Agilent Technologies CrysAlis Pro Quick User Guide
Summary
A comprehensive technical manual designed for professionals utilizing X-ray Diffractometers. This guide details the full workflow of CrysAlis data collection and processing software, providing step-by-step instructions on installation, operational controls, and advanced analysis. Users will learn to leverage powerful tools—including Lattice Wizard and complex image manipulation features—to ensure accurate data reduction and management of detailed experimental file structures. It is essential reading for crystallographers and research scientists needing expert guidance on high-quality crystallography data analysis.
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Crys Alis Pro Data Collection and Processing Software for X-ray Diffractometers User Manual
Read the main diffractometer user manual, in particular the Health and Safety information, before operating Crys Alis Pro with the diffractometer.
Version 4, September 2010
Agilent Technologies XRD Products
10 Mead Road, Yarnton, Oxfordshire. OX5 1QU, UK Tel: +44 (0)1865 291600 Fax: +44 (0)1865 291601 http://www.agilent.com/chem
Page Summary Contents For Agilent Technologies CrysAlis Pro Quick User Guide
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Crys Alis Pro Data Collection and Processing Software for X-ray Diffractometers User Manual Read the main diffractometer user manual, in particular the Health and Safety information, before operating ...
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CONTENTS Contents 1. Introduction ................................................................................... 1 2. Installation of Crys Alis Pro ..................................................
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CONTENTS 4.4.15 Autochem launcher ................................................................................................ 16 4.5. Diffraction / image display window .............................
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CONTENTS 8. Inspection and Manipulation of Data ............................................... 50 8.1. Refinalization ....................................................................................
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CONTENTS Table of Figures Figure 1 Crys Alis Pro layout and controls ................................................................................................... 4 Figure 2 Key to image control...
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INTRODUCTION 1. Introduction Crys Alis Pro has been designed to provide a user friendly, simple to use, graphical user interface for data collection and data reduction of single crystal X-ray diffract...
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INSTALLATION OF CRYSALISPRO 2. Installation of Crys Alis Pro To install the Crys Alis Pro software on your diffractometer PC you will need the following programme saved to your computer: Crys Alis Pro...
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STARTING AND CLOSING CRYSALISPRO 3. Starting and Closing Crys Alis Pro 3.1. Starting Crys Alis Pro To start Crys Alis Pro double click on the icon on the windows desktop. When the programme is started...
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CRYSALISPRO LAYOUT AND CONTROLS 4. Crys Alis Pro layout and controls The Crys Alis Pro GUI is comprised of a number of different areas. These include: 1. START / STOP button 2. Image control icon bar ...
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CRYSALISPRO LAYOUT AND CONTROLS • Start Data reduction only • Full auto analysis (cell, red) • Special data collection • Append special data collection • Resume data collection/pre-experiment • Resume...
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CRYSALISPRO LAYOUT AND CONTROLS • Zoom localiser window • Resolution rings • 2D Peak profile (a line profile) • 3D Peak profile (rocking curve) • Help • View (CCD/RED/USER) Figure 2 Key to image contr...
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CRYSALISPRO LAYOUT AND CONTROLS If the left mouse button is depressed and held a wire box can be drawn around an area / object in the diffraction image window and a semi-transparent window displays th...
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CRYSALISPRO LAYOUT AND CONTROLS 4.2.11 Zoom localiser The zoom localiser is a floating semi-transparent window which displays the full diffraction image (regardless of the zoom used in the main diffra...
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CRYSALISPRO LAYOUT AND CONTROLS In CCD view the images coming off the machine are displayed, but it is not possible to do anything with them when collecting data. In RED view visual feedback of the da...
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CRYSALISPRO LAYOUT AND CONTROLS improved) unit cell. Also displayed are information on the proposed data collection strategy, intensity statistics and a proposed exposure time for the data collection,...
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CRYSALISPRO LAYOUT AND CONTROLS • Space group • Information of face indexed absorption corrections. • Multi-component information from twin data reduction • Results (in terms of Rint, I/sig, Redundanc...
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CRYSALISPRO LAYOUT AND CONTROLS • Crystals launcher (if installed) • Jana launcher (if installed) • Autochem (if installed) Figure 4 Key to power tool icons 4.4.2 Lattice Wizard The lattice wizard ico...
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CRYSALISPRO LAYOUT AND CONTROLS commands and illustrations of typical usage are available by typing COMMAND HELP in the command line power tool. There is also an options button included which provides...
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CRYSALISPRO LAYOUT AND CONTROLS Figure 5 Service utility 4.4.6 Service This power tool collects those service commands most commonly accessed by the user into one defined area. These commands include ...
