AFRO Version 0.85 - Documentation

NAME

afro - multivariate substructure factor amplitude estimation for SAD/MAD and SIRAS.

SYNOPSIS

afro hklin foo.mtz hklout foo_out.mtz

Keyworded input

DESCRIPTION

This program will determine normalized substructure factor amplitudes (ie. E(A) values) which are needed for direct methods substructure determination programs. In this version, the multivariate formulas are not implemented, but just a standard approach is taken for finding SAD or SIR differences (and attempting to find the best wavelength to calculate the anomalous differences).

GETTING STARTED

The best way to start is to use the example scripts.

KEYWORDED INPUT

XTAL <ID>

<ID>

The crystal's name/identification string.

XTAL SUBKEYWORDS:

CELL

<a> <b> <c> <alpha> <beta> <gamma>

<a> <b> <c> <alpha> <beta> <gamma>

Cell parameters for the given XTAL. Default: take the values from the mtz file.

DNAMe <ID>

The dataset identifier. This keyword is required.

DNAMe SUBKEYWORDS:

COLUmn F=<f> SF=<sf> F+=<f+> SF+=<sf+> F-=<f-> SF-=<sf->

Diffraction data for the XTAL and DNAMe defined. If anomalous data is not to be used, set F and SF only. If using anomalous data, set F+, SF+, F-, SF-. Setting both F and F+ will result in an error. If only F and DANO is present in the mtz file, use the ccp4 program mtzMADmod to change F/DANO to F+/F-.

<f>

|F| (observed structure factor amplitude *if no anomalous data is present*).

<sf>

Corresponding sigma for <f>.

<f+>

|F+| (observed structure factor amplitude of positive Bijvoet pair).

<sf+>

Corresponding sigma of <f+>.

<f->

|F-| (observed structure factor amplitude of negative Bijvoet pair).

<sf->

Corresponding sigma of <f->.

RESO <hires> <lores>

Specify resolution limits for the given XTAL and DNAMe diffraction data. Do not use this keyword to specify a resolution cut-off for substructure detection, but use the HIREs keyword from AFRO instead. Only use this keyword if you wish to remove some data that you believe to be useless. Default: use all the data available in the mtz file.

EXCLude [ SIGF <nsigf> ] [ SANO<nsano> ] [SISO ]

Set criteria for excluding E-values to output for the given XTAL and DNAMe diffraction data. This is essential for correct substructure determination. The default is to use all the data available in the mtz file and this is not optimal for EA calculation.

The criteria and cutoff recommendations for the subkeywords are the following:

SIGF <nsigf>

exclude reflections if FP < <nsigf> * SIGF. The recommended setting is 3.

SANO <nsano>

exclude reflections if DANO < <nsano> * SDANO. The recommended setting is 1. (DANO = abs(|F+| - |F-|) and SDANO is the standard deviation of DANO in measurement.

SISO <nsiso>

exclude reflections if abs(|Fder| - |Fnat|) < * SDISO. The recommended setting is 1. SDISO is sqrt(SIGFder^2 + SIGFnat^2).

BINS

Number of bins for luzzati parameter estimation and refinement and output of statistics.

OPTIONAL KEYWORDS:

OUTPut <outputname>

<outputname> is the string associated with the ASCII file that afro writes out. The default <outputname> is "heavy".

ASCIi

Write out an unsorted drear file suitable for crunch2.

HIREs <hireslimit>

Only output FA values to the following high resolution limit. The default is for the program to calculate it automatically.

ACENtric

Only acentric reflections will be used. This is the default for SAD data.

CENTric

Only centric reflections will be used.

TITLe <title>

Title to be added to the mtz file. Default: "EA values from AFRO".

VERBose <n>

Specify amount of information to be outputted (where n is a positive integer). n = 0 is the normal output, n = 1 is more output and n = 2 is for debugging purposes. Default: n = 0.

OUTPUT:

COLUMNS in HKLOUT

EXAMPLES

Example 1 - SAD experiment

#!/bin/sh

set -e

afro HKLIN $CEXAM/tutorial/data/gere_MAD_nat.mtz \
    HKLOUT $CCP4_SCR/gere_SADEA.mtz << eof-afro

Xtal SeMET
 DNAME PEAK
   COLUmn F+=F_peak(+) SF+=SIGF_peak(+) F-=F_peak(-) SF-=SIGF_peak(-)
   EXCLUDE SIGF 3 SANO 1       # don't use data with F/SF < 3 or DANO/SIGDANO < 1
   RESOL HICUt 0.5             # only use data 0.5 Angstroms about hi res limit
ALLIn

eof-afro

Example 2: MAD EA value generation

#!/bin/sh

set -e

afro HKLIN $CEXAM/tutorial/data/gere_MAD_nat.mtz \
    HKLOUT $CCP4_SCR/gere_MADEA.mtz << eof-afro

