Here are a few notes about the 'LAUEGEN' program. As of 18/3/93 it has been released and is available as part of the Daresbury Laboratory Laue Software Suite. It is an X-windows based program and uses the library of X-windows based XDL_VIEW routines which is distributed along with the Daresbury Laboratory Laue software suite. Documentation for these routines is available and it would probably be a good idea to get a printed copy of Vol 1 of this documentation from Daresbury which has pictures illustrating the text. The text of the documents is in the directory $CCP4_MASTER/laue/xdl_view/doc These notes are for guidance if the program has been obtained separately from the suite. NOTES ON INSTALLING XDL_VIEW ============================ The following notes are extracts from the Laue installation notes and from Chapter 11 of Vol 3 of the XDL_VIEW documentation: (Machines currently set up vax, convex, sparc, sun3, iris, sgi) This X-windows based library may be built using the following commnad (from $CCP4_MASTER/laue/make): lmake xdl_viewlib If an individual module from the library needs to be recompiled and replaced in the library then execute the command 'lmake -x name' where 'name' is the name of the module in question. If the routines are to be installed on a new Unix system, the file xdl_systyp.h will need to be edited to set the values of a few parameters parameters as appropriate for the system on which the software is to be used. The C source code files (subdirectory 'src') should be compiled using the -D switch on the C compiler to define the machine type. The supplied Makefile may be used after appropriate editing of items as indicated in the file. The Makefile puts the object modules in a library in a user defined directory. Programs linked with this library or any xdl_view routines will also need to be linked with the 'Xlib' (X11) library. COMPILING AND LINKING 'LAUEGEN' =============================== The source code is in lauegen.for and the include files are in the composite file lauegen.inc. This latter file may be split into its component files with the 'isplit' program supplies with the Laue suite. If your compiler does not support the include statements as used then they may be 'included' in the source code file using the 'fincl' utility supplied with the Laue suite. Apart from these include statements and the use of long variable & subroutine names, the code should be in standard Fortran 77. It should be noted that the XDL_VIEW routines are written in 'C' and need to be installed as described above to ensure that the appropriate Fortran/C interfacing is done. The program needs to be linked with the following libraries which should be in the directory pointed to bt $CCP4_LIB liblaue, libxdl_view, libccp4 and also to the X11 library. SOME DOCUMENTAION ON 'LAUEGEN' ============================== The documentation of LAUEGEN is now available; however there follows some of the intoductory material which should get you started if you do not have access to the full documentation. INTRODUCTION LAUEGEN is an X-windows based program for carrying out the initial stages of data processing for Laue diffraction images. It has facilities for displaying Laue simulations, displaying film/image-plate images, and finding and refining crystal orientations. It incorporates the functions of the programs NEWLAUE, SPOTIN and GENLAUE from the Daresbury Laboratory Laue Software Suite. (Refs..... The program makes use of a library of X-windows based routines, called XDL_VIEW, written by John Campbell at the Daresbury Laboratory. Reference should be made to Volume 1 of the XDL_VIEW documentation to find detailed instructions on how to manipulate the various view-objects (menus, parameter tables, image displays etc.) used by the program. Some of the code has been taken, with varying degrees of modification, from the programs NEWLAUE (M. Elder, E. Pantos & T. Jhahjadi) and GENLAUE (I.J. Clifton, P.A. Machin & S. Zurek). In particular, M. Elder's auto-indexing code from NEWLAUE and the code for generating Laue patterns from GENLAUE, have been used. SCREEN~LAYOUT The basic screen layout for the program is divided into five areas. Top left: A menu area used for selecting the options currently available. The options within a menu are, in general arranged such that the normal order of access would be from the top downwards without necessarily using all the options available. The basic menu structure of the program is heirarchical and most menus have an item at the bottom which returns the program to the previous level. Top right: Parameter table 1. This is an editable parameter table which contains main crystallographic/film parameters which relate to the current crystal and are common for all films/plates of the current film/image-plate pack. Bottom left: Parameter table 3. This area is used at various stages for different tables of parameters relating to the current option selected (e.g. >>>>>>>>>) Bottom middle: This area is an input/output window. This is used to output textual information from the program when required and