Lesson 4 Crystal Structure Filesprofex.doebelin.org/wp-content/uploads/2018/07/Lesson-4...CIF Import...

Lesson 4

Crystal Structure Filesfor Profex / BGMN

Nicola Döbelin

RMS Foundation, Bettlach, Switzerland

June 13 – 15, 2018, Bettlach, CH

BGMN: Wavelength Distribution

2

Refinement

Control File

(*.sav)

Geometric

Instrument Data

(*.geq)

Wavelength

Distribution

(*.lam)

Diffraction

Pattern

(*.xy)

Structure

Models 1…n

(*.str)

Refined

Parameters

(*.lst)

Refined

Pattern

(*.dia)

Peak

Parameters

(*.par)

Refined

Structures(*.str, *.res, *.fcf, *.pdb…)

Run BGMN

STR Files Bundled with Profex

3

STR Files Bundled with Profex

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Public Structure Databases

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- STR files shipped with Profex (created manually by the Profex developer)

- http://www.bgmn.de/download-structures.html (created manually by BGMN team)

- Create manually from:

- ICSD (http://www.fiz-karlsruhe.de/icsd.html)

- PDF-4+ (http://www.icdd.com/)

- American Mineralogist Structure Database

(http://rruff.geo.arizona.edu/AMS/amcsd.php)

- Crystallography Open Database COD

(http://www.crystallography.net/)

- Cambridge Crystallographic Data Centre

(http://beta-www.ccdc.cam.ac.uk/pages/Home.aspx)

http://www.bgmn.de/download-structures.html

http://www.fiz-karlsruhe.de/icsd.html

http://www.icdd.com/

http://rruff.geo.arizona.edu/AMS/amcsd.php

http://www.crystallography.net/

http://beta-www.ccdc.cam.ac.uk/pages/Home.aspx

CIF File Format

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CIF (Crystallographic

Information File) Format:

- Standardized file format

- Contains structural information

- Contains references

- Specification available

at http://www.iucr.org

Problems with CIF Files

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Problems with CIF files:

1. May be (and very often ARE) incomplete

2. May use non-standard atomic settings

3. Must be converted to STR format for BGMN

With Profex:

• For complete CIF files: automatic import

• For incomplete CIF files: semi-automatic import

CIF Import

8

Major improvements in Profex 3.13:

- More meaningful and complete error messages

- Improved auto-recognition of space group symbols

- Instant STR file verification

CIF Import – Example 1: Vaterite.cif

9

Exercises Day 2 STR Files Vaterite.cif

No error messages Complete STR file

hkl stick

pattern

computed

on the fly

CIF Import – Example 2: Aragonite.cif

10

Exercises Day 2 STR Files Aragonite.cif

Profex 3.13: No user input requiredProfex ≤ 3.12: User input required

hkl Stick pattern = verification successful

«P m c n» from CIF file automatically

assigned to «P2_1/m2_1/c2_1/n» for BGMN

Slide from workshop 2017

CIF Import – Example 3: Calcite.cif

11

Exercises Day 2 STR Files Calcite.cif

Space group No. 167

automatically recognized

(since Profex 3.13)

1. Select correct setting

(here: Trigonal)

2. Add missing Wyckoff

symbols


12

«Tools BGMN SPACEGRP.DAT»

Select Number 167, Trigonal setting, and browse all Wyckoff positions.


13

Ca at 0,0,0: Wyckoff=b

C at 0,0,1/4: Wyckoff=a

O at x,0,1/4: Wyckoff=e

Fill in manually

“Save STR” to Structure Database directory


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1. Add missing Wyckoff symbols2. Run verification again

3. Stick pattern = verification successful


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Compare verification stick pattern with reference

Profex verification

ICDD PDF-4+

CIF Import – Example 4: Anhydrite.cif

16

Again: Wyckoff

symbols missing


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CA x=0.75 y=0.0 z=0.34760

S x=0.25 y=0.0 z=0.15556

O x=0.25 y=0.1699 z=0.01620

O x=0.08190 y=0.0 z=0.29750

Wyckoff=c

Wyckoff=c

Wyckoff=g

Wyckoff=f


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Verification sucessful


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Wrong hkl stick pattern

CIF Import – How BGMN works

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- Coordinates MUST be specified in the first symmetry of the list

- Special coordinates given in STR file will be ignored

- BGMN will always use hard-coded special coordinates


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CA x=0.75 y=0.0 z=0.34760

Wrong! Coordinates correspond to 2nd position





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CA x=0.75 y=0.0 z=0.34760

X and y in STR file ignored, using hard-coded coordinates:




CA x=0.25 y=0.0 z=0.34760


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CA x=0.75 y=0.0 z=0.34760 CA x=0.25 y=0.0 z=0.34760

CIF / STR file: Used by BGMN:

≠

Correct transformation from 2nd to 1st symmetry:

CA x=0.75 y=0.0 z=0.34760 CA x=0.25 y=0.0 z=-0.34760

CA x=0.25 y=0.0 z=0.6524=


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CIF Import – Example 5: Clinoptilolite.cif

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Pick one, verify later

Wyckoff symbols

missing

verification

failed


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Filter for lattice type «C»

SG #12

Setting 1 or 8?

