- + Frequently Asked Questions
- - Crystals Primer
- 1. Getting Started
- 2. Example Of A Simple Structure
- 3. Overview
- 4. Basic Data Input
- 5. The Model
- 6. Fourier Maps
- 7. Preparation Of The Model
- 8. Refinement
- 9. Seeing The Structure
- 10. Molecular Geometry
- 11. Publication Listings
- 12. Cif Files
- 13. Documentation
- 14. The Data Base
- 15. Tailoring The Program
- 16. Advanced Refinements
- 17. Scripts
- 18. Data Lists And Instructions
- 2. Example Of A Simple Structure
- + Crystals User Guide
- + Crystals Manual
- + Cameron Manual
- + Index
- Fri Jun 2 2000
- - Crystals Primer
Crystals Primer
Chapter 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. 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.
2.1: Script mode
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'.
2.2: Starting CRYSTALS
On a PC, type CRYSTALS
On a VAX type CRYSTALS [] compound_id
Summary of Screen Users 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 Dont 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 deaults, or insert
. real values
Reflection file name [-] nket.ref
Data type [FSQ] Fsqared 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, dont 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 comtrol 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 wont 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, oterwise
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 tham 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.
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, he may use either or
both input methods. 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