INSTALLING THE DARESBURY LABORATORY LAUE SOFTWARE SUITE ======================================================== INTRODUCTION This document contains details of how to obtain copies of the Daresbury Laboratory Laue Software Suite and how to install it. It is available for use on Unix platforms. Most of the suite has also been installed on a VMS platform though this is no longer fully supported. Information about the suite can be found via the WWW Laue Software Suite home page . URL http://wserv1.dl.ac.uk/SRS/PX/jwc_laue/laue_top.html List of sections: Important Notice General Notes List of Programs Anonymous FTP Facility Installing the Programs on a 'Unix' System Installing the Programs on a 'VMS' System Running the Programs Documentation Program Test Data IMPORTANT NOTICE The Daresbury Laboratory Laue Software Suite is made available free of charge to Academic Institutions subject to acceptance of the conditions of a Licence agreement. The form is available as a Postscript Format File. The use of the software is also permitted, for academics, if the user has signed the CCP4 Program Suite Licence Agreement. Again, for Academics, the suite may either be obtained separately or as part of the CCP4 Program Suite. For non-academic institutions, the suite may only be obtained as part of the CCP4 Program Suite and different conditions apply (Contact the CCP4 Secretary at the Daresbury Laboratory, Daresbury, Warrington, WA4 4AD for details). In publications describing work carried out using programs from the Laue software suite, appropriate acknowledgements should be made. For a general reference, the following may be quoted: Helliwell, J.R., Habash, J., Cruikshank, D.W.J., Harding, M.M., Greenhough, T.J., Campbell, J.W., Clifton, I.J., Elder, M., Machin, P.A., Papiz, M.Z. and Zurek, S. (1989) J. Appl. Cryst, 22483-497. The LAUEGEN program has the reference: Campbell J.W., (1994b) "LAUEGEN, an X-windows based Program for the Processing of Laue X-ray Diffraction Data" (1995) J. Appl. Cryst., 28228-236 and the Laue Data Module (LDM) has the reference: Campbell J.W., Clifton I.J., Harding M.M. and Hao Q. (1994) "A Laue Data Module (LDM) for use in the processing of Laue X-ray Diffraction Data" (1995) J. Appl. Cryst., 28635-640 GENERAL NOTES The Laue Software suite uses both FORTRAN 77 and 'C' compilers. Most of the programs contain only standard FORTRAN 77 code with the exception of allowing variable names which may be more than 6 characters long and which may contain underscores both in variable and subroutine names. Most have been restructured using the 'SPAG' utility and checked using the 'FORCHK' utility. The source code of many of the programs as supplied also contains 'INCLUDE' statements and all the sections to be included are given in a single file for the program; utilities are provided to deal with these as needed. Machine dependent functions are handled through the CCP4 and Laue library routines. A few programs such as INTLAUE still contain other non-standard FORTRAN 77 code. Distribution versions for Unix systems (with C shell scripts) and for VMS systems are available. Library routines from the CCP4 (Collaborative computational project in Protein Crystallography) program suite are used by the Laue programs. The source code for the relevant programs and routines should all be present on the distribution medium. The program LAUEGEN uses the X-windows based set of routines XDL_VIEW (J.W. Campbell, SERC Daresbury); this is now distributed as part of CCP4. A copy of the suite may be obtained from Daresbury, provided authorisation has been given, via an 'Anonymous ftp' service and this is now the preferred mode of distribution. Test data for the programs are now supplied with the suite with instructions for carrying out one or two basic trial runs on each of the main programs of the Laue Software Suite. Sample output log files are given for reference. LIST OF PROGRAMS The following programs are distributed as part of the Laue Software Suite: lauegen Predict Laue patterns, auto_indexing, image display & measurement, parameter refinement (X-windows based). newlaue Predict Laue patterns, auto-indexing. spotin Measure spot positions from a film