| X-PLOR 98.1 |
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.
You may note that it is no-longer necessary to use the keyword NREFL to create memory for the specified number of reflections before the reflection data is read. Memory allocation for reflection data is now completely automatic.
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.
2. 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
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:
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.
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.
Crystallographic map files
| 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.
2. Lines 2- 5
Title information written as character strings. These lines are written as 80-character strings in the formatted file map.
3. 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).
4. 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).
5. 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.
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.
2. 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)).