PARAMETER AND MATRIX FILES

INTRODUCTION

This chapter describes the first four program options which may be selected via the main menu. They are for reading and writing a keyworded parameter file and for reading and writing matrix data.

List of sections:

The 'Read Parameters File' Option
The 'Read Matrix File' Option
The 'Write Matrix File' Option
The 'Write Parameters File' Option
Usaved Parameters Warning on Quit

THE 'READ PARAMETERS FILE' OPTION

This option is used to read in the keyworded parameter values for the dataset. A description of the file format and parmeters available is given in Appendix 2. Most of the parameters are displayed in the program's main parameter table.

When the option is selected, the following prompt is output:

File name (default ext=.rdm):

The user replies with the name of the required keyworded parameters file; if no file extension is given, an extension of .rdm (rotation data module) is assumed. A blank reply will cancel the request. The program checks that the file exists and can be opened; if there is an error, an error message will be output and the prompt will be repeated.

The data are then read from the file and are checked by the program. Errors will be flagged. Values are reset for all the parameters shown in the main parameter table. Program parameter value default values will be set for all parameters not explicitly given in the keyworded data file. The current cystal set and image number will be set to one.

All program flags will be reset to the program startup values when a new parameters file is read in.

THE 'READ MATRIX FILE' OPTION

This option is used to read in crystal orientation data from a matrix file for example after the orientation has been determined via an auto-indexing procedure. Currently two types of matrix file may be read.

When the 'Read Matrix File' option is selected, the following menu is displayed:

   <MOSFLM Matrix File>
   <DENZO Matrix File>

   <Return to Previous Menu>

These options allow for the input of a matrix file as used by the MOSFLM suite (e.g. from the program REFIX) or from the HKL/DENZO suite DENZO program.

If the 'MOSFLM Matrix File' option is selected, the following prompt is output:

File name (default ext=.mtx):

The user replies with the name of the required MOSFLM suite matrix file; if no file extension is given, an extension of .mtx is assumed. A blank reply will cancel the request. The program checks that the file exists and can be opened; if there is an error, an error message will be output and the prompt will be repeated.

The matrix data are then read from the file and are checked by the program. Errors will be flagged. Values are read and reset for the following parameters.

The cell parameters
The U-matrix
The missetting angles phi1, phi2, phi3

A brief message indicates that these parameters have been updated. The program returns to the main menu.

If the 'DENZO Matrix File' option is selected, the following prompt is output:

File name (default ext=.x):

The user replies with the name of the required HKL/DENZO suite .x file which contains the matrix information in addition to integrated intensities; if no file extension is given, an extension of . x is assumed. A blank reply will cancel the request. The program checks that the file exists and can be opened; if there is an error, an error message will be output and the prompt will be repeated.

The matrix data are then read from the file and are checked by the program. Errors will be flagged. Values are read and reset for the following parameters.

The cell parameters
The missetting angles phi1, phi2, phi3

A brief message indicates that these parameters have been updated. In contrast to the MOSFLM case, the missetting angles and cell need to be derived from the matrix read in as the required values are not stored in the file. The program derives the missetting angles on the basis of the current value of the U-matrix and this remains unchanged again in contrast with the MOSFLM case.

The program returns to the main menu.

THE 'WRITE MATRIX FILE' OPTION

This option is used to write out the crystal orientation data to a matrix file or command file for subsequent input to another program. Currently two types of output data file may be written.

When the 'Write Matrix File' option is selected, the following menu is displayed:

   <MOSFLM Matrix File>
   <DENZO Commands File>

   <Return to Previous Menu>

These options allow for the output of a matrix file as used by the MOSFLM suite or a set of orientation commands suitable for input to the DENZO program of the HKL (/DENZO) suite.

If the 'MOSFLM Matrix File' option is selected, the following prompt is output:

File name (default ext=.mtx):

The user replies with the name of the required MOSFLM suite matrix file which is to be written. If no file extension is given, an extension of .mtx is assumed. A blank reply will cancel the request. The program checks that the file does not already exist and that it can be opened; if there is an error, an error message will be output and the prompt will be repeated. If the file already exists, the user is given the option of overwriting the file or selecting an alternative file name.

If the 'DENZO Command File' option is selected, a file name is requested as in the previous case. This time the default extension is .dzo. A series of DENZO commands will be written to the output file rather than a matrix file as such. This is because, for DENZO, the matrix is contained within a multi-purpose .x output file which also contains reflection data not available from ROTGEN.

The program prompts for the vectors defining the spindle and vertical axes as follows:

Spindle axis [0 0 1]:
Vertical plane axis [1 0 0]:

The data written to the output file are the CELL, SPINDLE AXIS, VERTICAL AXIS and CRYSTAL (ROTX, ROTY and ROTZ) commands.

After an output file has been written, the program returns to the main menu.

THE 'WRITE PARAMETERS FILE' OPTION

This option is used to write the current values for the dataset parameters to a parameters (.rdm - rotation data module) file to save them for future use. A set of standard parameters and any other parameters with non-default values are output.

When the option is selected, the following prompt is output:

File name (default ext=.rdm):

The user replies with the name of the required output parameters file; if no file extension is given, an extension of .rdm will be added. A blank reply will cancel the request. The program checks that the file does not already exist and that it can be opened; if there is an error, an error message will be output and the prompt will be repeated. If the file already exists, the user is given the option of overwriting the file or selecting an alternative file name.

USAVED PARAMETERS WARNING ON QUIT

When quitting the program, if any of the values for the keyworded parameters have been changed since last writing a parameters file, a popup notice warns of this fact and the user has the choice of returning to the main menu so that a parmeters file may be written or quitting the program anyway.