image. lchk Predict amount of reciprocal space coverage. genlaue Parameter refinement, spot prediction and preparation of .ge1 and .ge2 files to hold integrated intensity data. intlaue Intensity integration. intldm Intensity integration (LDM compatible) lscale Wavelength normalisation, scaling and absorption correction. afscale Scaling of films within a pack. unscram Deconvolution of harmonics. deconv Deconvolution of harmonics using direct methods. (A set of programs used in conjunction with programs from the CCP4 program suite. intanal Analyse intensities from .ge1 files or 'afscale' output files. lauescale Wavelength normalisation against a reference set of data. lauenorm Internal wavelength normalisation and film pack scaling. lauelam Split data into wavelength batches for CCP4 program 'rotavata'. lauediff Process Laue difference data method 1. difflaue Process Laue difference data method 2. difflmrg Combine 'difflaue' output files. exchge Convert .ge1/.ge2 binary files to an ascii format for interchange between machines. reorder Reorder the data in a film or image-plate (i2) file. genldm Convert a .gen parameters file to a .ldm parameters file. ldmge Create .gen/.ge1/.ge2 files from a .ldm parameters file. filmps Prepare a postscript output file of a film or image-plate image. pslaue Colour laue simulations to a Postscript output file afstats Analysis of .afout files with graphical option gnomconv Convert a Laue film or image-plate image to an image containing its gnomonic projection. tidytext Printing/formatting of 'tidytext' format documentation files (types .utx, .ptx) (lcf2mtz) Convert from LCF file to MTZ file (mtztona4, na4tomtz from CCP4) Convert between MTZ files and an ascii exchange format (na2) file. (mtzdump from CCP4) List the contents of an MTZ file ANONYMOUS FTP FACILITY The Laue suite is now available to Academic users who have signed the Daresbury Laboratory Laue Software Suite Licence agreement (or the CCP4 Program Suite Licence agreement) via 'ftp' from Daresbury. Three files are currently associated with the Laue suite. These are: LAUEINSTALL Installation notes (a plain text version of this document) laue.tar.Z Compressed 'tar' format file containing all the Laue software suite except the test data files. lauedata.tar.Z The Laue suite test data files. The CCP4 files lib.tar.Z and x-windows.tar.Z will also be needed if the CCP4 Program Suite has not been installed on your system. Note: The file LAUECHANGES is also available; this contains the latest version of a Laue news file + copies of an Updates file with a record of changes made to the Laue programs (starting June 1992) The logon 'id' is ftp and you are asked to give the name of your computer system as the password (this is not checked currently). First create a temporary directory to receive the files. This is referred to as 'tar_temp' in the example below and where this occurs, you must substitute your chosen directory name. The ftp address is ccp4a.dl.ac.uk and the session would be as follows (password 'email-address' is replaced by the user's own email address): Unix **Make sure you use the binary option for file transfer** cd tar_temp ftp ccp4a.dl.ac.uk Name: ftp Password: email-address ftp> cd pub/ccp4 ftp> binary ftp> get LAUEINSTALL ftp> get laue.tar.Z ftp> get lauedata.tar.Z ftp> cd ccp4 ftp> get lib.tar.Z (Not needed if CCP4 already installed) ftp> get x-windows.tar.Z (Not needed if CCP4 already installed) ftp> quit The compressed 'tar' files should then be uncompressed as follows: uncompress laue.tar uncompress lauedata.tar uncompress lib.tar (If fetched) uncompress x-windows.tar (If fetched) VMS Carry out the following in the CCP4_MASTER: directory (or another one if you wish, but bear in mind that the detailed instructions given in the VMS installation section will then need to be altered where appropriate). **Make sure you use the binary option for file transfer** ftp ccp4a.dl.ac.uk Name: ftp Password: email-address ftp> cd pub/ccp4 ftp> binary ftp> get LAUEINSTALL ftp> get laue.tar ftp> get lauedata.tar ftp> cd VMSutils/tar ftp> get vmstar.alpha_exe (for an Alpha or vmstar.exe for a Vax) ftp> cd ../.. ftp> cd ccp4 ftp> get lib.tar (Not needed