Reflection Data Analysis Tools in PLATON Problem from Bruker Discussion List: Triclinic or Monoclinic? Ni-complex In P-1,Z'=2: a = 11.869 b = 5.562 c =

Slides:



Advertisements
Similar presentations
Peer to peer and Social Web How Web 2.0 and File Sharing mix.
Advertisements

Twinning tools in PLATON Detection and Absorption Correction Martin Lutz, Bijvoet Center for Biomolecular Research Dep. Crystal and Structural Chemistry,
The MISSYM Family: Software for the detection of Missed or Pseudo Symmetry A.L.Spek Utrecht University The Netherlands.
PLATON, New Options Ton Spek, National Single Crystal Structure Facility, Utrecht, The Netherlands. Delft, Sept. 18, 2006.
PLATON TUTORIAL A.L.Spek, National Single Crystal Service Facility,
Fundamental Concepts Crystalline: Repeating/periodic array of atoms; each atom bonds to nearest neighbor atoms. Crystalline structure: Results in a lattice.
t1 t2 6 t1 t2 7 8 t1 t2 9 t1 t2.
Example 5.2: Anhydrous Sodium carbonate
CIF, PLATON-2014, SHELXL-2014, VALIDATION & SQUEEZE
Point Groups (Crystal Classes)
Erice 2011 Electron Crystallography – June Introduction to Sir2011 Giovanni Luca Cascarano CNR- Istituto di Cristallografia – Bari - Italy.
An Update on Current and New Structure Analysis Tools in PLATON Ton Spek, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands.
PLATON Validation and Analysis Tools Ton Spek National Single Crystal Service Facility, Utrecht University, The Netherlands. Sevilla, 14-Dec-2010.
Twinning. Like disorder but of unit cell orientation… –In a perfect single crystal, unit cells are all found in the same orientation. We can consider.
PLATON/SQUEEZE Ton Spek Bijvoet Center Utrecht University, The Netherlands. PLATON Workshop Chicago, 24-July-2010.
The PLATON Toolbox Ton Spek National Single Crystal Service Facility, Utrecht University, The Netherlands. Kyoto, 20-Aug-2008.
Automatic Detection of Poor or Incorrect Single Crystal Structures A.L.Spek Utrecht University The Netherlands.
Structure Validation Challenges in Chemical Crystallography Ton Spek Utrecht University, The Netherlands. Madrid, Aug. 26, 2011.
Software Tools for the Analysis of Z’ > 1 Structures A.L.Spek, Utrecht University, National Single Crystal Service Facility The Netherlands. BCA-Meeting,
Data Flow SADABS sad.hkl sad.abs sad.prp name.ins name.hkl SAINTXPREPSMARTSHELX n.xxx p4p n.raw n._ls m.p4p copy to sad.p4p.
The System-S Approach to Automated Structure Determination: Problems and Solutions Ton Spek National Single Crystal Service Utrecht University, The Netherlands.
Automated Crystal Structure Validation Ton Spek, National Single Crystal Facility, Utrecht University, Utrecht, The Netherlands Platon Workshop Chicago,
PLATON, AN OVERVIEW Ton Spek National Single Crystal Service Facility, Utrecht University, The Netherlands. Platon Workshop Chicago, 24-July-2010.
SYSTEM-S The Challenge of Automated Structure Determination Ton Spek National Single Crystal Service Utrecht University, The Netherlands.
Structure Validation in Chemical Crystallography Ton Spek, Bijvoet Centre for Biomolecular Research, Utrecht University, The Netherlands. CCP4-Leeds, 5-Jan
Structure Validation in Chemical Crystallography Principles and Application Ton Spek, National Single Crystal Service Facility, Utrecht University SAB-Delft,
Mastering OOA/OOD with UML. Contents Introduction Requirements Overview OOAOOD.
Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space Groups Michael Shatruk September 12, 2011.
MGT-491 QUANTITATIVE ANALYSIS AND RESEARCH FOR MANAGEMENT OSMAN BIN SAIF Session 19.
Twinning Non-merohedral twinning Merohedral twinning.
PLATON, A set of Tools for the Interpretation of Structural Results Ton Spek National Single Crystal Service Facility, Utrecht University,The Netherlands.
PLATON TUTORIAL A.L.Spek, National Single Crystal Service Facility, Utrecht, The Netherlands.
Ton Spek Utrecht University The Netherlands IUCr-Montreal Aug 11, 2014
The PLATON/TwinRotMat Tool for Twinning Detection Ton Spek National Single Crystal Service Facility, Utrecht University, The Netherlands. Delft, 29-Sept-2008.
PLATON, A Multipurpose Crystallographic Tool Ton Spek, National Single Crystal Service Facility, Utrecht, The Netherlands.
The PLATON Toolbox History and Applications Ton Spek Utrecht University, The Netherlands. Bruker User Meeting, UCSD La Jolla, March 22-24, 2012.
By: Luis Fuentes-Montero (Luiso) Esmeralda, program for treating Laue images.
Indexing. Q hkl = h 2 a* 2 + k 2 c* 2 + l 2 c* 2 + 2hka*b* cos gamma* + 2klb*c* cos alpha* + 2hlc*a* cos beta* = (1/d hkl ) 2.
Evolutionary Art (What we did on our holidays) David Broadhurst Dan Costelloe Lynne Jones Pantelis Nasikas Joanne Walker.
Thesis Project Process Brian Newberry Spring 2013.
PLATON/SQUEEZE Ton Spek Bijvoet Center Utrecht University, The Netherlands. PLATON Course Utrecht, April 18, 2012.
Absolute Configuration Types of space groups Non-centrosymmetric Determining Absolute Configuration.
Making the System Operational Implementation & Deployment
Updates on Validation and SQUEEZE Ton Spek Utrecht University Bruker User Meeting Jacksonville (FL), Jan 19, 2016.
This template can be used as a starter file for presenting training materials in a group setting. Sections Right-click on a slide to add sections. Sections.
Point Groups (Crystal Classes)
Images for reflection. Que
Judging the Quality of a Crystal. Determining the Best Exposure Time. Data Collection Strategy. From Crystal to Diffraction Pattern.
Parameters235 Formula MW cryst syst Space group a /Å b /Å c /Å α (°) β (°) γ (°) V /Å 3 Z T /K λ /Å ρ c (g/cm3) μ (mm-1) Goodness of fit θ range Total.
What is Needed for Proper Structure Validation and How to Act upon Validation ALERTS Ton Spek Utrecht University The Netherlands ACA-Denver, july 26, 2016.
The PLATON checkCIF and SQUEEZE Tools
(check)CIF, SHELXL-2014, SQUEEZE
What Makes a Crystal Structure Report Valid?
Math 4030 – 10b Inferences Concerning Variances: Hypothesis Testing
Crystal Structure Validation with PLATON
MSIS 2011 – Statistics Sweden
Why Crystal Structure Validation ?
Making the System Operational Implementation & Deployment
Theory and Practice of X-ray Crystal Structure Determination
Symmetry Elements II.
The Gamma PDF Eliason (1993).
Suggested/Recommended Project Process
Welcome to Utrecht and to the Netherlands
The SQUEEZE Tool in PLATON and its use with SHELXL2013
Which equation does the function {image} satisfy ?
Alpha Mu Gamma Past National Conventions
Mobile technologies, as tools to improve researches and communication in developing countries, Case of DRCongo.
Ton Spek Utrecht University The Netherlands Vienna –ECM
Evaluate the integral {image}
The PLATON/TwinRotMat Tool for Twinning Detection
Presentation transcript:

