Optimizing Your Data Collections in CrysAlisPro Strategy ... · PDF filescenarios (user...

Optimizing Your Data

Collections in

CrysAlisPro

Strategy Modes

Detector Binning

and Other Tools

Mathias Meyer

Agilent Technologies Poland

Oliver Presly

Agilent Technologies UK

Zoltán Gál

Agilent Technologies UK

X-ray Product Configurations

Modular Products - Tuned to Application

4-circle Goniometer X-ray Sources

CCD Detectors

2 04/07/2013

Agilent Confidential

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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PX

SM

04/07/2013


A Perfect Tool from Crystal to Structure!

Mounting Strategy Structure Experiment Screen/Pre

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Prerequisites to a Successful Experiment Strategy

5

Well centred crystals on suitable mounts - think orientation / material / glue / oil

Screening has identified best candidates for data collection - minutes spent here can often save hours (of data collection time)

Be aware of any phase transitions

- sample environment (temperature / photoreactivity / solvent loss)

Be as confident in the unit cell as possible – use Ewald Pro - think supercells / twins / modulations

Mounting Screen Pre-exp

04/07/2013


Typical Data Acquisition Sequence

CrysAlisPro ‘Centering assistant’

reduces centering error for

anisotropic samples

Height estimator ‘remembered’

for automatic shape generator

Movie registers sample shape

for later evaluation (triggered at

experiment time)

Mounting Screen Pre-exp Strategy Experiment

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Automatic Crystal Evaluation

CrysAlisPro now offers fast

SM and PX screening tools

Mount

Fast screen (10-60sec)

Judge sample quality,

resolution limit, mosaicity

Simple, customizable

scenarios (user

dependent)

Unit cell often found in only

1 or 2 frames, checked by

CellCheckCSD

Helps to set up most

effective pre-experiment

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CellCheckCSD

Cambridge Structural Database Interface

CrysAlisPro automatically links

to the CSD

Based on real-time unit cell

parameters, the CSD is

screened during a pre-

experiment to check for

published unit cell information

A CSD licence is not required

for basic screening!

Cell hits can easily be

visualised in Mercury or

WebCSD (CSD licence

permitting)

Now also with private local

data base

8 04/07/2013


Strategy Software – Defines How Data is Collected

Benefits of using a calculated strategy on a 4 circle kappa geometry:

Save up to 30% time, ensure complete data collected every time (even in P1), reach specific goals with data collection

Calculated by default once unit cell is found during pre-experiment

User editable (on-the-fly)

Highly flexible

Interactive or auto modes

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Mounting Screen Pre-exp Strategy Experiment

04/07/2013


Re-Calculating the Strategy is Already Very Fast

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Type of Strategy Orthorhombic Monoclinic Triclinic

Connectivity

(Mo, 0.8 Å, 98.5%) 2.9 seconds 3.7 seconds 4.8 seconds

Charge Density

(Mo, 0.4 Å, 10 fold) 26.6 seconds 39.3 seconds 39.5 seconds

Absolute Config.

(Cu, 0.84 Å, 10 fold) 11.2 seconds 19.1 seconds 22.3 seconds

S-SAD Phasing

(Cu, 2.0 Å, 20 fold) 0.9 seconds 1.0 seconds 1.2 seconds

And we are still working to make it faster…

04/07/2013


Basic Checks and Controls for Strategy

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Select :

Unit Cell

Resolution

Laue Group

Friedel Mates

Detector Distance

Calculate New Strategy!

Check :

Completeness

Redundancy

Total / Finish Time

04/07/2013


Which Strategy Mode To Use?

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Complete data (default mode)

Quick publishable connectivity

Complete redundant data

Fill specific redundancy (charge

density/ absolute configuration)

Total time constrained data

Time to fill without complete data

Complete total time constrained

Time to fill with complete data

Absorption Correction

For irregular shapes and or high

absorbers

Complete data for twins

For up to 4 components

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Exposure Time Prediction

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Signal-to-Noise Estimator:

Based on pre-experiment

Multi-theta aware

Individual / merged / total

I/sig updated on the fly

Predicts max resolution

Scan width control

Theta dependent binning

Strategy: q-Dependent Binning

Available for Detectors Built since 2003

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The user has free choice to

use it or not

The user should enable 4x4 binning:

04/07/2013


CCD Binning

1 x 1 2 x 2 4 x 4

Higher spatial resolution

Larger dynamic range

Lower detectivity

Longer processing time

Larger files

Lower spatial resolution

Smaller dynamic range

Higher detectivity

Shorter processing time

Smaller files

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CCD Binning

Reflections at Detector Front Face

4x4 4x4

2x2 2x2

Strong signal Weak signal

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CCD Binning

Reflections as Pixels

4x4 4x4

2x2 2x2


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Overloaded pixel

CCD Binning

Optimized Modes for Strong and Weak Signals

4x4 4x4

2x2 2x2


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Multi-Theta Settings

Cu and High Resolution Mo Datasets

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Changing the binning setting in

the same dataset is useful for

multi-theta settings; common in

Cu and charge-density Mo

datasets:

• Low angle = stronger data

• High Angle = weaker data

04/07/2013



Use of ‘soft-binning’