if CCP4 already installed) ftp> get x-windows.tar (Not needed if CCP4 already installed) ftp> quit Note that by giving the file names as 'name.tar' rather than 'neme.tar.Z', the compressed tar files will be automatically uncompressed during the ftp transfer. The VMSTAR utility is used to unpack the tar files into the appropriate directories. INSTALLING THE PROGRAMS ON A 'UNIX' SYSTEM Introduction The next few sections describe how to obtain the Laue Software Suite and how to install it on a Unix based computer system. List of subsections in this section: Basic Setup Unix Directory Structure Loading the Files Building the Suite Basic Setup The Laue software suite uses the same top level directory as that used by the CCP4 program suite. If the CCP4 suite has not been installed, then the user should create a top level directory under which the Laue software, and selected parts of the CCP4 suite, are to be stored. The top level directory is referred to in the remaining parts of this document as top_dir which should be replaced by the user where it occurs by the directory that was selected. The user needs to set the following environment variables and aliases (e.g. within his/her .login file). If the CCP4 suite has been installed then the setup procedure for that suite should be followed before installing the Laue software suite and these items should then have been set. CCP4_MASTER Top level directory. (e.g. setenv CCP4_MASTER top_dir) CCP4_SCR A directory for scratch files. CCP4_BIN A directory to hold the (binary) executables. CCP4_LIB A directory to hold the (binary) object file libraries. CLIBD Directory for the library data files such as the point groups data file. (normally $CCP4_MASTER/ccp4/lib/data) MCTYPE The type of machine (e.g. 'sgi' or 'convex') as used in the the conditional compilations when making the CCP4 libraries and in the Laue programs 'make' procedure (see below). The following aliases must also be set up: alias laue '$CCP4_MASTER/laue/cmd/laue.cmd' alias lget '$CCP4_MASTER/laue/cmd/lget.cmd' alias linkimages '$CCP4_MASTER/laue/cmd/linkimages.cmd' The first command is used for running the Laue programs. The other two are used in conjunction with the supplied test data and demonstration. To run jobs in batch it is necessary to set up a command 'lbatch'; this is invoked from within the 'laue' command. The 'lbatch' command must accept three parameters being (1) the script name, (2) the name of the output log fiole and (3) the maximum time in seconds. An example may be found in $CCP4_MASTER/laue/dl/lbatch_sgi which uses the NQS batch system. Unix Directory Structure The Laue files are in the following directories: |-lib--|-src Laue library routines. | | | |-dat Copy of symmety files for Laue programs | |-src Program source files | |-laue--|-doc Laue documentation files | | | |-utils Utility programs (needed by Laue make | | procedure etc.) | | | |-testdata Test data files etc. | | | |-make Laue programs & libraries make proc;edure. | | (for Unix) | | top_dir--| |-cmd Command files used in running Laue programs | | (for Unix) | | | |-vms Sub-directories contain VMS command files | | | |-gnom Gnomonic projection programs | | |-src CCP4 libraries source code & Makefile |-ccp4--|-lib--| | |-data CCP4 library data files (**) | | | |-doc CCP4 library routines documentation | |-x-windows-|-xdl_view-|-src X-windows based | | | XDL_VIEW routined | |-doc | | | |-templates . . Other CCP4 directories (not required by Laue suite) . (**) Selected files only for Laue suite. Note: Copies of the programs 'mtztona4', 'na4tomtz' and mtzdump' from the CCP4 program suite are included in the Laue programs source code directory. Copies of their documentation are included in the Laue suite documentation directory. Loading the Files a) Installation from 'ftp' distribution Assuming that the 'tar' files have been copied to the directory 'tar_temp' and uncompressed (See section below on 'Anonymous ftp' facility) then proceed as follows: Make the directory top_dir/ccp4 if not already present and then execute the following commands (substituting top_dir and tar_temp as appropriate): cd top_dir tar xvf tar_temp/laue.tar tar xvf tar_temp/lauedata.tar cd