ECALC (CCP4: Supported Program)

NAME

ecalc - calculate normalised structure amplitudes

SYNOPSIS

ecalc hklin foo.mtz hklout foo_e.mtz
[Keyworded input]

DESCRIPTION

The program ECALC is used to calculate normalised structure amplitudes for input to molecular replacement and direct methods programs and to calculate origin-removed Patterson coefficients. If the output is to an MTZ file, then it will contain all entries in the input file + F E SIGE F2OR E2OR, see below.

KEYWORDED INPUT

The various data control lines are identified by keywords, those available being:

EXCLUDE, LABIN (compulsory), LABOUT, MULTAN, REFLECTIONS, RESOLUTION, SCALE, SHELL, SNB, SPACEGROUP, TITLE

EXCLUDE [SIGP <nsigp>] [SIGPH <nsigph>] [FPMAX <fpmax>] [FPHMAX <fphmax>] [DIFF <diffmax>]

Set criteria for excluding data from the generation of E values. Large errors can distort the normalisation seriously.

Excluded data will still be written to the output file but there will be no associated value for E; it will be flagged as a "Missing number". The default is to include all data.

The following subkeys select the tests to be applied:

SIGP <nsigp>: exclude reflections if FP < <nsigp>* SIGP
SIGPH <nsigph>: exclude reflections if FPH < <nsigph>* SIGPH
FPMAx <fpmax>: exclude reflections if FP > <fpmax>
FPHMax <fphmax>: exclude reflections if FPH > <fphmax>
DIFF <diffmax>: exclude reflections if abs(FPH-FP) > <diffmax>

TITLE <title>

Title for the output file (up to 80 characters). The text PRODUCED BY ECALC will be appended to this title automatically.

SPACEGROUP <group>

The space group is read from file with logical name SYMOP. Default: Take the SPACEGROUP from the MTZ header. Group is the space group name or number in International Tables. Only the rotation part of the symmetry operations is used, so for example 177 (P622), 178 (P6122) and 179 (P6522) are all equivalent. This keyword is required only if the symmetry information in the reflection file header is missing or wrong.

RESOLUTION <resmax>

Default: take the maximum resolution from the MTZ header. The value <resmax> is the resolution cutoff in Angstroms. Usually 0 to include all reflections.

SHELL <number>

Specifies the approximate number (default 200) of reflections wanted per shell. If this is too small you are likely to get shells with no reflections and the program will stop with the message Empty shell. If it is too big there will be an insufficient number of shells to get sensible averages. Note this number refers to independent reflections; however the output shows the number in a hemisphere of reciprocal space.

MULTAN

No further data are required on this line. Outputs E values in a formatted ASCII file e.g., for Direct Method packages. Normally however, most Direct Method programs will calculate Es internally. Default is to output E values in standard MTZ format e.g., for ALMN.

SNB

No further data are required on this line. Outputs E values in a formatted ASCII file suitable for SnB (Shake-and-Bake).

REFLECTIONS <nwant>

This only applies when outputting reflections to a file and not an MTZ file i.e. in conjunction with the MULTAN/SNB cards. The largest <nwant> Es are written to HKLOUT, the default is to write all reflections. This cutoff may be necessary because some programs will only accept a limited number of reflections. Also, when getting Es from |FPH-FP|, small E values do not necessarily reflect the true E value calculated from the heavy atom sub-structure. For instance, all the centric reflections will have an E of zero.

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

Column label assignments for H, K, L, FP and optionally SIGFP, FPH and SIGFPH.
FP is the native structure amplitude, SIGFP is its standard deviation, FPH is the derivative structure amplitude and SIGFPH is its standard deviation. If FPH is assigned, the absolute difference between the columns assigned to FP and FPH (i.e., the isomorphous difference) corrected by the standard deviation (in columns SIGFP and SIGFPH) bias is used to calculate the F and E values for output. It is important that the standard deviations on the file are sensible, otherwise this won't work. Standard deviations (>0) are also used to check for the existence of measured data but unlike other programs no check is made on Fs. It is much better to use the missing number flag to check for unmeasured data. If FPH is not assigned, the column assigned to FP is used to calculate the E value. SIGFP>0 is used to check for existence of measured data. Similar to above FP is not checked.

LABOUT <program label>=<file label> ...

This card is only required when outputting reflections to an MTZ file. There are three items that can be used with LABOUT: F, E, and SIGE. These are the three extra columns that are output in the MTZ file, the terms are explained below. Basically you can change the column name of these three extra columns, the default names are F_ecalc, E, SIGE. It is essential to change the column names if they already exist in the input MTZ file.

SCALE <scale>

The output columns F will be scaled by the value <scale>. The default scale is 1.0.

INPUT AND OUTPUT FILES

The input files are

The control data file.

