IT'S EASY

• NKET.QCK
• NKET.LSQ
• NKET.ANISO
• NKET.FOUR

The main CRYSTALS documentation is in volumes 1 to 7 of the manual, which are more or less complete and definitive. An additional introduction to the program is available in the GUIDE. New users seem to want something even simpler, and this PRIMER has been written to try to meet this need. If you dont like this document, or the Guide or the Manuals, please let me know what should be changed.

These first few pages will illustrate how to take reflections and a trial structure from another system and get them into CRYSTALS, and then start refining the structure. The data is on the distribution media. You should create a subdirectory and then copy the data into it.

 
            VMS                                    DOS
 
     $CREATE/DIRECTORY      [.EXAMPLE]     MKDIR C:\EXAMPLE
     $SET DEFAULT           [.EXAMPLE]     COPY NKET.* C:\EXAMPLE\*.*
     $COPY CREXAMPLE:NKET.* []             CD \EXAMPLE
 

Start CRYSTALS in interactive mode. Answer NO (the default) in reply to the question about SCRIPT mode. That will be dealt with later. You will get the CRYSTALS prompt '!'. Enter the following commands in order each time you are prompted. You can print a listing file (132 characters wide) when you exit from CRYSTALS. The file will have the extension .LIS or .LIn.

 
           VMS Start                        DOS start
     $CRYSTALS   []    NKET                 CRYSTALS
 
                         !\USE NKET.QCK
                         !\USE NKET.LSQ
                         !\USE NKET.ANISO
                         !\USE NKET.FOUR
                         !\FINISH
                                    Note that the CRYSTALS commands
                                    are the same for both computers
 

The display on the terminal will look like:

 
 
      Issue   9 for DEC VAX under VAX/VMS 5.0   September 1986
       Copyright Chemical Crystallogaphy Laboratory, Oxford
 
        This is the interactive version of CRYSTALS
              incorporating a help facility
 
        To get help, type \HELP HELP
        To end, type      \FINISH
 
 ************************************************************
  A new direct access file has been created on unit 1 -- Data
 ************************************************************
 
     CCCC  RRRR   Y   Y   SSSS  TTTTT   AAA   L       SSSS
    C      R   R  Y   Y  S        T    A   A  L      S
    C      R   R  Y   Y  S        T    A   A  L      S
    C      RRRR    YYY    SSS     T    AAAAA  L       SSS
    C      R R      Y        S    T    A   A  L          S
    C      R  R     Y        S    T    A   A  L          S
     CCCC  R    R   Y    SSSS     T    A   A  LLLLLL SSSS
 
( YES NO )
 Do you want to use SCRIPTS? (YES or NO) [ NO ] : no     <--
 !\USE NKET.QCK                                          <--
 
    0001*  \USE NKET.QCK
    0002*  \QUICKSTART
    0003*  CELL 7.5330  7.5336 15.7802
    0004*  SPACEGROUP P 41
    0005*  CONTENT C 32 H 32 N 4 O 16
    0006*  DATA 1.5418 FSQ
    0007*  FILE CRDIR:NKET.REF
    0008*  FORMAT (3F4.0, 2F8.2 )
    0009*  END
 
Quick startup ends            Version  1.03
Disc file extended by   0 record(s) (      0 integer words )
**** Disc file on unit   1 extended by     1 records
 
 

The two line with the arrow, <-- , contain the user input. Other input is drawn from the specified files. The data in those files could have been typed into CRYSTALS directly at the '!' prompt, so that depending on the amount of input and the users confidence, he may use either or both input methods. The following pages explain the contents of the files.

NKET.QCK

 
 
 \ This is the startup file for NKET
 \QUICKSTART
 CELL 7.5330  7.5336 15.7802
 SPACEGROUP P 41
 CONTENT C 32 H 32 N 4 O 16
 DATA 1.5418 FSQ
 FILE CRDIR:NKET.REF
 FORMAT (3F4.0, 2F8.2 )
 END
 \LIST      5
 READ NATOM =     13
 ATOM C       1 X=0.819200   0.697300   0.118000
 ATOM C       2 X=0.502300   0.661800   0.030100
 ATOM C       3 X=0.809300   0.322200   0.053100
 ATOM C       4 X=0.739400   0.046200   0.091800
 ATOM C       5 X=0.936400   0.463600   0.025800
 ATOM C       6 X=1.059800   0.461400   0.171800
 ATOM C       7 X=0.836400   0.629600   0.033900
 ATOM C       8 X=0.634800   0.560100   0.004300
 ATOM C       9 X=1.106300   0.435500   0.091400
 ATOM C      10 X=1.180100   0.263500   0.070100
 ATOM C      11 X=1.048600   0.109000   0.096000
 ATOM C      12 X=0.857800   0.160100   0.077100
 ATOM C      13 X=0.630000   0.381500   0.040500
 END
 \SFLS
 SCALE
 END
 \ANALYSE
 END
 

The ANALYSE instruction gives an analysis of residuals, and shows the R factor (20%) for the model after Fo has been scaled to Fc.

NKET.LSQ

 
 
 \LIST 12
 FULL X'S U[ISO]
 END
 \SFLS
 REFINE
 REFINE
 CALC
 END
 \COLLECT
 END
 \EDIT
 SORT U[ISO]
 END
 \DISPLAY HIGH
 END
 \MOLAX
 ATOM FIRST UNTIL LAST
 PLOT
 END
 

 
 
 \EDIT
 RENAME C(1) O(1), C(2) O(2), C(4) O(4), C(6) O(6)
 REN C(3) N(3)
 EX
 END
 \LIST 12
 FULL X'S U'S
 END
 \SFLS
 SCALE
 REFINE
 REFINE
 END
 

 
 
 \FOURIER
 REFLECT  CALC=YES
 MAP TYP=DIFF
 PEAK HEIGHT=2
 END
 \PEAK
 END
 \COLLECT
 SEL TYPE=PEAK
 END
 \MOLAX
 ATOM FIRST UNTIL LAST
 PLOT
 END