top_dir/ccp4 tar xvf tar_temp/lib.tar tar xvf tar_temp/x-windows.tar b) Installation from tape The user must change directory to the top level directory for the suite (top_dir or $CCP4_MASTER). The contents of the supplied tape are then read in using the 'tar' command e.g. tar xvf 'device' (where 'device' is the relevant tape drive) Building the Suite If the CCP4 suite has not been installed, then the following steps should be taken (they are included as part of the CCP4 setup procedure): a) The file top_dir/laue/dl/laue.setup should be edited to give appropriate directories for the environment variables and aliases associated with the suite. b) This file should then be sourced from the .login files of the users needing to the suite by including the following line in the .login file (Note: the top level directory top_dir must be given explicitly here): source top_dir/laue/dl/laue.setup The compilation and linking of the Laue software needs to be done in the following order: * Compile the Laue utility programs * Compile the CCP4 libraries (if not already present) * Compile the Laue libraries * Compile the xdl_view routines (if not already present) * Compile & link the Laue progr;ams * Compile and link the Gnomonic projection programs c) The Laue Utilities and Make Procedure Unless you have a Silicon Graphics (MCTYPE=sgi) or Convex (MCTYPE=convex) machine, you will need to edit the command file 'lmake' in $CCP4_MASTER/laue/make to add in a section similar to those present for the sgi and convex. To choose an appropriate name, first examine the file library.c from CCP4 ($CCP4_MASTER/ccp4/lib/src) to see if it will cater for your system; if so use the appropriate system name from that file; if not you will need to select a new name and add appropriate code changes to library.c and make other changes outlined below. Systems catered for in library.c include sgi, sun, alliant, HP, ESV, convex, ultrix. (See also (c) below describing a subdirectory containing some machine dependent routines and the notes on the utility programs 'isplit', 'fincl' and 'splitf' later in this section) From that directory you should then execute the command 'lmake utils' to make the utility programs. The command 'lmake -h' shows what make options are available; If the CCP4 suite is already present (i.e. the CCP4 library files have been compiled) then it would be possible to make the Laue utilities, libraries and programs by executing the single command 'lmake all'; however it is probably wiser to do it in the separate stages described here. If the CCP4 suite is not present, then such a command cannot be used at this stage as the CCP4 library (partial) is not built until the next step. If an individual utility needs to be made then execute the command 'lmake -u name' where 'name' is the name of the utility. Mention should be made of three utilities: 1) 'isplit' is used to split a program includes file (ext = .inc) into its component files (ext = .finc) to be included in the program. 2) 'fincl' is used to include the 'include sections' within the source code files before compilation if the Fortran compiler does not accept 'INCLUDE' statements in the form used. 3) 'splitf' is a utility which splits a Fortran source file into its component subroutine files (ext = .f). It is analogous to the Unix utility 'fsplit' but will accept subroutines containing underscores in their names in a way that some versions of 'fsplit' do not. These three utilities are used as needed in the 'lmake' procedure. d) The CCP4 Libraries This step will not be needed if the CCP4 suite has already been installed. If the Laue suite is being installed on its own then only those parts of the CCP4 library needed are compiled (though the source code for the complete library is supplied) The source code is in the directory $CCP4_MASTER/ccp4/lib/src. The Fortran based machine dependent code should be confined to the routines in a file called unix.for. The file normally needs to be created from the file unix.m4 in the ccp4 libraries source code directory using the unix 'm4' pre-proccessor utility. However, in the present case, a number of versions of unix.for (unix.sgi, unix.sun, unix.convex etc.) have been