1 2 reso 10 2.5 (This wvlscl scaling group
               contains groups 1 and 2 and reso 10-2.5A)
  weighting_scheme prolsq/sigma prolsq/sigma(optional) <2 real values>(optional)
    example: weight prolsq
             weight prolsq -105.0 30.0
             weight prolsq sigma
             weight sigma
    default: no weighting
  xplor <function keyword> <file name>: output xplor file name for functions
    FA, MERGIT, PHASE, MADFAZ AND MADABCD.
    example: xplor madabcd phase.dat