3. Spot Finding 7(i). 2D Integration 2. Image Handling 7(ii). 3D Integration 4. Indexing 8. Results 1. Introduction5. Refinement Background mask and plane.

Slides:

Advertisements

Similar presentations

Protein x-ray crystallography

Advertisements

CCP4 workshop Argonne, June 2011 Strategy of diffraction data collection (at synchrotrons) Zbigniew Dauter MCL-NCI & ANL-BIO.

Not just a pretty picture Jul. 14 Hyunwook Lee.

Practice of analysis and interpretation of X-ray diffraction data

Acknowledgements Christine Gee Janet Newman Tom Peat Center for Structure of Membrane Proteins Membrane Protein Expression Center II Center for HIV Accessory.

Data Collection & Data Analysis Basic Processing with Mosflm Gwyndaf Evans Diamond Light Source, UK.

Automatic Identification of Bacterial Types using Statistical Image Modeling Sigal Trattner, Dr. Hayit Greenspan, Prof. Shimon Abboud Department of Biomedical.

Structure of thin films by electron diffraction János L. Lábár.

Two cases of chemometrics application in protein crystallography European Molecular Biology Laboratory (EMBL), Hamburg, Germany Andrey Bogomolov.

Data Collection and Processing Using APEX2, SHELXTL and the Bruker PHOTON 100 Kevin J. Gagnon

Constraining Astronomical Populations with Truncated Data Sets Brandon C. Kelly (CfA, Hubble Fellow, 6/11/2015Brandon C. Kelly,

Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.

Methods: Cryo-Electron Microscopy Biochemistry 4000 Dr. Ute Kothe.

A Novel 2D To 3D Image Technique Based On Object- Oriented Conversion.

Automated protein structure solution for weak SAD data Pavol Skubak and Navraj Pannu Automated protein structure solution for weak SAD data Pavol Skubak.

The goal of Data Reduction From a series of diffraction images (films), obtain a file containing the intensity ( I ) and standard deviation (  ( I ))

Data Analysis I19 Upgrade Workshop 11 Feb Overview Short history of automated processing for Diamond MX beamlines Effects of adding Pilatus detectors.

CHE (Structural Inorganic Chemistry) X-ray Diffraction & Crystallography lecture 2 Dr Rob Jackson LJ1.16,

Macromolecular Electron Microscopy Michael Stowell MCDB B231

Refinement with REFMAC

Protein Structure Determination Part 2 -- X-ray Crystallography.

Introduction to Macromolecular X-ray Crystallography Biochem 300 Borden Lacy Print and online resources: Introduction to Macromolecular X-ray Crystallography,

ACA meeting July 2009 Highlights. Small Angle Scattering (X-rays, Neutrons) Don’t need.

3. Spot Finding 7(i). 2D Integration 2. Image Handling 7(ii). 3D Integration 4. Indexing 8. Results Gwyndaf Evans 1, Graeme Winter 1, David Waterman 2,

MRC software for 2d crystal structure determination Henderson & Unwin (1975) Nature 257, Introduction Basic Functions and Principles.

Lars Ehm National Synchrotron Light Source

R. Keegan 1, J. Bibby 3, C. Ballard 1, E. Krissinel 1, D. Waterman 1, A. Lebedev 1, M. Winn 2, D. Rigden 3 1 Research Complex at Harwell, STFC Rutherford.

1. Diffraction intensity 2. Patterson map Lecture

The PLATON/TwinRotMat Tool for Twinning Detection Ton Spek National Single Crystal Service Facility, Utrecht University, The Netherlands. Delft, 29-Sept-2008.

POINTLESS & SCALA Phil Evans. POINTLESS What does it do? 1. Determination of Laue group & space group from unmerged data i. Finds highest symmetry lattice.

Conventions Special aspects of the scattering of high- energetic electrons at crystals Axel Rother*, Kurt Scheerschmidt**, Hannes Lichte* *Triebenberg.

Data Harvesting: automatic extraction of information necessary for the deposition of structures from protein crystallography Martyn Winn CCP4, Daresbury.

FROM IMAGES TO ANSWERS Live Cell Imaging - Practical Issues Silver Spring & San Diego, June 2005.

An Introduction to Mosflm (1) what Mosflm does (2) where it fits in the crystallography process (3) run through a typical job (4) introduction to the CCP4.

ELECTRON CRYSTALLOGRAPHY:

Computational Crystallography InitiativePhysical Biosciences Division First Aid & Pathology Data quality assessment in PHENIX Peter Zwart.

Pattersons The “third space” of crystallography. The “phase problem”

MOS Data Reduction Michael Balogh University of Durham.

Analyzing Expression Data: Clustering and Stats Chapter 16.

E. F. Eikenberry E. F. Eikenberry 1 Ch. Brönnimann 1 G. Huelsen 1 H. Toyokawa 2 R. Horisberger 3 B. Schmitt 1 C. Schulze-Briese 1 T. Tomizaki 1 1 Swiss.

Atomic structure model

Anomalous Differences Bijvoet differences (hkl) vs (-h-k-l) Dispersive Differences 1 (hkl) vs 2 (hkl) From merged (hkl)’s.

Developments in xia2 Graeme Winter CCP4 Dev Meeting 2008.

X-Ray Diffraction Spring 2011.