prepared and are held in the directory $CCP4_MASTER/laue/make/unixfor. The suffix represents the machine/operating-system type. You should copy the relevant file to $CCP4_MASTER/ccp4/lib/src/unix.for before attempting to compile the ccp4 library. If the required version is not present, you may be able to use the 'm4' pre-processor on the unix.m4 file or you should create your own version of unix.for based on one of the existing versions. If you need to take this latter approach you should, check the code carefully especially in the routines CCPOPN, USTIME, UTIME, and UBYTES. As indicated above, the MCTYPE variable in the Laue make procedure 'lmake' must have been set to one of the machine types catered for in the library.c file which contains the machine dependent 'C' functions required. The partial CCP4 library is built using the following command (from $CCP4_MASTER/laue/make): lmake libccp4 e) The Laue Libraries There may be some machine dependent routines present in subdirectories of $CCP4_MASTER/laue/lib/src. For a machine not already catered for, a similar subdirectory will need to be created for the new machine and the routines copied from the most appropriate subdirectory already present and modified as needed. When these routines are in place, use the following command (from $CCP4_MASTER/laue/make) to make the Laue library: lmake libs If an individual library module needs to be recompiled and added to the Laue library then execute the command 'lmake -l name' where 'name' is the name of the library module. f) The XDL_VIEW Library This step will not be needed if the CCP4 suite has already been installed. 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. g) The Laue Programs The following command (from $CCP4_MASTER/laue/make) is used to compile and link the programs of the Laue Software suite: lmake progs If an individual Laue program needs to be recompiled and linked then execute the command 'lmake name' where 'name' is the name of the Laue program. h) The Gnomonic Projection Programs The following command (from $CCP4_MASTER/laue/make) is used to compile and link the Gnomonic Projection programs: lmake gprogs If an individual Gnomonic Projrction program needs to be recompiled and linked then execute the command 'lmake -g name' where 'name' is the name of the Gnomonic Projection program. INSTALLING THE PROGRAMS ON A 'VMS' SYSTEM Introduction The next few sections describe how to obtain the Laue Software Suite and how to install it on a VMS based computer system. Note that this is not fully supported now. List of subsections in this section: Basic Setup 'VMS' Directory Structure Loading the Files Building the Whole Suite Fixing the Image Files from 'Unix' Distribution Re-building Parts of the Suite Basic Setup The Laue software suite uses the same top level directory as that used by the CCP4 program suite. If the CCP4 suite has not been installed, then the user should create a top level directory under which the Laue software, and selected parts of the CCP4 suite, are to be stored. The logical symbol CCP4_MASTER must be assigned to this top level directory. This may be done as follows (where 'disk' is substituted by the actual name and 'direct' is substituted by the actual directory): DEFINE/NOLOG/TRANS=CONCEALED CCP4_MASTER disk:[direct.] The logical name CCP4_SCR must also be set up to point to a scratch area. The following must also be set up: LAUE :== @CCP4_MASTER:[LAUE.VMS.CMD]LAUE LGET :== @CCP4_MASTER:[LAUE.VMS.CMD]LGET DEFINE LFILM: CCP4_MASTER:[LAUE.TESTDATA] The CCP4_MASTER, CCP4_SCR, LAUE, LGET and LFILM definitions must be set up via the login procedure (either in LOGIN.COM or a file executed by LOGIN.COM) for each user accessing the suite (or in a global login procedure). If the CCP4 suite has been installed, then these items should be set up following the procedures described for that suite. 'VMS' Directory Structure The directory structure, now used under VMS for the CCP4 and Laue program suites, maps on closely to that used under Unix systems. The Laue files are in the following directories: |BIN Laue program executables | |OBJ Temporary Laue object files | |LIB.