Xtal SeMET
 DNAME PEAK
   COLUmn F+=F_peak(+) SF+=SIGF_peak(+) F-=F_peak(-) SF-=SIGF_peak(-)
   EXCLUDE SIGF 3 SANO 1        # don't use data with F/SF < 3 or DANO/SIGDANO < 1
   RESOL HICUt 0.5              # only use data 0.5 Angstroms about hi res limit
 DNAME INFL
   COLUmn F+=F_infl(+) SF+=SIGF_infl(+) F-=F_infl(-) SF-=SIGF_infl(-)
   EXCLUDE SIGF 3 SANO 1 SISO 1 # don't use data with F/SF < 3 or DANO/SIGDANO < 1
                                # or isomorphous/dispersive difference < 1
   RESOL HICUt 0.5              # only use data 0.5 Angstroms about hi res limit
 DNAME HIGH
   COLUmn F+=F_hrm(+) SF+=SIGF_hrm(+) F-=F_hrm(-) SF-=SIGF_hrm(-)
   EXCLUDE SIGF 3 SANO 1        # don't use data with F/SF < 3 or DANO/SIGDANO < 1
   RESOL HICUt 0.5              # only use data 0.5 Angstroms about hi res limit

                                # NOTE! Afro takes only isomorphous/dispersive differences between
                                # the first two defined data sets!!!
                                # You could also define the low remote as well...
ALLIn

eof-afro

Example 3: SIRAS EA value generation

#!/bin/sh

set -e

afro HKLIN $CEXAM/tutorial/data/gere_MAD_nat.mtz \
    HKLOUT $CCP4_SCR/gere_SIRASEA.mtz << eof-afro

# define the native first!!

Xtal NATIVE
 DNAME NATIVE
   COLUmn F=F_nat SF=SIGF_nat
   EXCLUDE SIGF 3               # don't use data with F/SF < 3
   RESOL HICUt 0.5              # only use data 0.5 Angstroms about hi res limit

Xtal SeMET
 DNAME PEAK
   COLUmn F+=F_peak(+) SF+=SIGF_peak(+) F-=F_peak(-) SF-=SIGF_peak(-)
   EXCLUDE SIGF 3 SANO 1 SISO 1 # don't use data with F/SF < 3 or DANO/SIGDANO < 1
 	                        # or isomorphous difference/sigma < 1
   RESOL HICUt 0.5              # only use data 0.5 Angstroms about hi res limit

ALLIn

eof-afro

Example 4: MAD + Native EA value generation

#!/bin/sh

set -e

afro HKLIN $CEXAM/tutorial/data/gere_MAD_nat.mtz \
    HKLOUT $CCP4_SCR/gere_MADNATEA.mtz << eof-afro

# define the native first!!

Xtal NATIVE
 DNAME NATIVE
   COLUmn F=F_nat SF=SIGF_nat
   EXCLUDE SIGF 3               # don't use data with F/SF < 3
   RESOL HICUt 0.5              # only use data 0.5 Angstroms about hi res limit

Xtal SeMET
 DNAME PEAK
   COLUmn F+=F_peak(+) SF+=SIGF_peak(+) F-=F_peak(-) SF-=SIGF_peak(-)
   EXCLUDE SIGF 3 SANO 1 SISO 1 # don't use data with F/SF < 3 or DANO/SIGDANO < 1
 	                        # or isomorphous difference/sigma < 1
   RESOL HICUt 0.5              # only use data 0.5 Angstroms about hi res limit
 DNAME INFL
   COLUmn F+=F_infl(+) SF+=SIGF_infl(+) F-=F_infl(-) SF-=SIGF_infl(-)
   EXCLUDE SIGF 3 SANO 1 SISO 1 # don't use data with F/SF < 3 or DANO/SIGDANO < 1
                                # or isomorphous/dispersive difference < 1
   RESOL HICUt 0.5              # only use data 0.5 Angstroms about hi res limit
 DNAME HIGH
   COLUmn F+=F_hrm(+) SF+=SIGF_hrm(+) F-=F_hrm(-) SF-=SIGF_hrm(-)
   EXCLUDE SIGF 3 SANO 1        # don't use data with F/SF < 3 or DANO/SIGDANO < 1
   RESOL HICUt 0.5              # only use data 0.5 Angstroms about hi res limit

                                # NOTE! Afro takes only isomorphous/dispersive differences between
                                # the first two defined data sets!!!
                                # You could also define the low remote as well...
ALLIn

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Last modified: Fri Aug 12 19:22:44 CEST 2005