Contact Author:

Authors: Keith Watenpaugh, Debra Holland, Stephan Freer & Jim Stewart,

Contact: Keith Watenpaugh, Physical and Analytical Chemistry,

The Upjohn Company, Kalamazoo, MI 49001, USA.

BFOURR prepares a bdf containing coefficients and phases necessary for calculating a Fourier map with FOURR. Only the information required for the desired Fourier calculation is left in lrrefl:. Coefficients for Patterson, Fourier, isomorphous Fourier, Bijvoet difference Fourier, product and combined ismorphous/anomalous may be formed.

Description

Coefficients can be computed for one of four Fourier types; Bijvoet difference (F(+)-F(-)), or isomorphous (-), or combined (Matthew), or product (). Fourier phases can originate from one of four sources; MIR centroid phases, MIR most probable phases, calculated structure factor phases, or phases from inversion of a Fourier map (density modification phases).

Reflection output can be limited to specified ranges on reflection indices, sinθ/λ, Bragg spacing (resolution), magnitude of Fo, and absolute magnitude of coefficient. The program is designed so that the code for producing additional coefficient types can be added with relative ease.

Items Output Using COEFF Line

Lrrefl: records on the output bdf will consist of at least four items with an additional one or two items if phase data is being used. In addition to a non-negative coefficient stored as ID number 1304, the lrrefl: records will contain Miller indices, sinθ/λ, and the multiplicity factor (ID numbers 1,2 and 3). Phase data is read from the input bdf and output only in phase source information has been specified. An adjustment of 180° is applied to phases associated with coefficients that are initially calculated as negative, but are output as positive values.

In the case of bijvoet, isomorphous and combined coefficients, phase items input from the input archive bdf are output with 1801 and 1802 ID numbers. For the fc phase option, the structure factor phase and |F| items ( n700 and n800) are used if they exist on the input file and are output as 1700 and 1800; otherwise, items n801 and n802 are used and output as 1801 and 1802. In the case of product coefficient, only one phase item is calculated and is output to the output archive bdf as item 1700. A structure factor phase is calculated (in cycles using the specified phase sources for the two data sets involved. As with the other coefficients, two sources are possible when using the fc phase option. Structure factor phase data (ID number n700) will be used if it exists; otherwise, n801 and n802 will be used to calculate the structure factor phase to be output. Density modification phase data may also be input as id 1510 and 1511.

COEFF line options

bijvoet |F(+) - F(-)|

combined [() PROD]^1/2

where PROD = {1 - [ k ((+) -(-)) / 2 *]² }²

and k = Matthew(K)₂ * exp[ Matthew(B)₂]

isomorph ( - ) where =exp(ΔB )

product

Items Output Using The Ad Hoc Routine

Lrrefl: records on the output bdf will consist of a varied number of items depending on the option selected. For options 1-4, the hkl and calculated coefficient will be output as items 1 and 1304. Phase data will be output as 1801 and 1802 if required. For option 5, reflection records will consist of seven items: hkl (ID number 1), coefficient (1304), weight of best Fourier coefficient (700), cosα and sinα for best coefficient (701, 702), cosα and sinα for most probable Fourier coefficient (703, 704).

adhoc line options

This line causes an ad hoc routine, B499, to be called to prepare the output scratch bdf. A sample routine which will read output from the Rossmann MIR phase refinement program, as it is presently implemented at the University of Washington, is supplied to serve as a guide for the writing of B499.

kdb line options

The kdb line is used only for difference maps for which the coefficient is of the type -, where k = K exp(ΔB ). K and ΔB place the F values of the specified data set on the same relative scale as the F values of the parent dataset. Neither of these fields may be void. If the kdb line is omitted, K and DB are obtained from the bdf.

File Assignments

Reads reflection data from the input archive bdf

Writes fourier coefficients to the output archive bdf

Examples

title PREPARE FOR A 3F0-2FC ALPHACALC SYNTHESIS

BFOURR

coeff isomor parenthol parenthol

phase fc parenthol

kdb parenthol 2. 0.

In this example a 3*Fo - 2*Fc coefficient file is created.The coeff line specifies that difference Fourier will be set up using observed F's from the dataset named parenthol as and calculated F's from parenthol as. K and ΔB for will be 3. and 0. and for will be 2. and 0. Phases used will be calculated ones for parenthol.

title DERIVATIVE MINUS PARENT DIFFERENCE PATTERSON

BFOURR

kdb =i3triz= 20 -.2

kdb parent 10 .1

scale 3.

weight centroid

limhkl 2 10 3 9 4 8

limstl .005 .11

limco 10 100

In this example a difference Patterson will be set up with the coefficients

3 [ 20exp(-0.2) - 10exp(0.1) ], where s = sinθ/λ.

A number of criteria will be applied to each reflection to limit those which will be placed on the output scratch file.