| Laue object library | | | |SRC Laue library routines source code. | | | |DAT Symmetry files for Laue programs | |SRC Laue program source files | |LAUE.|DOC Laue documentation files | | | |UTILS Utility programs | | | |TESTDATA Test data files etc. | | | |MAKE Unix make files | | CCP4_MASTER:[] | |CMD Command files used in running Laue | | programs for Unix | | | |VMS.|MAKE Laue programs & libraries make | | | procedures for VMS | | | | | |CMD Command files used in running Laue | | programs for VMS | | | |GNOM Gnomonic projection programs | | |SRC CCP4 libraries source code | | |CCP4.|LIB.| CCP4 object library | | | |DATA CCP4 library data files (**) | | | |DOC CCP4 library routines documentation | |X-WINDOWS.|XDL_VIEW.|SRC X-windows based | | | XDL_VIEW routined | |DOC | | | |TEMPLATES . . Other CCP4 directories (not required by Laue . suite) . (**) Selected files only for Laue suite. Note: Copies of the programs 'mtztona4', 'na4tomtz' and 'mtzdump' from the CCP4 program suite are included in the Laue programs source code directory. Copies of their documentation are included in the Laue suite documentation directory. Loading the Files Note: The Suite from Daresbury is compiled on a DEC Alpha system and everything will need to be re-compiled if it is to be run on a Vax system. a) Installation from tape Assuming that CCP4_MASTER has been set up as described above, read in the VMS backup format tape on which the Laue suite is distributed. The name of the tape is LAUE and the name of the backup save set is LAUE.BCK. e.g. (where 'mdev' is the name of your tape device) MOUNT/FOR mdev: BACKUP/LIST mdev:LAUE.BCK CCP4_MASTER: DISMOUNT mdev: b) From 'ftp' distribution A Unix version of the Laue software suite is available to authorised persons via an 'anonymous ftp' account at the Daresbury Laboratory (see below for details). The VMSTAR utility, also available by ftp, can be used to read a tar file and place the files in the appropriate VMS directory structure. The option the stored compressed tar files should be uncompressed as part of the ftp transfer as described below. The procedure should be carried out in the directory CCP4_MASTER:. When the (uncompressed) tar files and the vmstar utility program have been retrieved, set up a VMSTAR command as follows: VMSTAR :== "$CCP4_MASTER:VMSTAR.ALPHA_EXE" (Dec Alpha) or VMSTAR :== "$CCP4_MASTER:VMSTAR.EXE" (Vax) then unpack the files as follows: VMSTAR XF LAUE.TAR VMSTAR XF LAUEDATA.TAR SET DEF CCP4_MASTER:[CCP4] VMSTAR XF CCP4_MASTER:LIB.TAR (If CCP4 suite not already present) VMSTAR XF CCP4_MASTER:X_WINDOWS.TAR (If CCP4 suite not already present) The .TAR files in CCP4_MASTER: may then be deleted, the VMSTAR program may be deleted or moved elsewhere for safekeeping. Note: The test data image files are in binary format. The film images are single bytes/pixel; The Lysozme image-plate image has two byte unsigned integers, the byte order in lys_swap.i2 should be in the byte order required by a VMS system. The record lengths of the image files will need to be 'fixed' as described in below. Building the Whole Suite You should build the suite in the following order: If you already have the CCP4 suite libraries set up then the following two steps should be omitted: 1) Make the CCP4 libraries using the command '@MAKEFILE' in CCP4_MASTER:[CCP4.LIB.SRC]; you will need to set up the logical names CLIB and CLIBS to point to the directories CCP4_MASTER:[CCP4.LIB] and CCP4_MASTER:[CCP4.LIB.SRC] respecively. 2) Build the XDL_VIEW library using the command '@MAKEFILE' CCP4_MASTER:[CCP4.X-WINDOWS.XDL_VIEW.SRC]. The Laue software is then built using command files in the directory CCP4_MASTER:[LAUE.VMS.MAKE]. * Build the Laue Utilities using the command '@MAKE_UTILS'. * Build the Laue Libraries using the command '@MAKE_LIBLAUE ALL'. * Build the Laue Programs (except for LAUEGEN) using the command '@MAKE_LAUE_ALL'. * Build the LAUEGEN program using the command '@MAKE_LAUEGEN'. * Build Gnomonic Projection Programs using the command '@MAKE_GNOM ALL' Note: The utility 'isplit' is used to split a program includes file (ext = .inc) into its component files (ext = .finc) to be included in the program at compile time. Fixing the Image Files from 'Unix' Distribution If the