New Features in Agilent's CrysAlis Pro X-ray Diffractometer Software
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1 New Features in Agilent's CrysAlis Pro X-ray Diffractometer Software Mathias Meyer Agilent Technologies Poland Oliver Presly Agilent Technologies UK 1
2 30+ Years of Innovation Sapphire2- First Back illuminated CCD Kuma launch First CCD Collaboration with Oxford Instruments Launch of Helijet Helium cooler First synchrotron CCD shipped to SNBL First dual wavelength Gemini system CrysAlis Pro software First dual microsource system Launch 2 nd generation Nova source Kuma Diffraction formed Our first diffractometer Launch of Xcalibur diffractometer Oxford Diffraction formed Launch first sealed tube & multi-layer optics Protein system Launch of higher intensity protein system Launched range of fast read out CCDs Launch of AutoChem Varian Inc. acquired by Agilent Technologies First Gradient Vacuum System high brilliance for proteins KM6-4 synchrotron End station Installed SNBL Launch first in-situ X- ray screening device Oxford Diffraction acquired by Varian, Inc. 2
3 X-ray Product Configurations Modular Products - Tuned to Application 4-circle Goniometer X-ray Sources CCD Detectors 3
4 Crystallographic Software: CrysAlis Pro CrysAlis Pro 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 SM PX 4
5 Typical Data Acquisition Sequence Mounting Screen Pre-exp Strategy Experiment CrysAlis Pro 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) 5
6 Automatic Crystal Evaluation CrysAlis Pro now offers a fast SM screening tool Mount Fast screen (~10sec) Judge sample Simple, customizable scenarios (user dependent) Unit cell often found in only 1 or 2 frames 6
7 Experiment Flowchart 7
8 Automatic Crystal Evaluation Mounting Screen Pre-exp Strategy Experiment Unit cell (CellCheckCSD) Quality Diffraction power 8
9 CellCheckCSD Cambridge Structural Database Interface CrysAlis Pro automatically links to the CCDC Based on real-time unit cell parameters, the CSD is screened during a preexperiment 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 9
10 Automatic Strategy Software Mounting Screen Pre-exp Strategy Experiment Rapid calculation Generates new strategies in seconds Strategy modes Automated or userdefined for specific experiment scenarios User editable limits Resolution (Å, Θ or 2Θ) Detector distance Laue symmetry Exposure times Angular constraints Modes Interactive vs. auto 10
11 Strategy: q-dependent Binning The user has free choice to use it or not 11
12 Strategy: q-dependent Binning Use of soft-binning Better compromise of dynamic range and detectivity Important for multi-q data sets CCD 1x1 2x2 Disk 2x2 1x1 2x2 Disk 4x4 4x4 12
13 Strategy: q-dependent Binning 2x2 4x4 4x4/2x2 (thetadependent) Total time 5h10m28s 5h23m58s 5h3m22s Frames Frames remeasured successfully Overflows (frames not remeasured successfully) 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% 13
14 Experiment Flowchart 14
15 Data Collection Concurrent data reduction begins after 25 frames Integration updated every 25 frames Real-time reporting Real-time structure solution and refinement with AutoChem (where installed) Automatic cryo- or heating-device shutdown at end of experiment (if requested) 15
16 AutoChem
17 AutoChem 2.0 New solution evaluation and structure completion algorithm More solution programs integrated (SuperFlip, SIR in addition to Shelxs, Shelxd) Multi-space group support Higher yield than AC 1.0 Stand-alone installer 32 and 64 bit Limited account support. 17
18 AutoChem
19 Feature Normal and Admin users Normal users can get info on their experiment Pre/experiment results Laue change Door open... Admins get admin related infos on every experiment of all users Par file change User change Tube life time (one time events) 19
20 Feature 20
21 A Perfect Tool from Crystal to Structure! Mounting Screen/Pre Strategy Experiment Structure 21
22 Power Tools Ewald Pro User-friendly, powerful reciprocal lattice viewer Twin/Multi-lattice visualisation Drag filter tools simple & intuitive Lattice IT tool for defining periodicity Reflection grouping Incommensurate overlay tools 22
23 Ewald Pro Functional Tabs 23
24 Ewald Pro Ice Ring Example 24
25 Ewald Pro Groups Groups: Indexation quality Twin components Resolution range Incommensurates Specific features (weak/strong peaks, powder rings, etc.) 25
26 Ewald Pro Lattice It 26
27 Key Element in Data Quality: Empirical corrections Scaling Empirical absorption based on spherical harmonics Decay Detector sensitivity I corr,1 = C 1 I 1 D 1 = I aver I corr,1 I corr,2 = C 2 I 2 D 2 = I aver I corr,2 I aver = S I corr_prev,i I corr,n = C n I n D n = I aver I corr,n Note: Strategy generated redundancy is the key ingredient! 27
28 Play Modes Scales Empirical sample absorption Decay A, B Sensitivity Decay Absorption Batch scales Sensitivity 28
29 Power Tools Refinalisation Tools Analysis and visualisation of processing results Auto graphing of results Face-indexed absorption corrections Beam Profile Correction Advanced space group options 29
30 Shape Building Takes Time Automatic? Auto shape 30
31 Systematic Effects/Noise sources Absorption (sample/holder) Beam illumination effects Sample centring Sample decay Experiment effects: cryo, generator Mounting technique 31
32 Empirical vs. Numeric Absorption dusekdc (Michal Dusek) inorganic (Cs 2 SeO 4 ), Mo, m=17.9mm -1, redundancy = 4.5 (Pna2 1 ) R int I/σ R 1 No correction 14.4% % Empirical 4% % 32
33 Empirical vs. Numeric Absorption dusekdc (Michal Dusek) inorganic (Cs 2 SeO 4 ), Mo, m=17.9mm -1, redundancy = 4.5 (Pna2 1 ) R int I/σ R 1 No correction 14.4% % Empirical 4% % Numeric (faces) 2.6% % Both 1.85% % 33
34 Twin Recognition and Data Reduction 34
35 Twin Types Easy twin Super lattice faker 35
36 Easy Twin in Ewald Pro 36
37 Easy Twin in Ewald Pro 37
38 Easy Twin in Ewald Pro 38
39 Incommensurates in Ewald Pro Na 2 CO 3 39
40 Power Tools Precession Image Reconstruction Extremely rapid calculation Single-click multiple image generation (e.g. hk0, h0l, 0kl) Generates both point and integrated layer images 40
41 Power Tools High pressure data reduction made easy Absorb program integrated to CrysAlis Pro for: Absorption Gasket shadowing Backing plates Video tool to measure sample Angel, R. J. (2004). J. Appl. Cryst.. 37,
42 Power Tools High pressure data reduction made easy Absorb program integrated to CrysAlis Pro for: Absorption Gasket shadowing Backing plates Video tool to measure sample 42
43 Power Tools Command Line Window Full manual control 100 s of specialist commands Complete log of data collection and data reduction 43
44 Solution and Refinement Links to External Software Packages Crystals WINGX OLEX2 44
45 External Frame & File Formats CrysAlis Pro can process frames from most detector manufacturers 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 45
46 Software Updates CrysAlis Pro 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, Free multi-user, multi-site license 46
47 47 Please type your question into the chat box. Send it to host if you want to remain anonymous
48 Thank you for listening! All feedback and comments are welcome The live CrysAlis Pro Webinar series continues on May 8 th 2013 Register at: 48
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