Data Reduction in CrysAlisPro - Agilent€¦ · incommensurate structures • Can visually analyse any diffuse scatter present • Can apply additional corrections to improve data

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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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

PX

SM

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A Perfect Tool from Crystal to Structure!

Mounting Strategy Structure Experiment Screen/Pre

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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

2

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

place

• 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

more

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

• Twin indexing matches 96.8%

of reflections

… but twin integration doesn’t help


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No slip Intentional sample slip

Reference

data

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

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

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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

data

Refinalisation New window teaser

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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

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

UK

September 18th 2013

10:00 am ET (Americas)

4:00 pm CET (Europe)

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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

F2

Theta

• 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

B A

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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

With

B-factor

R1 3.92% 3.77%

Rint 7.5% 7.2%

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Advanced Features Incommensurates

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Output a .hklmno file for

structure solution in

external programs

More in the next webinar!

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Advanced Features High pressure

• Designed primarily for high-pressure data for filtering out reflections

overlapped by diamond diffraction spots

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Advanced Features High pressure

No

filtering With filtering

no. of

reflections 10535 10450

Rint 6.4% 10%

R1

34%

(no structure) 9%

With filter

Higher value for Rint after filtering!

• Diamond reflections are

symmetrically equivalent and falsify

Rint value.

• Standard outlier rejection filter fails.

Profile agreement = 0.8

I/s= 10

No filter Example – HP data:

• Structure unsolvable although data

seem to be of sufficient quality (Rint)

• After filtering structure solved

Profile agreement

Bad Profile Rejection SM example

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Simulation of cryo-failure

(shield flow turned off)

Bad Profile Rejection SM example

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No ice Large ice build-up

Reference Data Auto

analysis

d range and run

Filtering

Bad profile

filtering

Rint (%) 2.6 10.5 3.2 4.0

I/σ 17.7 8.4 14.0 12.7

R1 (%) 3.83 6.11 4.11 4.50

Comp (%) 99.9 99.9 92.6 98.6

Advanced Features Batch processing

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Multi-temperature experiments problem – there are many data sets to process

Advanced Features Batch processing

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• XX PROFFITBATCH

• Browse for the folder

• Set PROFFIT parameters

• Click Finish

• A script “proffitbatch.mac” gets

created in the directory selected at

the start

• You can edit it or run as is using

SCRIPT command

Advanced Features Synchrotron/External frame formats

Massive dataset from synchrotron: 4 runs of 10,000 images

each; making a total of 40,000 images

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• Possible to read in a large variety of

external frame formats into CrysAlisPro

• Full auto-analysis on protein sample

successful even with very small diffraction

spots

More details on Protein Webinar and future

applications note!

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Summary

• Automatic data reduction during experiment

• Full override control in manual mode

• Fully accessible statistics from tables and graphs

• Easy-to-use face-indexing tool

• Many options in data reduction and re-finalisation to improve data quality

• Can handle twins, incommensurates, HP data, SM, PX, synchrotron etc.

• Outputs everything you need for structure solution/refinement

• Read in many external formats

• Come along to the Agilent booth at the ACA in Hawaii – we can process your data for you with our software

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Constantly being updated and improved

Software Updates

CrysAlisPro is frequently

updated with fixes for known

problems

New features are introduced in

annual major updates

All updates are Free and

available from our user forum,

www.agilentxrdforum.com

Free multi-user, multi-site

license

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http://www.agilentxrdforum.com/

Please type your question into the chat box. Send a direct chat to the

“Host” which is private, or a chat to “All Participants” which is public

Q&A

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New applications note on data recovery

Go to www.agilent.com and click on the “Library” tab,

and the “Literature” link. Search for “CrysAlisPro” to find

relevant app notes

http://www.agilent.com/

Thank you for listening!

All feedback and comments are welcome

[email protected]

The live CrysAlisPro Webinar series

continues on September 18th 2013

Register at:

www.agilent.com/chem/x-ray_eSeminars

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Documents

Data Reduction in CrysAlisPro - Agilent€¦ · incommensurate structures • Can visually analyse any diffuse scatter present • Can apply additional corrections to improve data