Reflection Data Analysis Tools in PLATON Problem from Bruker Discussion List: Triclinic or Monoclinic? Ni-complex In P-1,Z'=2: a = b = c = Alpha = Beta = Gamma = R1 = 10% WR2 = 31% Ton Spek, Utrecht University, The Netherlands Bruker User Meeting Bad Herrenalb, Sept. 23, 2012

Triclinic, Monoclinic ? -The New SHELXT program offers a starting model in P-1 and Pn and P21/n -PLATON/ADDSYM happily offers a structure in P21/n that resembles the solution in P-1

Alternative Monoclinic Model In P21/n, Z'=1: A = B = C = Alpha = 90 Beta = Gamma = 90 R1 = 17% WR2 = 53% Poor ADP's

Monoclinic Model ADP's

Looking at the Data - Investigate thePrimary Data - Images, Integration - HKL File - Redundancy, Laue Symmetry (Rav) - Space Group Extinctions - Investigate the Refinement Data - Analysis of Variance - Twinning With Tools Available in PLATON

Test P-1 Model for Twinning

Overlapped k = 0 Layer

Rav (Monoclinic – 2/m) = 21% on F(calc) Model

Refined Model in P-1 All H-atoms Found and rerined

In Conclusion -Three additional parameters had to be introduced to obtain a nice looking refinement result in P-1: -- A twinning parameter -- Two population parameters Ni1 0.88, Ni The residual problem: explain the non 1.0 population parameters for Ni. - Go back to the chemist …..

Thanks ! Example taken from the very active and interesting Bruker User Discussion List Maintained by Ilia Guzai Problem and data communicated by Babu Varghese