wilson - Wilson plot, absolute scale and temperature factor
wilson hklin input.mtz
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'.
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.
Specify the TITLE to write to the log file.
<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 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).
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.
- use observed reflection count to determine average intensity (default). This is the normal option.
- use total number of possible reflections to determine average intensity (i.e. assume missing data are all zero). THIS IS NOT NORMALLY CORRECT.
<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 hydrogens
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.
<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> is the volume per atom, default 10.
Controls printout from reading file and batch headers.
- no header printed
- brief header (default)
- brief + history
- full header printed
- no batch header printed
- batch titles printed (default)
- batch orientation data also printed
The default is to use the symmetry from the input HKLIN file. Normally OMIT this command.
Column assignments for the program columns.
- standard deviation of amplitude
- 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.
dm, rwcontents (1), xloggraph.
Eleanor Dodson, Phil Evans
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