image files have been obtained from the 'Unix' ftp distribution then they will need to be 'fixed' as follows: In the directory $CCP4_MASTER:[LAUE.TESTDATA] rename the file LYS.I2 as LYS_UNIX.I2 and then rename the file LYS_SWAP.I2 as LYS.I2 In the directory $CCP4_MASTER:[LAUE.DL] compile and link the program VMS_IMGFIX.FOR as follows: FOR VMS_IMGFIX LINK VMS_IMGFIX Then back in the directory $CCP4_MASTER:[LAUE.TESTDATA] run this program (RUN $CCP4_MASTER:[LAUE.DL]VMS_IMGFIX) for each or the three image files LYS.I2, PF1A.DAT and PF1B.DAT. In each of these cases the required record length is 2400. Re-building Parts of the Suite The following command files are available for re-compiling and linking parts of the suite if and as needed (these are in the directory CCP4_MASTER:[LAUE.VMS.MAKE]): @MAKE_LAUE name makes the Laue program 'name' (except for LAUEGEN and INTLDM) @MAKE_LAUEGEN makes the Laue program LAUEGEN (uses X-windows) @MAKE_INTLDM makes the Laue program INTLDM @MAKE_UTILS makes all the Laue utility programs @MAKE_LIBLAUE ALL makes the Laue libraries @MAKE_LIBLAUE module re-compiles the Laue library module 'module' @MAKE_XDLVIEW ALL makes the complete XDL_VIEW library @MAKE_XDLVIEW module re-complies the XDL_VIEW library module 'module' @MAKE_GNOM name makes the Gnomonic projection program 'name' Note: The utility 'isplit' is used to split a program includes file (ext = .inc) into its component files (ext = .finc) to be included in the program at compile time. RUNNING THE PROGRAMS All the programs may be run by typing the command: laue program where 'program' is the program name e.g. laue lauenorm When the 'laue' command is invoked, a command file program.com (where 'program' is the name of the program being run e.g. lauenorm.com for lauenorm) is created. An option is available, for most programs, to save this command file. This may then be re-submitted (after editing if required) for processing by typing the command: laue program.com The 'laue' command, in general, gives options for running the program interactively (with output to the terminal or a file), in background mode (Unix systems) or in batch mode (if available). Most require some kind of control data file of parameters files as described in the relevant documentation. Examples may also be found in the test data directory. The basic versions of 'genlaue' supplied will handle up to 100000 reflections. A version for up to 300000 reflections is also supplied as as genlaue_300k. The CCP4 programs MTZDUMP, MTZTONA4, NA4TOMTZ and LCF2MTZ and the document tidying and printing program TIDYTEXT may also be run via the 'laue' command. DOCUMENTATION The Laue documentation was originally written in a variety of styles and formats. All the documents have now been converted to use the same basic format (a pre-html format) from which a number of other formats can be generated. The generated 'html' files will be available on the World Wide Web. The distribution copy of the Laue software suite will contain plain text files. For graphics image files the master copies are in .gif format and these will be accessible via the Web. The distribution copy of the suite will contain Postscript equivalents of those referred to in the distributed documents. The documentation files for the Laue programs are in $CCP4_MASTER/laue/doc on Unix systems and CCP4_MASTER:[LAUE.DOC] on VMS systems. PROGRAM TEST DATA . Some standard test data files are supplied to enable some basic testing of the Laue programs to be carried out (in $CCP4_MASTER/laue/testdata on a Unix system or in CCP4_MASTER:[LAUE.TESTDATA] on a VMS system). They may be used in two ways, either as test data sets just to check that the programs seem to be running OK or as part of a learning process about the programs. The data sets come from three sources: a) Proflavin hemisulphate (smallish molecule) - film (pf...) b) Tetragonal HEWL Lysozyme (protein) - image-plate (lys...) c) 4 Zinc Insulin (protein) - film (zn...) Their use is documented in the file 'laue_tests.txt'. This is in the directory $CCP4_MASTER/laue/doc on a Unix system and in the directory CCP4_MASTER:[LAUE.DOC] on a VMS system. The documentation is also accessible via the Web.