Crystals Primer

Chapter 17: Scripts

17.1: Escaping from SCRIPT mode.

17.2: Entering SCRIPT mode

17.3: Principal Menued Scripts - Feb 1997

17.4: Available Scripts - Feb 1997

The CRYSTALS SCRIPT environment is similar to the menus found in many modern PC programs. Superficially it is rather like a command tree, with a root, branches, twigs and finally leaves which perform discrete crystallographic or data management operations. This sort of structure is adopted so that related operations may be grouped together, making them easy to locate. However, a basic operation may be strongly related to several groups of operations, and must therefore appear on the menu for each of these groups. The same leaf can be found on several different branches! In addition, it is sometimes usefull to execute a 'leaf' quite out of its normal context.

This structured flexibility is provided by the SCRIPT processor, and the CRYSTALS program is issued with a sample set of scripts. These have developed to meet some of the needs of Oxford students, and so they may well not be suitable in other environments. However, the scripts themselves are only plain text data files, and users are free to modify them in any way they wish, and add new ones. It is not possible for a script to corrupt the CRYSTALS program.
 

Control can be passed to the command mode at any time by replying DIRECT (in full) to any SCRIPT question. The users is passed to the CRYSTALS prompt '!'.
 

Control can be passed to script mode by issuing the CRYSTALS command.

          \SCRIPT    scriptname

where scriptname is the name of the script required. The master script is called CONTROL, but entry can be to any branch of the tree directly. Script mode is entered automatically by a call '\SCRIPT CONTROL' in the CRYSTALS startup file 'CRYSTALS.SRT', but can be deactivated by a call '\USE CONTROL' in the users CRYSINIT.DAT file.

 e.g.
        \SCRIPT  DATA

Passes control to the branch concerned with list input, examination and editing. The help facility \HELP SCRIPTS Lists the available scripts on-line.

Numerical data for a structure is stored in a CRYSTALS data-base, filename.DSC. This accumulates information as an analysis progresses. In this file, data is grouped by function into 'LISTS'. Most of the scripts refer to data by its type (e.g. CELL parameters), but occasionally they refer by LIST number (in this case, LIST 1), and many CRYSTALS output messages refer to lists. A table of the lists and the data they contain is appended to this document.
 

  This is the master control SCRIPT
     HELP          Display this help text
     DATA          Input, examination and modification of data LISTS
     SCRIPT        Execute the named SCRIPT immediately
     NEWSTART      Starting a new structure analysis
     STRUCTURE     Solving a structure or inputting a solution
     MAPS          Computing and using Fourier maps
     LEASTSQ       Setting up and performing least squares refinement
     GEOMETRY      Computing molecular parameters
     PUBLISH       Preparation of tables
     ROUTINE       A script for routine structures
     GENERAL       Information about CRYSTALS
     FINISH        Exit from CRYSTALS
     DIRECT        Go to CRYSTALS direct command input

     This script assists in the examination, modification
     and input of CRYSTALS LISTS
     BACK        End this script
     HELP        Display this help text
     INDEX       List the possible CRYSTALS LISTS
     INPUT       Input new lists
     LOOK        Print the contents of the current LISTS
     MODIFY      Modify the contents of some lists
     PERHYDRO    Perhydrogenate the carbon atoms
     DISK        Access the CRYSTALS DSC file
     USE         Single step though a data file
     DIRECT      Go to CRYSTALS direct command input

     This script helps you get in the basic data for a new structure
     BACK        End this script
     HELP        Display this help text
     INCAD4      Input CAD4 data from the RC85 or RC93 program
     DIPIN       Input data from DIP2000
     QUICKSTART  Simplified startup using reflections in SHELX format
     Y290        Input format for Hilger & Watts Y290 'Nottingham' format
     INITIAL     Generalised startup for non-RC85 data formats
     DATA        General data input script
     MODIFY      Modify existing lists
     LOOK        Examine existing lists
     DIRECT      Return to command mode

      BACK        Finish with this facility
      HELP        Display this help text
      INEMAP      Input model found by Direct Methods run
      PATTERSON   Prepare data for, or compute a Patterson map
      SHELXS      Prepare data for SHELXS86
      SIR88       Prepare data for SIR88
      SIR92       Prepare data for SIR92
      PLOT        A join the dots plot on screen and printer

      BACK        Finish with this facility
      HELP        Display this help text
      INEMAP      Input the results of a Direct methods run
      AUTO        A cyclic procedure for Fourier refinement
      GUIDE       A SCRIPT to guide you through Fourier calculations
      SF          Compute structure factors and phases
      FOURIER     Compute Fourier map
      CONVERT     Convert peaks list to atoms list
      COLLECT     Collect atoms and peaks together
      REGROUP     Reorder atoms to form molecules
      PLOT        A join the dots plot on screen and printer
      EDIT        Delete or rename groups of atoms and peaks
      DISTANCE    Compute interatomic distances.
      SLANT       Compute a general Fourier section
      SECTION     Define the asymmetric part of the cell
      RFACTOR     Show the current R factor
      CONTOUR     Produce contouring files
      DIRECT      Go direct to command mode

