CSDS Commands QUEST(L) NAME quest - search the Cambridge Crystallographic Database SYNOPSIS quest [ -j ] jobname [ -help ] [ -nbg ] [ -ini init_file ] [ -v virtual_database ] [ -tem template_file ] [ -version ] [ -fig fig_file ] [ -if input_file ] [ -of output_file ] [ -reorderbytes order ] [ -db database_file1 [ ... database_fileN ] ] [ < infile ] [> outfile] DESCRIPTION quest searches the Cambridge Structural Database or any database subset. Unless redirected, quest interactively reads instructions from standard input and writes to stan- dard output. If the name jobname is specified all files created by quest will have the form jobname.ext. OPTIONS -j jobname Specify a jobname for this run of quest. Output files will be given the root name jobname. -db database1 ... databaseN Search these databases instead of the default `Master' database. This flag must appear after all others (see ENVIRONMENT below). quest will search the database specified by the triplet databasen.ind, databasen.msk and databasen.ind (The extensions .ind , .msk and .tcd are invariant). If more than one database is specified on the command line the specified databases will be searched in the order given (See BUGS). The keywords `Master' (case sensitive) can be used to refer to the default master database and the Database Use database, respectively. -tem template_file Specify an input chemical templates file (see QUESTTEM- PLATE below). -ini initialisation_file Initially read quest commands from the file initialisation_file instead of the default before read- ing commands from standard input. (See QUESTINIT in the ENVIRONMENT section.) -v virtual_database Use only those REFCODEs in the file virtual_database for searching. (See QUESTVIRTUALDB in the ENVIRONMENT section.) -fig fig_file Configure the graphics for quest from the file CSD System Last change: $Date: 1999/08/17 11:52:34 $ 1 CSDS Commands QUEST(L) fig_file. (See QUESTFIG in the ENVIRONMENT section.) -nbg Do not fork a background process when searching the database. In interactive mode, unless `-nbg' is speci- fied, quest will fork a background process after each request to search the database. -version Print version information for the current CSDS. -reorderbytes Flag the database files as having a non-native integer format. Note that all subset databases created using the SAVE ASER option are in native format and that you cannot mix native and non-native databases. Valid values for are permutations of the string "1234". You do not need to specify this unless quest is unable to determine the ordering for itself. See the CSD_DB_REORDER_BYTES environment variable in the ENVIRONMENT section. -help Display these manual pages. -if input_filename Read instructions from input_file instead of standard input. -of output_filename Write output to output_file instead of standard out. Useful for batch runs with the at(1) command. ENVIRONMENT quest 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 expli- citly defining them within the current environment. 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 quest. CSDMACHINE Use the executables and database for machine type $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 System Last change: $Date: 1999/08/17 11:52:34 $ 2 CSDS Commands QUEST(L) 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 quest recognises the environment variables: CSDVIRTDB, QUESTVIRTUALDB, QUESTTEMPLATE, QUESTINIT and QUESTFIG. These environment variables, when set, should point to particular input files. See the FILES section for more details. FILES Input Files: jobname.virtual_db Contains a list of refcode names that act as a filter. If it doesn't exist then it is linked to the first file found, if at all, in the following list: `-v' virtual_db, CSDVIRTDB, $QUESTVIRTUALDB. jobname.fig The quest graphics configuration file. (Allows users to change the colours used by the graphics, for example and specify pagesizes for Postscript output files.) If it doesn't exist it is linked to the first file found in the list: command-line $QUESTFIG, ./quest.fig, $HOME /quest.fig, $CSDHOME /csds/quest.fig. jobname.ini File containing quest instructions to be executed before any user instructions. If it doesn't exist it is linked to the first file found in the list: command-line `-init' init_file, $QUESTINIT, ./quest.ini $HOME /quest.ini, $CSDHOME /csds/quest.ini. 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, $QUESTTEMPLATE, ./quest.tem, $HOME /quest.tem, $CSDHOME /quest.tem. You can add templates to this file using quest but only if template file resides in one of your subdirectories. Therefore you will have to copy the original from $CSDHOME /csds/quest.tem. $CSDHOME/csds/db_*.dbl If one of these files exists, then it is understood to CSD System Last change: $Date: 1999/08/17 11:52:34 $ 3 CSDS Commands QUEST(L) contain a list of names of the files that constitute the Cambridge Crystallographic Database. Database file names explicitly specified by the command line `-db' database_file, override the use of this file. $CSDHOME/csds/quest.hlp The quest on-line help file. Output files: jobname.{fser,bib,con,dat,gcd,ps,bcc,mol2,cmf,gls,mdl,cor} ASCII SAVE files. Files are created using the SAVE ( FSER, FBIB, FCON, FDAT, REFCODE, POSTSCRIPT, BCCAB, MOL2, CIF ), GLIST, MODEL and COORD commands before a search. These files contain lists of varying kinds of data, one packet per hit. jobname.ss.{ind,msk,tcd} Database subset created using the SAVE ASER command. These files can be reused and input in a subsequent run of quest using the command line `-db' jobname.ss jobname.rco This enables you to set up a quest instruction document which will be read by quest when you issue the RECOVER instruction. jobname.{fgn,fgd} Fragment numbers (binary) and fragment definition (ascii) files. These files are the input files for gstat(l) or vista(l). They are created whenever a search is conducted with geometric (3D) constraints. The auxiliary files jobname.tab and jobname.sum are also created. jobname.jnl Journal file. jobname.sve STORE-FRAGMENT file. SEE ALSO The "Unix Installation Notes", CCDC. DIAGNOSTICS The diagnostics produced by quest are intended to be self- explanatory. The output of quest is explained in Volume 2 of the "CSD System documentation.". BUGS The virtual database QUESTVIRTUALDB will not be used if the `-nbg' flag is set. CSD System Last change: $Date: 1999/08/17 11:52:34 $ 4 CSDS Commands QUEST(L) The BEGIN command works inefficiently when the database is not in REFCODE lexical order. In some circumstances, quest may produce other output files. (e.g. .ins, .fg_to_bg_x, .csd, .stats etc.); these files may be ignored. CSD System Last change: $Date: 1999/08/17 11:52:34 $ 5