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 useful 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.

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17.1: Escaping from SCRIPT mode

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 '!'.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

17.2: Entering SCRIPT mode

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.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

17.3: Principal Menued Scripts - Feb 1997

The SCRIPT CONTROL is the master controlling script. Most of the sub-scripts called from it are also menued.

CONTROL.SCP

   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

DATA.SCP

    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

NEWSTART.SCP

   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

STRUCTUR.SCP

       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

MAPS.SCP

       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

LEASTSQ.SCP

    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.

GEOMETRY.SCP

    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.

PUBLISH.SCP

    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.

GENERAL.SCP

    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.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

17.4: Available Scripts - Feb 1997

 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

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