Anafcf

• Introduction
  
• How it works
  
• Invocation
  

Introduction

How it works

1. You specify name.fcf or name.fco
2. weights
   • commandline
     • If weighta and weightb are specified on the commandline, use them.
     • If weighta is specified on the commandline, use it, and set weightb to zero.
     • If weightb is specified on the commandline, use it, and set weighta to zero.
   • name.cif or name_lsum.cif
     • If weighta and weightb are found in the ciffile, use them.
     • If weighta is found in the ciffile, use it, and set weightb to zero.
     • If weightb is found in the ciffile, use it, and set weighta to zero.
   • reflections from .fcf or .fco file
     • weighta=0.0
     • weightb=0.0
   • otherwise
     • weighta=0.1
     • weightb=0.0
3. read name.fcf The following items are extracted:

   fcfname	item
   _cell_length	a b c
   _cell_angle	α β γ
   _refln_index_h	h
   _refln_index_k	k
   _refln_index_l	l
   _refln_F_squared_calc	Icalc
   _refln_F_squared_meas	Iobs
   _refln_F_squared_sigma	σobs
   _refln_observed_status (fcf file)	status
   _refln_status (fcf file)	status
   _refln_XD_refine_code (fco file)	status
   _shelx_refinement_sigma	σ (weights applied)

4. Calculate σ
   • if the fcf file contains a _shelx_refinement_sigma item, the corresponding value is used (unless --ignorefcfsigma is specified on the commandline)
   • if I_obs, I_calc and σ_obs are available:
     p = max(I_obs,0.0) + 2/3*I_calc
     σ = √( σ_obs² + (weighta*p)² + weightb*p)
   • use σ_obs
5. Ignore reflections if:
   • too weak (I_obs/σ < c
     c can be specified on the commandline using crit=c.
   • status <> 0 (fco file)
   • I_obs < 1.0
   • I_calc < 1.0
6. Calculate various variables.
   • from cell parameters a, b, c, α, β and γ construct an rmatrix R
     resolution = 0.5*|R·hkl|
   • d=0.5/resolution
   • if wavelength is set: θ = asin(λ/2d)
   • log(I_obs)
   • √(I_obs)
   • log(I_calc)
   • √(I_calc)
   • Δ = I_obs - I_calc
   • I/σ = I_obs/σ
   • delsig = Δ / σ
   • delsig2 = Δ / σ²
   • del2sig2 = Δ² / σ²
7. You specify what to plot

Invocation

• --verbose (-v)
  verbose output. ( -vv is even more)
• --bins ......
  Set the upper resolution limits for every bin. This option expects 10 arguments, one for each bin. (Do not use the option --nbin to change the number of bins.)
• --cell f f f f f f
  Set the cell parameters: a, b and c (in Å) and alpha, beta and gamma (in degrees).
  The cell parameters are normally extracted from the fcffile.
• --crit (-c) f
  Set the minimum I/σ to f
  Default is -2.0
• --dotsize (-d) n
  Set the dotsize in the scatterplots to n pixels.
  Default is 4.
• --ignorefcfsigma
  When reading from an fcf file, ignore the value of _shelx_refinement_sigma item, and calculate σ using I_obs, I_calc, σ_obs, weighta and weigthb.
• --ignorestatus
  When reading from an fco file, reflections with a nonzero status will be ignored, unless --ignorestatus is set.
• --lsparameters n
  Set the number of parameters in the refinement to n
  The default value is extracted from the corresponding ciffile.
• --margin f
  Set the margin (fraction of range) for the axes. The default is 0.01, expanding both axes by 1%.
• --mode (-m) m
  m is the number (starting from 0) of the variable of the first plot. The available variables depend on the input data.
  0. scatterplot I_obs vs I_calc
  1. scatterplot log(I_obs) vs log(I_calc)
  2. scatterplot √(I_obs) vs √(I_calc)
  3. scatterplot σ vs I_obs
  4. scatterplot Δ/σ vs log(I_calc)
  5. scatterplot Δ/σ vs resolution
  6. normal probability Δ/σ
  7. histogram <I_obs> vs resolution
  8. histogram √<Δ/σ)²> vs resolution
  9. histogram √<(Δ/σ)²> vs I_calc
  10. histogram <I_obs/I_calc> vs resolution
  11. histogram <I_obs/I_calc> vs I_calc
• --nbin (-n) n
  Set the number of bins for the histogram plots. Default = 10
• --pagehor f
  Set the horizontal page dimension (in mm) to f
  The default is 29.7mm
• --pagever f
  Set the vertical page dimension (in mm) to f
  The default is 21.0mm
• --savetype s
  Set the filetype for the save command to s
  possible values are: png eps jpg pdf pgf ps svg tif
  The default is png
• --unit (-u) s
  Set the unitcell contents to s, a list of atoms. For example Zn1C20H16
• --wavelength f
  Set the wavelength to d Å
  The default value is extracted from the corresponding ciffile.
• --weighta (-a) f
  Set weighta to f
• --weightb (-b) f
  Set weightb to f
• --wc s
  Write fcalc to file s
• --wo s
  Write fobs to file s
• --z n
  Set cell content Z to n
  
• fcffile
  reflection file