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Crystals PrimerChapter 2: Example Of A Simple Structure
CRYSTALS can be run in two modes:
COMMAND-LINE in which the user enters commands in the order he chooses.
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 modeThe 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
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]
[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.
[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. [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.3: Command modeThe 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.
!\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
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 ] |
© Copyright Chemical Crystallography Laboratory, Oxford, 2006.
Comments or queries to David Watkin -
david.watkin@chem.ox.ac.uk Telephone +44 1865 285019.
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