chem cryst
CRYSTALS manual
University of Oxford

Crystals Primer

Chapter 3: Overview

3.1: Modes of Use

3.2: Data Formats

3.3: Output

3.4: Starting the program

3.5: Getting out of the program

3.6: Getting out of SCRIPTS

3.7: Stopping the program

CRYSTALS is a single program for performing most calculations required in single crystal structure analysis, including graphics, but with the exception of direct methods. Simple links connect CRYSTALS to SIR and SHELXS for direct methods.
 

The program has the same command set for both interactive and batch use. In batch mode the program executes commands taken from data files, and the results are returned as files.

In interactive mode, the user types commands directly into the running program, and results are both displayed on the screen and saved as files.

The program can also be run on-line with commands taken from data files and results displayed on the screen. There is a mixed mode, in which the program is used interactively, with the user entering some commands directly, and briefly passing control to pre-prepared files containing frequently used combinations of commands, after which control is returned to the user.

There is also an interrogative mode, in which the program leads the users through the analysis. See the section SCRIPTS for details, and the chapter Example of a Simple Structure.
 

All the user input to CRYSTALS is in normal ASCII characters. Reflection data can be input in fixed format to speed processing, but in general all data is free format with <space> or <cr> as delimiters. For most commands the interpretation of a value may be taken either from its position on the line, or from a preceeding keyword. The two methods may be intermixed. Default values are provided for many parameters.

 e.g.
            REAL  10.4 12.3 19.5 90.0 113.7 90
      or
            REAL a=10.4 b=12.3 19.5  beta=113.7
 

All commands, keywords and alphbetic data is case insensitive. Decimal points are optional for exact real values.

The program can be run so that all data is loaded each time from ASCII files for every new job, but if permanent filestore (disc space) is available the user can accumulate a binary data base for each structure which is automatically loaded for each run of the program. In this case the program can be started and stopped at will, and will usually survive a machine crash without loss of data.

The crystallographic data is grouped into LISTs for both ASCII and binary representations. When data in a LIST is modified or reinput to the data base, it usually over writes a previous LIST of the same type. The main exception is LIST 5, the refinable coordinate list, which always generates a new version. See the chapter DATA BASE for details. A list of the contents of the LISTS is given at the end of this document.

All COMMANDs begin with the character \ (or the hash symbol) followed without a space by the command name. Additional data may be given on the same or subsequent lines, and the whole command is terminated with END on a line by itself. \ followed by a space then text is taken as a comment in the data.

      \  This is a comment
      \COMMAND     (parameters)
      (DIRECTIVES)    (parameters)
      END
 

There are two main plain text output channels. One, *.LI*, is intended as a detailed record of a task, and may be printed on a lineprinter. The other, *.MON, is displayed on the terminal during interactive or on-line sessions, and directed to a file during batch working. The file may be listed on a printer. Other files are used for special purposes. See the section FILES for details.
 

It is intended that a subdirectory will be used to hold the files associated with a structure. Most of the permanent files created by CRYSTALS have the same filename, and extensions indicating their function.

For example, if you are working on a copper compound, create a suitable subdirectory.

             VAX                              DOS
 
      $CREATE/DIRECTORY      [.CU]            MKDIR CU
      $SET DEFAULT           [.CU]            CD CU
 

CRYSTALS automatically creates the data base file, *.DSC if it has not been created by a previous run. If commands have already been put into a file using a text editor, the file (e.g. JOB.DAT) may be executed online by issuing:

  (VMS only)     $CRYSTALS      []      CUCPD      JOB
 

or submitted to a batch stream with:

  (VMS only)     $SUBMIT/PARAM=(CU, CUCPD, JOB)      CRPROC:CRYSTALS
 

Finally, the program can be started interactively and control be passed to the data file.

Answering 'NO' to the question about SCRIPTS (see the section on SCRIPTS) will bring you to the CRYSTALS prompt, '!'. Commands may now be entered directly to the program. The \USE command passes control to the specified file. The \SET commands tailor the volume of program output. See the section on Tailoring the Program.

 (VMS start)     $CRYSTALS [] CUCPD
 (DOS start)     >CRYSTALS
 
 (all systems)   !\SET WATCH 5
                 !\SET LISTS BOTH
                 !\USE JOB.DAT
 

If you are running CRYSTALS and suddenly wish to do something with SCL, e.g. list a directory to find a file name, it is not necessary to close down the program (SCL means the System Control Language, such as DOS or DCL).

Issuing $SCLcommand activates the SCL command, and returns you to CRYSTALS on its completion, e.g.

!$EDIT datafil.dat

Typing $ without an SCL command on VAX systems passes you to the DCL prompt, at which you may issue any DCL commands. When you wish to return to CRYSTALS, logout of the subprocess (type LO).

Under VMS a subprocess can also be initiated by typing CTRL/C and then S (for subprocess). You are passed to the DCL prompt, $, while CRYSTALS waits for you. When you wish to return to CRYSTALS, logout of the subprocess (type LO), and answer C (for continue) to the CRYSTALS question.
 

CRYSTALS is stopped by issuing:

         !\FINISH
 

If the program is stopped using <ctrl>/C, <ctrl>/Y or <ctrl>/BREAK there ia a small chance that the binary data base will not be correctly closed, and become corrupted.
 


[Getting Started | Example Of A Simple Structure | Overview | Basic Data Input | The Model | Fourier Maps | Preparation Of The Model | Refinement | Seeing The Structure | Molecular Geometry | Publication Listings | Cif Files | Documentation | The Data Base | Tailoring The Program | Advanced Refinements | Scripts | Data Lists And Instructions ]