Setting 1

Setting 8

Step 1: all general

positions are Wyckoff=j

(regardless of the setting #)


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E=SI(0.8700) Wyckoff=j x=0.178900 y=0.170500 z=0.095300 TDS=0.011171

E=AL(0.1300) Wyckoff=j x=0.178900 y=0.170500 z=0.095300 TDS=0.011171







E=SI(0.9100) Wyckoff= x=0.000000 y=0.216000 z=0.000000 TDS=0.011640

E=AL(0.0900) Wyckoff= x=0.000000 y=0.216000 z=0.000000 TDS=0.011640

E=NA(0.5000) Wyckoff= x=0.147800 y=0.000000 z=0.666100 TDS=0.058006

E=CA(0.5000) Wyckoff= x=0.147800 y=0.000000 z=0.666100 TDS=0.058006



E=K(0.6400) Wyckoff= x=0.234400 y=0.500000 z=0.025200 TDS=0.087203

E=O Wyckoff= x=0.197300 y=0.500000 z=0.457100 TDS=0.025813

E=O Wyckoff=j x=0.232000 y=0.121200 z=0.613800 TDS=0.024212









E=O(0.9800) Wyckoff= x=0.079800 y=0.000000 z=0.853100 TDS=0.303934

E=O(0.8900) Wyckoff=j x=0.079800 y=0.419000 z=0.965500 TDS=0.073226


E=O(0.3600) Wyckoff=j x=0.020200 y=0.090100 z=0.525000 TDS=0.155461


x y z: Wyckoff=j


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…









…


…


…


…


The rest: various

special coordinates

Step 2: Find Wyckoff

positions for special

coordinates

Search in Settings #1 and #8


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…









…


…


…


…


Symmetry

0 y 0

x 0 z

x 1/2 z

0 y 1/2

x 0 z

0 1/2 1/2

x 0 z


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Symmetry Wyckoff Setting 1 Wyckoff Setting 8

0 y 0 g g

x 0 z i i

x ½ z ? ?

0 y ½ h ?

0 ½ ½ d ?

x y z j j

Neither of the two

settings is correct…?


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…





…

Symmetry

x 1/2 z

Possible explanation:

If x ½ z is not known as a special position,

maybe the symmetry is x y z (general position)?

Try Wyckoff=j

Error message


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C 1 2/m 1:

C-face centered

Centering translation


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…

E=NA(0.3900) Wyckoff= x=0.040400 y=0.500000 z=0.216700

E=CA(0.3900) Wyckoff= x=0.040400 y=0.500000 z=0.216700

E=K(0.6400) Wyckoff= x=0.234400 y=0.500000 z=0.025200

E=O Wyckoff= x=0.197300 y=0.500000 z=0.457100

…

Translated by (-1/2, -1/2, 0)…

E=NA(0.3900) Wyckoff= x=-0.4596 y=0.000000 z=0.216700

E=CA(0.3900) Wyckoff= x=-0.4596 y=0.000000 z=0.216700

E=K(0.6400) Wyckoff= x=-0.2656 y=0.000000 z=0.025200

E=O Wyckoff= x=-0.3027 y=0.000000 z=0.457100

…

Unknown Wyckoff Positions

«x 0.5 z» does not exist

«x y z» invalid

«x 0 z» = Wyckoff=i


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Symmetry Wyckoff Setting 1 Wyckoff Setting 8

0 y 0 g g

x 0 z i i

x ½ z ? ?

0 y ½ h ?

0 ½ ½ d ?

x y z j j

Correct Space Group Setting = 1


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CIF Import: Summary

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If requested, select space group number and Hermann Mauguin

symbol from dialog.

If no Wyckoff symbols are found:

Select symbols from «Tools Browse BGMN Space Groups»

Make sure the first Symmetry is used, transform if necessary

Run verification.

Compare stick pattern with reference.

Save in Structures repository.

Import CIF file:

CIF Import: Summary

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If no Wyckoff symbol for a special position is available:

Try to figure out why, and fix it.

or…

Find a better CIF file.

I will keep on improving CIF import

in future versions of Profex

Lesson 4 Crystal Structure Filesprofex.doebelin.org/wp-content/uploads/2018/07/Lesson-4...CIF Import...

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