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CRYSALISPRO LAYOUT AND CONTROLS 4.4.7 Powder diffraction The powder diffraction power tool performs different functions depending on the Crys Alis Pro operating thread (CCD/RED/USER). When in CCD view...
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CRYSALISPRO LAYOUT AND CONTROLS 4.4.12 Olex2 launcher This button launches the crystallographic structure solution and refinement software Olex2, where installed. Assuming the data have been processed...
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CRYSALISPRO LAYOUT AND CONTROLS active. When automatic data reduction is active then the RED thread allows the user to visualise the data reduction in progress. 3. USER thread – this thread provides f...
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CRYSALISPRO LAYOUT AND CONTROLS 4.8.2 CCD detector head controller Clicking on this icon opens the software device controller for the CCD detector head. The display should show the running temperature...
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CRYSALISPRO LAYOUT AND CONTROLS Figure 8 Generator ramping control Clicking the right mouse button on the X-ray button gives access to Generator options (Figure 19). This menu controls automatic gener...
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CRYSALISPRO LAYOUT AND CONTROLS • Pixel integration Select a peak by hovering over it, then right-click. Information such as integrated I/sigma and so on is displayed so that you can check that you ha...
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NORMAL OPERATION 5. Normal operation In normal operation Crys Alis Pro is designed to work in automatic mode. The automatic mode consists of the following three major components: 1. Pre-experiment – a...
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NORMAL OPERATION Figure 9 Pre-experiment setup dialog window 3. Click on the Mount Sample button to mount a sample WARNING Press ‘STOP’ on the remote control on the keyboard to stop movement of the eq...
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NORMAL OPERATION NOTE The settings lower and upper refer to the glass stick position on the video monitor • Use the tool provided with the goniometer head to adjust the vertical height and horizontal ...
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NORMAL OPERATION 9. The automode settings area of this window allows the user to put some restraints / constraints on the final data collection strategy. The Auto Start tick box (when selected) instru...
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NORMAL OPERATION • At the end of the pre-experiment the strategy module will open and will display the preferred data collection strategy based on the unit cell, detector distance, Laue class, user co...
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NORMAL OPERATION 5.3. Protein Screening The protein screening features can be accessed from the START/STOP menu. Figure 11 Protein screening dialog Protein screening normally involves exposure times s...
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NORMAL OPERATION Figure 12 Screening information card The Peaks button invokes the peak hunting dialog box. Here you can quickly tune the peak hunting parameters in case of difficult samples. Figure 1...
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NORMAL OPERATION Figure 14 d-value tool Crys Alis Pro Crys Alis_Pro_manual_v4 Page 28 USER MANUAL
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NORMAL OPERATION 5.4. Strategy The strategy module will automatically pick up the Laue class, detector distance, resolution target and exposure time from the pre-experiment and will determine an optim...
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NORMAL OPERATION These provide a quick and easy graphical feedback. Alternatively, you can display the corresponding statistics tables by pressing the appropriate radio button just above the graphs. T...
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NORMAL OPERATION If you have bypassed the pre-Experiment, but wish to set up crystal movie generation and Auto Chem, you may do so by launching the Strategy module and pressing the 'Autochem/Movie/Cry...
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NORMAL OPERATION • The strategy module will automatically adjust the scan width of the frames depending on the unit cell axis dimensions, mosaicity and overlap parameters found in the pre-experiment. ...
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NORMAL OPERATION 5.6. Stop all processes Working On-Line 1. Press the START/STOP button. 2. A dialog window appears with the option ‘Stop All’. Press ‘Stop ALL’ and all processes will stop. NOTE Stopp...
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NON-STANDARD OPERATION 6. Non-standard operation 6.1. Start special collection This utility is located under the menu accessed from the START/STOP button and is used for experiments generated without ...
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NON-STANDARD OPERATION 2. Define a strategy to collect as much data as is required for full evaluation at various temperatures. More data than normal may be needed in order to take account phase chang...
Manual Details
| Brand | Agilent Technologies |
|---|---|
| Pages | 74 |
| File Size | 2.34 MB |
| Published | May 13, 2026 |
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Frequently Asked Questions
What must I read before operating CrysAlis?
You must read the main diffractometer user manual, specifically the Health and Safety Pro information.
Where does the 'CrysAlisINI' directory store files?
This directory contains initialisation and user defined setup files for CrysAlis, ODBench, and ODShell programs.
What file extensions are found in an experiment root folder?
Required definition files include *.par, *.run, *.ffiinffit, *.ffi, *.tab, among others.
How can I perform task automation within CrysAlis?
You can use macro files with the extension *.mac, which are stored in this directory.