also, at some stages, for prompt and reply sequences e.g. for inputting file names. Bottom right: Parameter table 2. This is an editable parameter table which contains parameters relating to the current film/plate in the pack being processed. Additional windows e.g. windows for displaying Laue simulations or film/image-plate images are used at various stages of the programs. These may be positioned independently of the main program window. Normally they will initially be positioned just to the right of the menu area. SOME~BASIC~CONCEPTS a) Crystallographic/film parameters. The program works with a basic set of parameters associated with the current crystal and a pack of films (or image plates) to be processed. Essentially they belong to three categories: 1) The parameters relating to the crystal cell and setting and the Laue soft limits. (Left hand two columns of parameter table 1) 2) The parameters describing the film/image-plate pack which is to be processed and which are common to all films/plates of the pack. e.g.>>>>>>> (Right hand column of parameter table 1) 3) The parameters relating to each individual film/plate in a pack. e.g. >>>>>>>>>>>> (Parameter table 2) The setting up of these parameters is done prior to the actual input of pack details and processing of a specific pack of films/image-plates. Laue simulations may be carried out when these parameters have been set as desired. b) Film/image-plate Pack When a film/image-plate pack is to be processed, further details about the pack need to be input to the program. Such details include the number of films/plates in the pack, the film/image-plate file names and details of film/image-plate spacings. >>>>different data orders >>>Standard packs comment here?? c) Key Film/Plate For a pack with more than one film/image-plate, one of the films/plates in the pack, normally the first, is considered to be the reference or 'key' film. This film/image plate will be the one used with the auto-indexing option and will be the first one used in refinement of the crystal orientation. It will normally be the first one in the pack though there may be cases where another one is used e.g. because a film is over-exposed or missing. OUTLINE OF MAIN OPTIONS The following are the main options available in LAUEGEN selectable via options in the program's main menu: a) Setting up the crystallographic/film parameter tables The parameters in parameter tables 1 and 2 are assigned default values when the program is started. Individual parameters may be reset by editing the values directly in the parameter table (see XDL_VIEW documentation). Alternatively, all parameters may be set to some alternative sets of standard values provided ('Setup/Reset Options' option) or read in from a parameters file ('Read Parameters File' option). When the required parameters have been set up, they may be saved in a parameters file for future use ('Write Parameters File' option). b) Laue simulations Two basic types of simulations are available, 'colour' simulations and 'interactive' simulations. In each case a window is created with a display area for the simulation, an area to list details of a selected reflection, a control panel and an area used for requesting hard copy (Postscript) output of the simulation. 'Colour' simulations show the show the Laue patterns with the spots colour coded in a number of different ways. 'Interactive' simulations are in black and white and have sliders which allow the user to investigate the effects of changing the lmin, lmax and dmin soft limits; spot labelling is also available. c) Input Film/Image-Plate Pack Details Details are given of the film/image-plate pack to be processed; these details are in addition to any parameters already set up in the main parameter tables. The information includes the number of films/plates in the pack, the names of the image files and details of the film/plate spacings. The order of the data in the image files may also be specified. Reduced input is available for two special cases, a 'standard' six film pack and a single 'i2' format image plate. d) Display/Measure Image This option enables a film or image-plate image to be displayed with options for inputting or determining the image centre, calculating a background image and measuring spot positions. A predicted Laue pattern, based on the current parameters, may also be displayed superimposed on the image. e) Find Orientation This option enables the crystal orientation to be determined by M. Elder's auto-indexing method. The option allows spot positions to be read from a previously generated spot positions file or measured from the image. f) Refine Orientation This option allows for the refinement of the crystal orientation, first for the key film/image-plate of the pack and then, if required, for other films/plates in the pack. Options are available for visually matching calculated and observed spot positions or for automatically searching for matches for selected reflections. When the refinement is complete, the .ge1/.ge2 files may be written for use by the integration program.