Data Reduction in CrysAlisPro - Agilent€¦ · incommensurate structures • Can visually analyse...

Data Reduction in

CrysAlisPro

Mathias Meyer

Agilent Technologies Poland

Oliver Presly

Agilent Technologies UK

Daniel Baker

Agilent Technologies UK

Layout

• Introduction: CrysAlisPro overview

• Part I: Automatic data reduction

• Part II: Manual data reduction

• Part III: Refinalisation

• Part IV: Twin data reduction

• Part V: Protein data reduction

• Part VI: Advanced features (Incommensurate, HP, batch processing, synchrotron, external formats)

• Conclusion: Summary

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Layout

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X-ray Product Configurations

Modular Products - Tuned to Application

4-circle Goniometer X-ray Sources

CCD Detectors

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Crystallographic Software: CrysAlisPro

CrysAlisPro has been designed to be as simple to use as possible:

User friendly GUI

Simple workflow

Fully integrated platform

Supporting SM and PX

Highly automated......

...but full of manual features for those who want them

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A Perfect Tool from Crystal to Structure!

Mounting Strategy Structure Experiment Screen/Pre

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Layout

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Automatic Data Reduction How it works

• Turns raw experimental data into a format that allows for structure solution and refinement

• Requires unit cell

• Produces reflection file (*.hkl), processing information file (*.lst) and crystal summary info file (*.sum)

• Uses unit cell to predict where peaks should appear on each frame

• Automatic profiling calculation followed by masking of peaks to collect intensity for .hkl file

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h k l Fobs2 sFobs

0 0 1 2356 45

0 1 1 218 17

1 1 0 77 9

1 0 1 3001 101

Automatic Data Reduction Example

Sucrose crystal

• 13 minute experiment

• Every 25 frames data reduction takes

• AutoChem gets structure before

experiment has finished (if installed)

• Excellent Rint and R1 with zero user

intervention

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Automatic Data Reduction Example

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Rint = 1.48%

Rint = 1.40% R1 = 2.86%

R1 = 2.22%

I/s = 34.2

Automatic data reduction and structure solution

Automatic vs. Manual Data Reduction

Why do a manual data reduction?

• Can do concurrent automatic processing of twins or

incommensurate structures

• Can visually analyse any diffuse scatter present

• Can apply additional corrections to improve data

• Presence of weakly-diffracting peaks may make automatic

selection of space group difficult

• e.g. weak superstructure reflections

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Sometimes the user knows best!

Layout

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Manual Data Reduction Introduction

• CrysAlisPro allows the user full control of the data reduction procedure

• Data reduction wizard steps the user through the various steps

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Manual Data Reduction Inputs

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• View orientation matrix for unit

cell to be used

• Twin/incommensurate features

Quasi-crystals

Manual Data Reduction Inputs

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• Choose which runs to use for

data reduction

Manual Data Reduction Reflection model & special options

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• Automatic model

refinement

• Sample wobbling (cold

stream)

• Sample slippage

• Access to special

parameters

PROFFIT

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For every run

Manual Data Reduction Model refinement options

Per-run

refinement

Integration Per-frame refinement

Global

cell & model

refinement Model 1

Model 2

Frame1 Frame2

Prediction

accuracy

evaluation

Prediction

accuracy

evaluation

Choose

accurate

approach

No need to decide now

– program does it for you!

Manual Data Reduction Sample slippage example

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• Superficially gives impression of

• Twin indexing matches 96.8%

of reflections

… but twin integration doesn’t help

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No slip Intentional sample slip

Reference

Slip Data

(Pre-Treatment)

Slip Data

(Post-Treatment)

Rint (%) 1.6 14.7 1.6

I/σ 22.0 5.0 22.9

R1 (%) 3.32 43.88 3.46

Comp (%) 98.5 95.2% 98.4%

Manual Data Reduction Reflection model & special options

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Several special features for:

• Weak samples – adjust masks

according to prediction

uncertainty

• Twin data – Increase/decrease

mask size

• Protein – Single wavelength only

integration

• High pressure – Bad profile

rejection

• Also useful for twins, multi-

crystals, iced samples,

SM/PX etc.

Manual Data Reduction Background correction

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Choice of background correction:

• Average background

• Define range and frequency

• Smart background

• Combination of local and

average background

• Improves statistics (I/s) for

samples with varying

background features

• Can’t be used for twin data

(yet…)

Manual Data Reduction Background correction example

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100μm

Well-mounted

sample

Intentionally

badly-mounted

sample

Standard peak-hunting

produces many non-lattice

peaks.

Manual Data Reduction Background correction example

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Well-mounted Badly-mounted

Reference Data Auto analysis Smart Background

Time 3h 8m 16h 18m 16h 18m

Diff. Limit 0.92 1.41 0.97

Rint (%) 3.1 14.4 5.8

I/σ 13.5 3.0 7.8

R1 (%) 5.28 - 6.22

Comp (%) 99.5 99.5 99.5

Space Group Determination (GRAL) Monoclinic cell choices

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• Automatic selection from 3 possible cell choices for particular monoclinic

space groups (GRAL)

- In Auto mode, a setting with β angle closest to 90° is selected

- In Interactive mode, all 3 choices are presented with the same default as in Auto mode

Data Reduction Tab

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Summary of information regarding the

data reduction process

• Shortcuts to Frame/run list,

absorption options window, and

space group options

• Information updates after every

automatic data reduction cycle

during experiment, or after any

manual re-finalisation

Data Reduction Output

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Data Reduction Output graphs

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Scale factor Sample temperature

Layout

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Refinalisation Introduction

• Refinalisation is a repeat of the finalisation step of the data

reduction

• Able to apply several additional corrections

• Absorption

• Filters

• Resolution

• Space group change

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Refinalisation Face-indexing

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Two different methods (point or drag) to quickly draw shape of crystal

Video guide coming soon

on user forum…

Refinalisation Absorption correction

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No problem running large crystal

with micro-focus source

Refinalisation ABSPACK

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Refinalisation Filters

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Main filters: Rint / d-spacing / I/s

Used to remove outliers and improve

Refinalisation New window teaser

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Layout

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Twin Data Reduction Introduction

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• 53% indexed as single

crystal

• 91% indexed as twin

• Software recognises that

sample is modelled as

Twin Data Refinalisation Example

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Rint = 4.15% R1 = 14.29%

I/s = 11.1

Rint = 3.9% R1 = 4.52%

I/s = 18.0

HKLF4 – no twin modelling HKLF5 – twin data reduction

Twinning and

Incommensurate

Data Processing in

CrysAlisPro

Dr Fraser White

Agilent Technologies

September 18th 2013

10:00 am ET (Americas)

4:00 pm CET (Europe)

Layout

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Protein Data Reduction

• CrysAlisPro has a dedicated PX mode for running protein

experiments

• Extra features specifically for protein samples

– .mtz files

– A/B scale factors

– Import/export of data

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Protein Data Reduction A/B-factor refinement

• New correction in ABSPACK

• Designed for correcting crystal decay in time

• Added extra factor to ABSPACK scaling

model:

CrysAlisPro only!

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No decay correction With decay correction

Example from beamline

protein data

A/B-coefficients plots show decay of the sample

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• Unexpected usefulness for some high theta small molecule data:

– can correct for some resolution-dependent effects, e.g. prediction uncertainty at high angle

Without

B-factor

R1 3.92% 3.77%

Rint 7.5% 7.2%

Layout

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Advanced Features Incommensurates

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Output a .hklmno file for

structure solution in

external programs

Data Reduction in CrysAlisPro - Agilent€¦ · incommensurate structures • Can visually analyse...

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