      The SCRIPT to help set up refinement jobs.
      BACK        End this script
      HELP        Display this help text
      AUTO        Automatic choice of variables
      VARIABLES   Define the variables to be refined
      SFCONTROL   Modifications applied to structure factor calculation
      SCALE       Compute structure factors/ scale factor
      CYCLE       Perform refinement cycles
      SIXCYCLE    Perform six unconditional refinement cycles
      RESTRAINTS  Define restraints
      ANALYSE     Produce analysis of residuals
      CHECK       Check that the matrix is properly defined
      WEIGHTS     Optimise the reflection weighting.
      DIFABS      Run the empirical absorption correction
      DISK        Examine the disk file
      RFACTOR     Show the current R factor
      PLOT        Show the current structure on the screen
      EXCHANGE    Exchange results with anothe computer
      DIRECT      Go to CRYSTALS direct command input.

      The SCRIPT to help produce tables for publication
      BACK        End this script
      HELP        Display this help text
      LOOK        List the contents of the active lists
      DISK        Examine the disk file
      DISTANCE    Compute distances and angles
      PLOT        Join-the-dots plots on the vdu
      PLANE       Best plane and best line computations
      TORSION     Compute torsion angles
      TLS         Analyse rigid body thermal motion
      AXES        Compute principal axes of temperature factors
      DIRECT      Go to CRYSTALS direct command input.

      The SCRIPT to help produce tables for publication
      NOTE that under some operating systems, the output from successive
      entries to this SCRIPT will overwrite previous output.
      BACK        End this script
      HELP        Display this help text
      XYZ         Coordinate listing
      ANISO       Temperature factor listing
      REFLECTIONS Reflection listing
      DISTANCES   Distance-angle listing
      SUMMARY     A summary of all data stored
      ANALYSE     A full analysis of residuals
      GEOMETRY    The SCRIPT for evaluating molecular parameters.
      CIF         Prepare a 'cif' format paper submission file
      ARCHIVE     A SCRIPT to save the best of the goodies.
      DIRECT      Go to CRYSTALS direct command input.

 This script gives general information about SCRIPTS and CRYSTALS.
      BACK        End this script
      HELP        Display this help text
      VERBOSE     Switch the verbose text display on/off
      PURGE       Purge the .dsc file of old data.
      CRYSINIT    A brief description of CRYSINIT.DAT
      SCRIPTS     A brief description of SCRIPTS
      CRYSTALS    The CRYSTALS HELP system
      TERMINAL    Lets you tell CRYSTALS your terminal type
      TYPE        Displaying a file on the terminal
      VERIFY      Enable/disable display of SCRIPT execution
      QUESTIONS   Format of SCRIPT questions
      DIRECT      Go to CRYSTALS direct command input.

AFOUR      ANALYSE    ARCHIVE    AUTO12     AXES       BATCHLSQ
CADQUICK   CADSLOW    CHECK      CIF        COLLECT    COMMANDS
CONTOUR    CONTROL    CRYSHELP   CRYSINIT   DATA       DATRED
DIFABS     DIPIN      DIRECT     DISK       DISTANCE   EDLIST1
EDLIST12   EDLIST16   EDLIST29   EDLIST5    ELEMENTS   EXCHANGE
EXPORT     FGUIDE     FINDH      FINISH     FOPTWT     FOURIER
FSQWT      GENERAL    GEOMETRY   GETEXP     IMPORT     INATOMS
INBASICS   INCAD4     INCOMP     INEMAP     INEMAP01   INITIAL
INLIST1    INLIST12   INLIST13   INLIST14   INLIST16   INLIST2
INLIST23   INLIST28   INLIST29   INLIST3    INLIST30   INLIST31
INLIST5    INLIST6    INPUT      INRC93     INSHELXS   INSPACE
INXYZ      INY290     LEASTSQ    LIST1      LIST12     LIST13
LIST16     LIST2      LIST23     LIST30     LIST31     LOOK
MAPS       MODEL      MODIFY     MULTAN     NEWSTART   NFOUR
NULL       PARTIAL    PATTERSN   PEAKS      PERHYDRO   PHEN16
PLANE      PLOT       PRINIT     PRRESET    PUBANISO   PUBDIST
PUBLISH    PUBREFL    PUBXYZ     QUESTION   QUICKST    REFINE
REGROUP    RELEASE    RENAME     RFACTOR    ROUTINE    SCALE
SCRIPT     SECTION    SFLS       SHELXS     SIR        SIR88
SIR92      SIXCYCLE   SLANT      SNOOPI     SORT       STRUCTUR
TERMINAL   TEXT       TIDYUP     TLS        TODOS      TORSION
TPP16      TYPE       USE        VALIDATE   VERIFY     WEIGHTS