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CRYSTALS manual
University of Oxford


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Crystals Primer

Chapter 2: Example Of A Simple Structure

2.1: Script mode
2.2: Starting CRYSTALS
2.3: Command mode


CRYSTALS can be run in two modes:

COMMAND-LINE in which the user enters commands in the order he chooses.
SCRIPT, in which CRYSTALS tries to help by asking questions.

This example 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 in a subdirectory NKET. You should create a subdirectory and then copy the data into it. The directory NKET contains files for a simple structure determination. Some of them are for Command mode, others for Script mode.


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

2.1: Script mode

The file to be used is:

       NKET.DOC      A brief description of the structure
       NKET.REF      Pre-processed reflection in SHELX format
 

The general information about the anaylsis is:

       Colourless crystal, .2x.2x.2 mm
       Molecular formula C8 H8 N1 O4
       Space Group P 41, 4 formula units in cell
 
           OH\        /OH
               Ch    Ch
             /  \  /    \
           /      CH     CHH
       OH-CH      |      |
           \      N      CHH
             \ /     \ /
              CHH     C=O
 
 

In the following example, the left column summarises the question CRYSTALS asks, the middle column is the users response, and the right column are comments. User responses shown in square brackets [YES] indicate a response chosen from a menu list. DO NOT include the '[]'. <cr> represents 'ENTER' or 'RETURN'.


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

2.2: Starting CRYSTALS

On a PC, type CRYSTALS or double click the CRYSTALS icon.

 Summary of Screen             User's response         Comments
 
 The CRYSTALS banner, an
 invitation to use SCRIPTS     [YES]
 Type of analysis              [NON-ROUTINE]
 The main menu                 [NEWSTART]     Starting a new structure.
 Structure title               'Nket at 0 C'  Some text as a title.
 The newstructure menu         [QUICKSTART]   Startup for SHELX reflections.
 Input LIST 30                 [YES]          These are general items.
 A series of general questions                If there is a value in [] at
                               <cr>           the end of a question, this is
                                 .            the default value. Use 'ENTER'
                                 .            to accept default, or enter a
                                 .            real value.
                               <cr>           If the line ends [-], there is
                                              no default. You MUST give an
                                              answer to continue.
 Number of formula units [-]   4              This question must be answered.
 Colour                        Clear
 Shape                         Cube
 Cell Parameters [-]           7.533          No defaults available.
                               7.533 15.78    You can often insert all the
                                              answers at once.
 Cell angles [90]              <cr>           Accept default.
 
 Space group                   P 41           Separate each component by <space>.
 
 Experimental conditions file  [NO]
 Radiation                     [CU]
 Friedels Law                  [YES]
 Crystal Orientation           [NO]
 Cell Contents                 C 32           4 formula units in this case.
                               H 32           Don't forget the spaces.
                               N 4 O 16       Type ahead.
                               END            Use 'END' to end input.
 Refinement against Fsquared?  [NO]           You could choose YES.
 Input Cell esds, List 31      [YES]
 Cell esds [.001]              <cr>           Accept the defaults, or insert
                                .             real values.
 Reflection file name  [-]     nket.ref
 Data type                     [FSQ]          F-squared data.
 Change any LISTS              [NO]
 Free Format data?             [NO]
 Standard format?              [YES]
 Sigma values                  [YES]
 Format [(3F4.0,2F8.0)]        <cr>           If you change it, don't forget
                                              the ( ).
 Merge?                        [YES]
 Sigma threshold               3.0            All reflections are stored, and
                                              the level can be reset later
                                              if required.
 Sort/Merge [YES]              <cr>           Remove systematic absences and
                                              merge equivalents.
 SHELX atoms [NO]              <cr>
 Solve [YES]                   <cr>
 Method [SIR92]                <cr>
 First try [YES]               <cr>           If the structure doesn't solve,
                                              choose [STRUCTURE] from main menu,
                                              and when you get here, try [NO].
                                              CRYSTALS will prepare a more
                                              intensive job
 


Crystals now closes down. To run SIR92, type SIR92. When SIR shows a menu, click QUIT until it closes down. Restart CRYSTALS.