Fourier transform from r to k: Ã(k) =  A(r) e  i k r d 3 r Inverse FT from k to r: A(k) = (2  )  3  Ã(k) e +i k r d 3 k X-rays scatter off the charge.

Advisor : Ku-Yaw Chang Speaker : Ren-Li Shen /6/12.

AN INTRODUCTION TO GENE EXPRESSION ANALYSIS BY MICROARRAY TECHNIQUE (PART II) DR. AYAT B. AL-GHAFARI MONDAY 10 TH OF MUHARAM 1436.

Crystallography : How do you do? From Diffraction to structure…. Normally one would use a microscope to view very small objects. If we use a light microscope.

AUTOMATION OF MACROMOLECULAR DATA COLLECTION - INTEGRATION OF DATA COLLECTION AND DATA PROCESSING Harold R. Powell 1, Graeme Winter 1, Andrew G.W. Leslie.

Why are. we not solving more struct tures? James Holton University of California San Francisco and Advanced Light Source Lawrence.

Tracking Under Low-light Conditions Using Background Subtraction Matthew Bennink Clemson University Clemson, SC.

Presentation Outline ANAELU: 2-D XRD texture analysis Experimental 2D XRD patterns Representation of structure Simulation of single-crystal XRD Polycrystal.

Methods in Chemistry III – Part 1 Modul M. Che

Mathematical Derivation of Probability

Serial Femtosecond Crystallography

CHARACTERIZATION OF THE STRUCTURE OF SOLIDS

Score maps improve clarity of density maps

The Crystal Screening Interface at ALS

Crystallography images

Organic Chemistry Lesson 21 X-ray crystallography.

Signal processing.

CCP4 6.1 and beyond: Tools for Macromolecular Crystallography

IIS for Image Processing

Data Reduction using SORTAV

X-ray detectors and diagnostics for HED instrument

Protein Structure Determination

Basics of Photometry.

Experimental phasing in Crank2 Pavol Skubak and Navraj Pannu Biophysical Structural Chemistry, Leiden University, The Netherlands

Analysis of crystal structures

The PLATON/TwinRotMat Tool for Twinning Detection

Presentation transcript:

3. Spot Finding 7(i). 2D Integration 2. Image Handling 7(ii). 3D Integration 4. Indexing 8. Results 1. Introduction5. Refinement Background mask and plane determination using background pixels, equivalent to that of MOSFLM Default refinement parameterization in DIALS, where the detector, sample and beam are refined: extensions allow for more complex detectors such as CS-PAD at LCLS and the Dectris P12M Background pixel identification via outliers similar to that used in XDS 6. Background Determination Spot finding – raw image, mean, variance map… … dispersion map, threshold map and final centroids Indexing of six lattices from 1° sweep of micro-crystal data 2D profile fitting: averaging of background subtracted reflection profiles to determine optimum 3D profile fitting: background subtracted reflection data mapped to reciprocal space before averaging and fitting Low resolution limit High resolution limit Rmerge (within I+/I-) Rmeas (within I+/I-) Rpim (within I+/I-) Total number of observations Total number unique Mean((I)/sd(I)) Mn(I) half-set CC(1/2) Completeness Multiplicity Anomalous completeness Anomalous multiplicity DelAnom correlation half-sets Mid-Slope of Anom Probability References: Evans, P. R. & Murshudov, G. N. (2013). Acta Crystallogr. D. Biol. Crystallogr. 69, 1204–1214. Grosse-Kunstleve, R. W., et al. (2002). J. Appl. Crystallogr. 35, 126–136. Kabsch, W. (2010a). Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 133–144. Kabsch, W. (2010b). Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 125–132. Leslie, A. G. W. (1999). Acta Crystallogr. Sect. D Biol. Crystallogr. 1696–1702. Leslie, A. G. W. & Powell, H. R. (2007). Evolving Methods for Macromolecular Crystallography, pp. 41–51. Experimental electron density from fast_ep (SHELX C/D/E) and merging statistics from AIMLESS, from DNA / ligand complex Low resolution limit High resolution limit Rmerge (all I+ and I-) Rmeas (all I+ & I-) Rpim (all I+ & I-) Total number of observations Total number unique Mean((I)/sd(I)) Mn(I) half-set CC(1/2) Completeness Multiplicity R* Rfree* *non protein atoms removed from refinement for difference map calculation Difference density from glucose isomerase test sample, calculated using dimple (CCP4 / REFMAC5) Time varying refinement of unit cell parameters of a 720° radiation damaged thaumatin data set DIALS is a collaborative initiative to produce an open source software toolbox encompassing all aspects of diffraction data analysis. DIALS has been developed as a modular framework that permits flexibility not only in the development of new methods and algorithms but also in the application of these methods to data analysis as illustrated above. DIALS builds on the computational crystallography toolbox cctbx. Positional (i.e. pixel offset x, y) and parallax correction tables for DECTRIS Pilatus 6M SN 100 at Diamond Light Source, I04 (x)(y) (x)(y) Gwyndaf Evans 1, Graeme Winter 1, David Waterman 2, James Parkhurst 1, Luis Fuentes-Montero 1, Richard Gildea 1, Aaron Brewster 3, Nicholas Sauter 3, 1 Diamond Light Source, 2 CCP4, 3 Lawrence Berkeley National Laboratory Diffraction Integration for Advanced Light Sourceshttp://dials.sourceforge.net Correlation of reflection profiles with reference, over detector and intensity