WILSON (CCP4: Supported Program)

NAME

   wilson - Wilson plot, absolute scale and temperature factor

SYNOPSIS

   wilson hklin input.mtz
   [Keyworded input]

DESCRIPTION

   This program reads a file of amplitudes (or of intensities), and
   performs  a  Wilson  plot of the observed intensities against
   resolution to determine an absolute scale and temperature factor.

   If the atoms are randomly distributed in the cell, then
  <f**2> = Scale * <Fobs**2> * exp (-2B (sin theta/lambda)**2)

   where <f**2> is the mean squared atomic form factor summed over all
   atoms in the unit cell. Thus a plot of ln(<f**2>/<Fobs**2>) against
   2(sin theta/lambda)**2 will have slope -B and an intercept Scale.
   The program derives Scale and B by a least squares fit.

   There may be a problem in evaluating <Fobs**2> if all the weak data
   have been systematically omitted (which should NOT be the case for
   data  measured in any proper manner). If weak reflections are
   missing from the data, use the WILSON ALL option. The program then
   estimates the expected number of reflections in each resolution
   shell and then calculates <Fobs**2> by dividing by the number of
   predicted reflections. The program also produces a log graph of the
   numbers of observed and missing reflections against resolution, and
   will work with either amplitudes or with intensities directly
   depending upon which labels are specified in the LABIN keyword.

   Note  that  the  scale  determined  by this procedure is very
   approximate, unless very high resolution data are available. See
   also the determination done by `dm'.

KEYWORDED INPUT

   The available keywords are:

     CONTENTS, END, HEADER, LABIN, NRESIDUE, RANGES, RESOLUTION,
     RSCALE, SYMMETRY, TITLE, VPAT, WILSON.

   N.B., one of CONTENTS or NRESIDUES is compulsory.

  TITLE <title>

   Specify the TITLE to write to the log file.

  RANGES <Nbin> | <Range>

   <Nbin> is number of resolution bins over the resolution range of
   the  Wilson  Plot.  <Range> is the width of ranges on 4sin**2
   theta/lambda**2 and is an alternative to <Nbin>. The resolution
   range of the Wilson PLot is defined by RSCALE. The default if this
   card is absent is <Nbin>=30.

  RESOLUTION <Dmin> <Dmax>

   Resolution limits, either 4(sin theta/lambda)**2 or d in Angstrom
   (either order). Reflections outside these limits will be excluded
   from all analysis and omitted on output. Defaults are taken from
   the range of data in the input file (i.e. all data are included).

  RSCALE <Dmin> <Dmax>

   Resolution limits for scaling, specified as for RESOLUTION. This
   option allows you to exclude low resolution reflections from the
   Wilson  plot: it is probably a good idea to include only high
   resolution data (beyond 3Å, if you have any data there) in the
   Wilson plot. This is because the assumptions made in determining
   the  Wilson  statistics  are not valid for the low resolution
   reflections. The default for the high resolution is the same as
   that for the RESOLUTION card. The default low resolution is 4.0Å if
   the high resolution limit is less than 3.5Å.

  WILSON OBSERVED | ALL

   OBSERVED
          use observed reflection count to determine average intensity
          (default). This is the normal option.

   ALL
          use  total number of possible reflections to determine
          average intensity (i.e. assume missing data are all zero).
          THIS IS NOT NORMALLY CORRECT.

  CONTENTS <element> <natoms> ...

   <element> is an element name (including hydrogen) for which there
   are <atoms> atoms in the asymmetric unit, e.g.
  CONTENTS  H 746 C  454  N 115    O 139   S 12  ! Must include hydrog
ens

   NOTE the program RWCONTENTS reads a PDB file and finds out how many
   Carbons, etc. there are in the file, and gives an estimate of the
   number of hydrogens.

  NRESIDUE <Nres>

   <Nres> is the number of residues expected in the asymmetric unit. A
   very approximate atom composition is calculated using:
   mean mass of an amino acid = 110
   add on one ordered water per amino acid = ca. 128

   This is then taken as 5 C + 1.35 N + 1.5 O + 8 H /residue as number
   of atoms in asymmetric unit.

  VPAT <vpat>

   <vpat> is the volume per atom, default 10.

  HEADER [NONE | BRIEF | HISTORY | ALL] [NOBATCH | BATCH |
  ORIENTATION]

   Controls printout from reading file and batch headers.
    a. file header printing:

        NONE
                no header printed

        BRIEF
                brief header (default)

        HISTORY
                brief + history

        ALL
                full header printed

    b. batch header printing:

        NOBATCH
                no batch header printed

        BATCH
                batch titles printed (default)

        ORIENTATION
                batch orientation data also printed

  SYMMETRY <space group>

   The default is to use the symmetry from the input HKLIN file.
   Normally OMIT this command.

  LABIN <program label>=<file label> .....

   Column assignments for the program columns.

   FP
          amplitude

   SIGFP
          standard deviation of amplitude

   IP
          intensity

   SIGIP
          standard deviation of intensity

   Note that the FP/IP labels are mutually exclusive - you specify if
   the program uses either amplitudes or intensities, but not both.

  END

   Terminate input

SEE ALSO

   dm, rwcontents (1), xloggraph.

AUTHORS

   Eleanor Dodson, Phil Evans

EXAMPLE

wilson  hklin u1afobs  <<EOF-wil
title U1A native, Weis (3/91), 2.5A, pass 3.2
wilson
resolution  20 2.4
rscale      4.5 2.4
nresidues   190
labin  FP=FP SIGFP=SIGFP
EOF-wil