HKLIN: The input reflection data file in standard MTZ format.
HKLOUT: If no MULTAN/SNB keyword is specified, the output file is a reflection data file in MTZ format containing the items H K L (all input) + F E SIGE where F=FP is copied from the input file if only FP is asigned, or F=sqrt(max((FPH-FP)^2 - SIGFP^2-SIGFPH^2,0)) if FPH is assigned as well. E is the normalised structure amplitude, SIGE is its standard deviation.

For the MULTAN option the output is H K L 1000*E in FORMAT(3I4,I6) terminated by E=-1.

SYMOP: The library symmetry data file, normally defaulted.

PRINTER OUTPUT

The line printer output may be divided into the following sections:

Echo of the input control data.
A table showing the distribution of the reflections in shells (chosen to give roughly equal numbers per shell) with mean d*^3, F^2, E^2-1 and (E^2-1)^2.
Scatter plot of F versus d*^2 with a smoothed plot of r.m.s. F versus d*^2 superimposed.
Mean values of E^2 and (E^2-1)^2 by parity groups.
Mean values of E^n where n = 1 to 6.
Mean values of |E^2-1|^n where n = 1 to 3.
For each mean the theoretical value for the acentric, centric and hypercentric distributions is also tabulated.
Cumulative distribution of E's for centric and acentric with theoretical values. This table can also be graphed with xloggraph.

PROGRAM FUNCTION

The program ECALC is used to calculate normalised structure amplitudes for a reflection data set. The normalised structure amplitude for a reflection is the structure amplitude divided by the product of epsilon (a factor dependent on the Laue group symmetry) and the r.m.s. value of the structure amplitudes at its sin(theta)/lambda value. The rotation and translation functions calculated using these normalised structure amplitudes result in sharper maps and the peak positions and heights are less susceptible to changes in resolution limits than the corresponding functions calculated with structure amplitudes.

EXAMPLES

Example of the control data for calculating a set of normalised structure factors.

 
ecalc hklin junk1.mtz hklout junk2.mtz << eof
TITLE TEST OF PROGRAM ECALC WITH C2HKL REFLECTION DATA
LABI FP=FO  SIGFP=SIGFO 
eof

 
ecalc hklin junk1.mtz hklout junk2.ref << eof
TITLE TEST OF PROGRAM ECALC WITH C2HKL REFLECTION DATA
LABI FP=FO  SIGFP=SIGFO
SNB
eof

 
$ecalc hklin junk1.mtz hklout junk2.dat
TITLE TEST OF PROGRAM ECALC For isomorphous differences
LABI FP=FO  SIGFP=SIGFO  FPH=FPH1 SIGFPH=SIGFPH1
MULTAN
REFLECTION 1500


ecalc hklin junk1.mtz hklout junk2.mtz << eof
TITL Es from isomorphous differences without sigma bias
LABI FP=FP FPH=FPHderv1
SCAL 0.001
SHEL 150
eof

Using coefficients from ECALC for origin-removed Patterson map

ECALC produces squared F's as the F2OR column in the output file, which can be used as input to FFT to produce a Patterson function directly, i.e. without using the PATT keyword.

In this case it is necessary to explicitly specify both the symmetry and the fftspacegroup as the appropriate Patterson spacegroup, using the SYMMETRY and FFTSPACEGROUP keywords. The Patterson spacegroups are given in the FFT documentation: "For a Patterson the space group should be P1bar(2) (for all space groups), P2/m(10) (for all monoclinic space groups, b axis unique), or Pmmm(47) (for all orthorombic space groups)."

For example:

ecalc hklin nat_der_scal.mtz hklout nat_der_scal_e.mtz << eof-ec
exclude SIGP 2 SIGPH 2 DIFF 100.
scale 1.
shell 50
labin FP=F_CNAT2 SIGFP=SIGF_CNAT2   FPH=F_CEMS SIGFPH=SIGF_CEMS
labout F=DISO E=E F2OR=F2OR E2OR=E2OR
eof-ec

fft hklin nat_der_scal_e.mtz mapout pat_der.map << eof-fft
title diff-patterson 
fftspace 47 
symm 47
LABIN F1=F2OR 
END
eof-fft

(With thanks to Steve Prince)

PROGRAM STRUCTURE

The program structure is straightforward and involves three passes through the input reflection data file. The structure is outlined below:

Open files
Pass 1 through reflection data: Find maximum F and S values and count the number of reflections. Print these values.
Pass 2 through reflection data: Collect F^2 values in bins of d*^3 (sums and numbers of reflections). Print a table of these results. Apply adjacent channel smoothing for points giving the average F^2 and d*^3 values for these bins.
Open the output mtz file.
Pass 3 through reflection data: Calculate E values (using the function AVF, write the output reflection data and collect data for the statistics.
Print scatter plot, average values of E^1 to E^6 and cumulative distribution of E's.

AUTHOR

Originator: Ian Tickle
Contact: Ian Tickle, Birkbeck College