 Use SCRIPTS                   [YES]          Return to SCRIPT mode
 Structure type                [NON-ROUTINE]
 Main Menu                     [STRUCTURE]
 Structure Sub-menu            [INEMAP]       Input results of direct methods
 How solved [SIR]              [SIR]
 Version                       [SIR92]        The SIR92 atoms are read in
 See the structure?            [YES]          In graphics, edit the structure
                                              using 'rena(me)' to change atoms.
                                              Remember each instruction needs
                                              two <cr>. Use 'END' to end.
 Save changes [YES]            [YES]
 Structure fragmented?         [NO]
 Resequence [YES]              [YES]          Renumber atoms so that adjacent
                                              atoms have sequential numbers.
 Compute over all scale        [YES]
 
                               [BACK]
 


This is the end of this branch of the process. A message suggests the next step. If all atoms were revealed in the e-map the next step is least squares, other wise try Fourier Maps. In this case the structure is OK, so you can jump directly to the refinement section below.

                               [MAPS]
                               [AUTO]         CRYSTALS chooses the 'best' map
                                              The atoms may be resequenced to
                                              include newly-found ones, and
                                              assembled into a molecule.
 Reject by rho                 [YES]
 Resequence atom numbers       [NO]
 Collect into molecule         [NEW]          Only apply symmetry to newly found
                                              peaks.
 
 Graphical mode                [YES]
                                              Relabel Q to real atoms, etc. END
                                              to end.
 Save the changes              [YES]
 Repeat Fourier cycle          [NO]
                               [BACK]         Back to main control menu.
 


Refinement. If the structure is routine, least squares will finish the job.

                               [LEASTSQ]
                               [AUTO]         CRYSTALS chooses the next task on
                                              the basis of R factor and
                                              previous history.
 R factor intermediate
 Refine x's & Uiso online?     [YES]
 How many cycles               [5]            If 5 is too many, CRYSTALS will
                                              stop anyway.
 Refine x's Uaniso online
 How many cycles               [5]
 
 Locate H atoms                [YES]
 Info or continue              [NO]
 Delete existing H atoms       [YES]          It won't matter if there are none.
                                              CRYSTALS computes structure factors,
                                              computes potential H sites and does
                                              a difference map. The computed H
                                              should be near found ones.
 Graphics                      [YES]
                                              Tidy up the map. Delete computed if
                                              you prefer the found, otherwise
                                              ignore the found. They will be
                                              eliminated later. Change any found
                                              peaks to H if there is no
                                              equivalent computed (eg H bonds).
                                              Some OH H should appear.
                                              'END' to end.
 Save changes                  [YES]
 Keep Geometric                [YES]
 How many cycles                [5]
 Continue                      [YES]
 Locate Hydrogens              [YES]          If there still are some missing.
 Delete existing H atoms       [NO]           We are looking for additional ones.
 Graphics                      [YES]          Try to find H amongst soup of peaks.
                                              Try:
                                     DIST (click O and q) and rename
                                  or PACK CELL COMPLETE INCL CELL VIEW
                                     ALONG AXIS A VIEW
                                     CONNECT HBOND O 0.0 3.0 VIEW
                                     EXCLUDE AREA <cr><cr>
                                              (use mouse to exclude some
                                              of the diagram - left button to
                                              mark corner of polygon)
                                     VIEW
                                     EXCLUDE ....
                                     UNPACK   (otherwise CRYSTALS will get all)
                                     END
 Save                          [YES]
 Geometric                     [YES]
 Refine                        [5]
 Locate H atoms                [NO]           We have them all.
 Check for exinction           [YES]          The program explains how.
 Check refinement weighting    [NO]           No, since we just included
                                              extinction.
 Number of cycles              [5]
 
 Locate hydrogen atoms         [NO]           If they are not all found by now,
                                              ask an expert.
 Check refinement weighting    [YES]          The program explains how.
 Type                          [OPTIMAL]
 Change the final parameter    [NO]           The 3 parameter scheme is fine.
 How many cycles               [5]
 Locate Hydrogen               [NO]
 Cycles                        [5]
 Continue refinement           [NO]           Now choose CYCLE off LSQ menu.
 See the structure             [YES]
                                              Use ELLIPS TYPE ALL 4 VIEW to
                                              check the adps.
 