Better compromise of dynamic

range and detectivity

Important for multi-q data sets

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1x1 Disk

2x2

4x4

4x4

1x1

CCD

Disk

2x2 2x2

04/07/2013



Mixed theta setting

is optimal:

Least re-measured

frames

Lowest number of

overflow reflections

Best Rint

Best refined data

Potential time saver

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2x2 4x4 4x4/2x2 (theta-

dependent)

Total time 5h10m28s 5h23m58s 5h3m22s

Frames 2583 2583 2583

Frames

remeasured

for overflows

252 634 246

Remaining

overflows

20 155 19

Rint 1.6% 1.4% 1.4%

R1 (all) 2.4% 2.37% 2.33%

R1 (first shell) 1.8% 2.0% 1.8%

R1 (last shell) 5.7% 5.3% 5.3%

04/07/2013


Advanced Strategy Options - Constraints

Setting Constraints

Applies to individual

experiments only*

Phi Scans

Kappa ranges

Theta ranges

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*NOTE – This feature is for individual data sets only. Where an additional hardware component effects the

collision model (LASERS, HP cells, gas cells etc.) please contact Agilent before proceeding

Advanced Strategy Options – Overlap Evaluation

Overlap Calculation

Guide appropriate

scan width

Iso / Aniso options

Use observed

mosaicity based on

pre-experiment

Or define one by hand

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Advanced Strategy Options – Symmetry / Scaling

Symmetry options

Longest axis first

Any symmetry axis

UB matrix scaling

Precision vs. speed

Locked runs

Protect frames already

collected

Use additional theta

Better for scaling multi-

theta experiments

(charge density / absolute

configuration)

24 04/07/2013


Advanced Strategy Options – Jet / HP / Quasi Xtals

Select:

JetShadow

High Pressure

opening angle

Do not tilt

Do not reverse

To be used only on HP

hardware setups

Quasi Crystals

User defined HKL list

Up to 6 dimensions

icosahedral symmetry

25 04/07/2013


Experiment Settings

Manual Control

Image correlation / binning

Dark image options

Data processing options

Movie / AutoChem options

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Manually Editing Run Lists

Complete Control

Create / modify / export /

import run lists

Collision checks / maps

Reference frames

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Tips and Tricks for Speeding Things Up

Things to consider

Turn off correlation

Reduce completeness

(from 100% to 98.5-99%)

Use as close a detector

distance as possible

Remove reference frames

Enable speed-up options

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Specialist Experiments

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Available from Start Menu

Expanding capability of the

instrument with multi-

disciplinary techniques

User inspired

Part of CrysAlisPro

Fully GUI driven

Concurrent data reduction

wherever possible

Powder Experiment Dialog

Medium resolution PXRD

Multi-theta automated

concurrent integration

Use of 4 circle gonio to reduce

preferred orientation effects

Multi temperature capable

Use long, calibrated detector

distance, 1x1 binning for best

results

Azimuthal plots

External data formats for

Rietveld refinements

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Multi Wavelength / Temperature Setup

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Compatible with CryoJet, CryoStream, Cobra, DTC and HeliJet

Multi Temperature Setup

Simple GUI for complex scans

Temperature / stabilisation

control

Dual strategy option

Movie at each temperature

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200K 180K

160K 140K 150K

170K

Single Scans and Axial Photographs

Image control for:

Still images

Phi and Omega scans

Rotation photos

Axial photographs

33 04/07/2013


High Pressure Experiments

Aware of HP cell opening angle

Easy pre-experiments / unit cell finding

Accurate strategy / completeness

Straightforward data integration

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Power Tools

High Pressure Data Reduction Made Easy

Absorb program integrated to

CrysAlisPro for:

Absorption

Gasket shadowing

Backing plates

Video tool to measure sample

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Angel, R. J. (2004). J. Appl. Cryst.. 37, 486-492

04/07/2013


Useful things to set up beforehand…

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Instrument / Software Setup

Generator ramping

Parking position

De-icing runs

Run list size

Email Features

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What to do when things go wrong?

Stopping

Choice for stopping all / collection / data reduction

Resuming

Choice for restarting all / pre-exp / data collection

Appending Data Collections

Previously collected frames are locked

38 04/07/2013


AutoChem2.0

39 04/07/2013


AutoChem2.0

New solution evaluation and

structure completion algorithm

More solution programs

integrated, where installed

(SuperFlip, SIR in addition to

Shelxs, Shelxd)

Fourier-type atom assignment

Multi-space group support

Higher success rate than

AutoChem1.0

Can work with or without a

chemical formula

40 04/07/2013


External Frame & File Formats

This includes:

Simple tools for importing frames

Esperanto feature for defining new

frame formats

These features are ideal for

processing synchrotron data

Data can also be exported in

various file formats for use in

other programs, such as Jana

CrysAlisPro can process frames from most detector manufacturers

41 04/07/2013


More on this in the next webinar…

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

42 04/07/2013


http://www.agilentxrdforum.com/

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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

04/07/2013


44

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

04/07/2013


Thank you for listening!

All feedback and comments are welcome

[email protected]

45

The live CrysAlisPro Webinar series

continues on July 3rd 2013

Register at:

www.agilent.com/chem/x-ray_eSeminars

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