RADDOSE

NAME

   raddose - calculations of absorbed X-ray dose by protein crystals

SYNOPSIS

   raddose
   [Keyworded input]

KEYWORDED INPUT

   The available keywords are:

     CELL, VOLUME, NMON, NRES, NDNA, NRNA, PATM, SATM, SOLVENT, ENERGY, WAVLENGTH,
     PHOSEC, BEAM, CRYSTAL, IMAGES, EXPOSURE, REMARK,,CONVH, HEAT, END
 
   In the description below, optional items are in [], keywords are in
   uppercase, parameters are in lowercase. The input is case-insensitive.

  CELL a b c [alpha beta gamma]

   Cell dimensions in Angstroms, alpha beta and gamma default to 90 degrees.

  VOLUME v
 
   If the CELL card is not given, the unit cell volume may be given in
   cubic Angstroms.

  NMON n

   Number of monomers, n in the unit cell. (N.B. NOT the asymmetric unit).

  NRES n
  
   Number of amino acid residues in a single chain. The number and
   types of atoms are calculated assuming an average amino acid content defined as
   amino acid = 5 C + 1.35 N + 1.5 O + 8H
   Sulfur atoms should be added explicity with the PATM keyword  

  NRNA n 

  Number of RNA nucleotides in a monomer. The number and types of
  atoms are calculated assuming an average nucleotide content defined as.
  mean nucleotide = 11.25H + 9.5C + 3.75N + 7O + 1P 
  If a more accurate estimate is required individual atoms may be
  entered explicitly with the PATM keyword.
   
  NDNA n 

  Number of DNA deoxynucleotides in a monomer. The number and types of
  atoms are calculated assuming an average deoxynucleotide content defined as.
  mean Nucleotide = 11.75H + 9.75C + 4N + 6O + 1P 
  If a more accurate estimate is required individual atoms may be
  entered explicitly with the PATM keyword.

  PATM  no-atoms [ no-atoms]...
  
  Define atoms to add to the protein part of the scattering as no. of
  atoms per monomer

  e.g. PATM  S 10 Se 2 !Add 10 sulfur and 2 selenium atoms per monomer

  SATM  conc-mM [ conc-mM]...

  Define the concentration of elements (not including water) in the
  solvent in millimoles per litre. Do not define these for oxygen and
  lighter elements (ie no PEG, but yes for ammonium sulfate).

  e.g. SATM Na 1000 Cl 1000 ! 1M sodium chloride

  SOLVENT solv_proportion

   The fraction of the unit cell that is occupied by solvent. If not
   given explicity, this value is estimated from NRES, NRNA and NDNA
   using 1.35 g/ml for protein, 2.0 g/ml for RNA and DNA.
 
  SPLINOR Element filename
 
  Optional keyword, to use empirical absorption coefficients from a
  CHOOCH splinor file. Only one SPLINOR keyword may be used.

  e.g. SPLINOR Se se_scan.splinor

  ENERGY energy_keV
  
   The energy of the beam in keV. The beam energy may also be input
   with the WAVELENGTH keyword.
  
  RANGE low_keB high_keV [step_keV]

  Optional range of energies for which to calculate doses. The step
  size defaults to 0.01 keV

  HENDLI dose_Gray

  The radiation dose limit in Gray. Defaults to 2E7 Gray. 

  WAVELENGTH wavelength

   The wavelength of the incident beam in Angstrom.

   If no ENERGY or WAVELENGTH card is given, a wavelength of 1.54 A
   (8.05 keV) is used, corresponding to copper K_alpha radiation.

  PHOSEC psec

  The flux of the beam in photons per second.

  BEAM xbeam ybeam 

  Beam size in mm

  GAUSS x-fwhm y-fwhm

  Optional keyword, giving the full-width-half-maxima in mm of a Gaussian beam profile. If
  this keyword is not given, a uniform beam is assumed.

  CRYSTAL xcryst ycryst zcryst

  Crystal dimensions x,y,z in mm.

  IMAGES no_images

  The number of images taken.

  EXPOSURE exp_time 

  Exposure time per image in seconds.

  CONV convh 
	
  Optional - the convective heat transfer coefficient in 
  W m-2 K-1. Default value 320. Don't change unless you think you know
  what you are doing.
  
  HEAT cp
  
  Optional - Specific Heat Capacity of the Crystal in J/kg/K. Defaults
  to 500. Don't change unless you think you know what you are doing.

  END 

    The end of input tokens


AUTHOR

   James Murray, LMB, Oxford
   Raimond Ravelli, EMBL Outstation, Grenoble, August 2003

BUILDING

compile with something like. 
g77 -O -w -fno-second-underscore -fno-globals -fno-automatic -o raddose name2z.f z2name.f mucal.f upcase.f raddose.f -L$CCP4_LIB  -lccp4

A CCP4 environment must be present.

EXAMPLES


# HEWL Dose calculations #################################
#!/bin/sh
raddose <