 Continue refinement           [NO]           Now choose CYCLE off LSQ menu.
                               [CYCLE]        Cycle until full convergence.
                               [BACK]         To main menu.
 
                               [PUBLISH]      Select what you want, eg CIF.
                               [FINISH]
 


Very few real analyses will run exacly like this.

Potential Problems

Fourier recycling does not complete the structure. Try some least squares before more Fourier recycling.

Some atoms are 'physically unreasonable'. Check the atomic type assignments. Many atoms are physically unreasonable. Incorrect data reduction, serious absorption.


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

2.3: Command mode

The files to be used in Command mode are:

 NKET.REF    Reflections in SHELX format
 NKET.QCK    Initial data, including a set of trial coordinates
 NKET.LSQ    Isotropic refinement and molecule assembly
 NKET.ANI    Anisotropic refienement
 NKET.FOU    Difference Fourier
 


In Command mode, the user can enter commands and data directly from the keyboard, or read them in from pre-prepared files.
Start CRYSTALS as above, but answer NO in reply to the question about SCRIPT mode. You will get the CRYSTALS prompt '!'or '>'. Enter the following commands in the order given each time you are prompted. Note that interactive commands can be mixed with the use of pre-prepared files, and that individual SCRIPTS can be activated. You can print a listing file (132 characters wide) when you exit from CRYSTALS. The file will have the extension .LIS or .LIn.

       !\USE NKET.QCK
       !\CAMERON
       !END            (In CAMERON, type MENU ON <cr><cr>
                         Type END <cr> to end the graphics)
       !\USE NKET.LSQ
       !\USE NKET.ANI
       !\USE NKET.FOU
       !\SCRIPT PLOT  (Rename some of the Q to H atoms)
       !\PERHYDRO
       >END
       !\LIST 12
       >BLOCK SCALE O(1,X'S,U'S) UNTIL C(9)
       >END
       !\SFLS
       >REFINE
       >REFINE
       >END
       !\FINISH
                                           Note that CRYSTALS commands are
                                           the same for all computers
 


The display on the terminal will look something like:

 
       Issue  10 for PC486 under DOS 6.0   September 1996
        Copyright Chemical Crystallogaphy Laboratory, Oxford
 
         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, either or both input methods may be used. The following pages explain the contents of the files.

NKET.QCK
This contains the basic data, the name of the file containing the reflections and a trial model obtained from somewhere else.
  \ 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
This file sets up isotropic refinement, and requests several cycles of least squares. The COLLECT assembles the atoms into a molecule.
 
  \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
 


The sort on U[iso] will help you decide which atoms to change from carbon, and the MOLAX (molecular axes) produces a simple plot on the terminal.
 

NKET.ANISO
This file starts by changing the selected atoms, and then doing anisotropic refinement.
 
  \EDIT
  RENAME C(1) O(1), C(2) O(2), C(4) O(4), C(6) O(6)
  REN C(3) N(3)
  EXECUTE
  END
  \LIST 12
  FULL X'S U'S
  END
  \SFLS
  SCALE
  REFINE
  REFINE
  END
 



 

NKET.FOUR
This file computes a difference Fourier, and then collects the new peaks to chemically suitable positions.
 
  \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
 



 



[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 ]

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© Copyright Chemical Crystallography Laboratory, Oxford, 2006. Comments or queries to David Watkin - david.watkin@chem.ox.ac.uk Telephone +44 1865 285019. This page last changed on Wednesday 8 November 2006. The website was re-generated on Wednesday 8 November 2006. Choose your nearest mirror for faster access: [ Original | CCP14 UK Mirror | CCP14 Canadian Mirror | CCP14 USA Mirror | CCP14 Australian Mirror ]
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