X-PLOR



B       File Formats

 This appendix describes the file formats for X-ray reflection data and electron density maps that are read and written by X-PLOR 98.


Crystallographic data files

X-PLOR reflection files are ASCII formatted files in which each data item is tagged by a keyword that indicates the meaning of the data item. Data items may be written in any order on each line.

Section 12.4 of the X-PLOR 3.1 manual describes the crystallographic data file format. An important difference between the current version of X-PLOR and X-PLOR 3.1 is that the data item for the observed structure factor, FOBS, is now a complex array that contains both amplitude and phase components and the PHASe keyword is no longer used to specify the phase associated with this amplitude.

A difference between this version of X-PLOR and X-PLOR 3.851 is that data items HLA, HLB, HLC, HLD, which correspond to Hendrickson-Lattman ABCD phase probability coefficients, have been added to the reflection data model. This permits use of a maximum likelihood target for phase probabilities in macromolecular refinement. Note that these phase probability coefficients correspond to the reflection data read by the X-PLOR program and that operations that map reflection data to a different asymmetric unit are not currently implemented to automatically change the values of the phase coefficients.

File header

Reflection files are not required to contain header information since all this information may be entered within the X-PLOR script or assumed as default. However, it is usually logical and convenient to include the following information at the start of each reflection file.

  1. Number of reflections in the file - keyword NREFlections.

It is essential to include this line in either the reflection file or the X-PLOR script. The NREFL parameter specifies the amount of storage space that will be required for the reflection data. The NREFL parameter must equal or exceed the number of reflections that are to be read.

Example: NREFlections=7985

  1. Treatment of Bijvoet reflection mates - keyword ANOMalous.

This keyword is used to specify whether the Bijvoet reflection pairs have been merged together. Expansion of the reflection set by the crystal symmetry operators includes the generation of Bijvoet mates if ANOMalous=FALSe (the default). This expression has the same meaning as the HERMitian=TRUE expression in X-PLOR 3.1.

Example: ANOMalous=FALSe

  1. Specification of the type of data object.

Each kind of data item in the reflection file may be defined by a statement of the type

DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END

In this example the data items FOBS are declared as complex reciprocal-space objects. These lines are optional for the standard set of data items that may be contained within the reflection file (see below).

Standard data items

Each reflection is specified by the INDEx tag follow by three Miller indices (integers). The following standard data items may be provided for each reflection:

FOBS=<real><real>

These two items correspond to observed structure factor amplitude and phase. It is permissible to supply only the structure factor amplitude (that is, a single value) when experimental phase information is not present.

FCALc=<real><real>

These two items correspond to a calculated structure factor amplitude and phase.

FPARt=<real><real>

These two items correspond to a partial structure factor amplitude and phase. This item may be used, for example, to supply a structure factor contribution for a bulk solvent model obtained in a separate calculation.

SIGMa=<real>

This item is the standard deviation for the observed structure factor amplitude.

FOM=<real>

This item specifies the figure of merit for a phased reflection.

WEIGht=<real>

This item specifies a weight that may be applied to the X-ray energy term for this particular reflection.

HLA=<real>

This item specifies the Hendrickson-Lattman `A' phase probability coefficient.

HLB=<real>

This item specifies the Hendrickson-Lattman `B' phase probability coefficient.

HLC=<real>

This item specifies the Hendrickson-Lattman `C' phase probability coefficient.

HLD=<real>

This item specifies the Hendrickson-Lattman `D' phase probability coefficient.

TEST=<integer>

This item is used to flag a reflection as belonging to the working set (if 0) or the test set used for Rfree calculations (if 1).

Example reflection record
This record specifies as single reflection with Miller indices 3,0,1 an observed structure factor amplitude of 1930, an experimental phase angle set to 0 and a standard deviation on the structure factor amplitude of 12.

INDE 3 0 1 FOBS= 1930.000 0.000 SIGMA= 12.000


Crystallographic map files

The X-PLOR program is able to write electron density map files in either a binary format or in an ASCII format. The binary format is more compact and may be read more quickly than the ASCII format but has the disadvantage that it may not be readable when transferred between different kinds of computer. The ASCII formatted file is written if the FORMatted keyword is set TRUE (the default); setting FORMatted=FALSE will cause a binary map file to be written.

See Chapter 14 of the X-PLOR 3.1 manual for more information on map writing options

Note

The description given here of the map format supersedes the format described in the X-PLOR 3.1 manual.  

Map header

The X-PLOR map file begins with an eight-line header.

  1. Line 1

An empty line written by the `/ ` FORTRAN format descriptor in the formatted map file.

  1. Lines 2- 5

Title information written as character strings. These lines are written as 80-character strings in the formatted file map.

  1. Line 6

A series of nine integers NA, AMIN, AMAX, NB, BMIN, BMAX, NC, CMIN, CMAX. The values NA, NB and NC indicate the total number of grid points along the a,b, and c cell edges. The items AMIN, AMAX, BMIN, BMAX, CMIN, CMAX indicate the starting and stopping grid points along each cell edge in the portion of the map that is written. In the formatted map file this line is written using the FORTRAN format statement (9I8).

  1. Line 7

A series of six double-precision items corresponding to the crystal cell dimensions a, b, c, alpha, beta, gamma. In the formatted map file these items are written using the FORTRAN format statement (6E12.5).

  1. Line 8

A three-letter character string which always reads `ZXY'.

Density array

Following the map header, the density matrix is then written section-by-section with c moving slowest (in z-sections). Each section of the density map is preceded by a section number.

Thus, for the formatted map file each section of the density map is written using FORTRAN statements of the type

WRITE(OUNIT,'(I8)') KSECT

WRITE(OUNIT,'(6E12.5)') ((SECTON(I,J),I=1,ISECT),J=1,JSECT)

and the resulting map is written with six pixels on each line. The binary format is identical except the format statements are missing, so that each line that is written contains the entire length of map along the `fast' (a-axis) direction.

Map footer

Two lines follow the density array.

  1. Line 1

The integer `-9999' is always written. For the formatted map file, The FORTRAN format statement (I8) is used to write this value.

  1. Line 2

Two double-precision items corresponding to the average electron density and the standard deviation of the map. For the formatted map file these items are written using the FORTRAN format statement (2(E12.4,1X)).



Last updated May 05, 1998 at 11:52AM Pacific Daylight Time.
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