CSDS Commands PREQUEST(L) NAME prequest - create Cambridge Structural Database ASER files SYNOPSIS prequest [ -j jobname ] [ -if input_file [ -ifmt BCCAB|ASER|FSER2|MOLFILE|MOL2|SHELX|CIF ] ] [ -mfe refcodes_file ] [ -of output_file [ -ofmt BCCAB|ASER|FSER2 ] ] [ -auto ] [ -term X|T420|T41|T40 ] [ -help ] [ -tem template_file ] [ -fig fig_file ] [ -dbg ] DESCRIPTION prequest validates Cambridge Structural Database entries, and optionally creates and edits database ASER search files. When invoked without -auto , prequest prompts the user to select an input file from a scrolling list. The input file format is detected automatically. The user may then select entries from the scrolling refcode list at the top right corner of the window. Entries are colour-coded according to their current status, where red means "in error", yellow means "warnings" issued, green means "perfect", and white means "not yet examined". Output files are created by selecting the "Export..." com- mand, and choosing the required fileformat and name. OPTIONS -if input_filename Read data from input_file instead of offering the default scrolling list of files. -if MASTER may be used as a shortcut to denote the MASTER (READONLY) ASER file. -ifmt BCCAB|ASER|FSER2|MOLFILE|MOL2|SHELX|CIF Specify format of input data. This option is not usu- ally required, as the script checks the given input_filename to determine the file format. -mfe refcodes_file Specify an input file containing refcodes (one-per- line, upper-case) of entries to be loaded from an ASER input database. If no -if option is given, -if MASTER is assumed. -of output_filename CSD System Last change: $Date: 1998/01/14 09:56:25 $ 1 CSDS Commands PREQUEST(L) Write output to output_file instead of offering the default scrolling list of files. Useful in conjunction with the -auto option. -ofmt BCCAB|ASER|FSER2 Specify format of output data. If -of output_filename is used, the default output format is ASER. -auto Turn off the prequest graphical user interface. When this option is specified, -if input_filename , -of output_filename and -ofmt BCCAB|ASER|FSER2 are manda- tory. -j jobname Specify a jobname for this prequest session. Some out- put files will be given the root name jobname. The default jobname is prequest. -term X|T420|T41|T40 Specifies the type of graphics device in use. -tem template_file Specify an input chemical templates file (see PREQUEST- TEMPLATE below). -fig fig_file Configure the graphics for prequest from the file fig_file. (See PREQUESTFIG in the ENVIRONMENT sec- tion.) -version Print version information for the current CSDS. -dbg Writes extra debug information to jobname{.dbg} -help Display these manual pages. ENVIRONMENT prequest recognises a number of environment variables. When the CSDS was configured (using config.sh) default values were (implicitly) assigned to the environment variables: CSDHOME and CSDMACHINE. They can, however, be overridden by explicitly defining them within the current environment. CSD System Last change: $Date: 1998/01/14 09:56:25 $ 2 CSDS Commands PREQUEST(L) CSDMASTERFILE Look for the READONLY master ASER file triplet in the file pointed to by $CSDMASTERFILE by adding {.ind,.msk,.tcd} to $CSDMASTERFILE. CSDNEWREFCODES Create new refcodes (when reading from non-CCDC file formats, such as CIF, MOLFILE, MOL2, SHELX) using the 8 lines of information in the file pointed to by $CSDNEWREFCODES. If $fCSDNEWREFCODES is not set, ~/prequest.refcodes is used instead. The n'th line of the file lists the allowable charac- ters for the n'th character of the new refcode. For example, to generate refcodes of the form 0001AB, 0002AB, 0003AB etc., create a file containing 8 lines, as follows: 0123456789 0123456789 0123456789 0123456789 A B prequest appends a line of counters to this file, each time a new refcode is built, so if $CSDNEWREFCODES is defined, to be shared amongst several users, it must be writable by all. If no input refcode definition file is found, a default one will be created, with refcodes beginning "000001 ", "000002 ", etc. CSDHOME Look for auxiliary executables, scripts and tables in the directory pointed to by $CSDHOME. This directory should be accessible to all potential users of the Cam- bridge Crystallographic Data System and must be acces- sible by prequest. CSDMACHINE Use the executables and database for machine type CSD System Last change: $Date: 1998/01/14 09:56:25 $ 3 CSDS Commands PREQUEST(L) $CSDMACHINE. It is possible, especially with the net- work file system (NFS), to have different types of machines accessing the database. This variable speci- fies the current machine type to the CSDS. CSD_CDROM_FILENAMES This should be set to the name of a script that con- verts actual filenames to filenames that quest under- stands. See cdcopy(l) for details and examples. CSD_DB_REORDER_BYTES Forces all database files to be interpreted in non native format. Integer bytes will be reordered accord- ing to the value of this variable. In addition prequest recognises the environment variables: PREQUESTTEMPLATE and PREQUESTFIG. These environment vari- ables, when set, should point to particular input files. See the FILES section for more details. FILES Input Files: $HOME/.prequest.prf prequest preferences file. This file is used to automatically remember various options (such as paper size, and levels of checking) between prequest ses- sions. jobname.fig The prequest graphics configuration file. (Allows users to change the colours used by the graphics, for exam- ple.) If it doesn't exist it is linked to the first file found in the list: command-line `-fig' config_file, $PREQUESTFIG, ./prequest.fig, $HOME /prequest.fig, $CSDHOME /csds/prequest.fig, $CSDHOME /csds/csds.fig. jobname.tem Template file. If it doesn't exist the file is linked to the first file found in the list: command-line `-tem' template_file, $PREQUESTTEMPLATE, ./prequest.tem, $HOME /prequest.tem, $CSDHOME /prequest.tem. You can add templates to this file using prequest but only if template file resides in one of your subdirectories. Therefore you will have to CSD System Last change: $Date: 1998/01/14 09:56:25 $ 4 CSDS Commands PREQUEST(L) copy the original from $CSDHOME /csds/prequest.tem. $CSDHOME/csds/prequest.hlp The prequest on-line help file. $CSDHOME/csds/prequest.edt The prequest edit layout file. This file determines the layout of editable text fields in the main PreQuest window. $CSDHOME/csds/pluto.hlp The CHECK-3D on-line help file. $CSDHOME/csds/pluto.sym The CHECK-3D symmetry-operators data file. $CSDHOME/csds/groups.def The prequest data file containing definitions of 26 chemical functional groups, used by the MAKE2D command. Output files: jobname.ps Postscript output, created when the "print to file" option within the Print command is used. The default filename may be changed by the user in the Print dia- log. jobname.lis Listing file. This contains all messages written to the prequest message area during the session. jobname.log Log file. This lists any changes made to ASER files during the prequest session, detailing which entries were added, modified and deleted. jobname.dbg Debug file. This file may be disregarded and deleted. BUGS In some circumstances, prequest may produce other output files. These files may be ignored. CSD System Last change: $Date: 1998/01/14 09:56:25 $ 5