Fast, Intuitive Structure Determination V: Structure Refinement and Report Generation. January 28, 2014

Transcription

1 Fast, Intuitive Structure Determination V: Structure Refinement and Report Generation January 28, 2014

2 Welcome Dr. Michael Ruf Product Manager Crystallography Bruker AXS Inc. Madison, WI, USA Bruce C. Noll, Ph.D. Sr. Applications Scientist Crystallography Bruker AXS Inc. Madison, WI, USA 2

3 Structure Refinement

4 Overview Refine structural model by least-squares method to improve fit of calculated structure factors to observed structure factors. Locate atom sites that may have been missed in initial solution. Add hydrogen atoms. Allow for anisotropic thermal motion. Add detail on disorder and twinning. 4

5 Least-Squares Refinement Create instruction file (.ins) containing program instructions and parameters for refinement model Adjust fit of parameters (model) to observations by minimizing sum of differences Review results file (.res) Edit results to new instruction file Repeat to convergence 5

6 From Structure Solution to Structure Refinement Initial solution from Direct Methods, Patterson, Intrinsic Phasing, or Dualspace Intrinsic phasing Space group Atom types 6

7 From Structure Solution to Structure Refinement Initial solution from Direct Methods Top 23 peaks comprise target molecule Next, open result in Refinement plug-in 7

8 The Structure Refinement Plug-in Latest result loaded 8

9 Loading Files Latest result loaded or Load from browser 9

10 The Structure Refinement Road Map Interface to SHELX 10

11 The Structure Refinement Road Map Interface to SHELX Tabs select SHELX files and structure viewer Presents instructions, program listing, results, and a viewer 11

12 The Structure Refinement Road Map Interface to SHELX Tabs select SHELX files and structure viewer Presents instructions, program listing, results, and a viewer Allows for refinement, editing, and editing with external programs Buttons for file management and program control 12

13 Analysis of Initial Solution Examine peak heights 13

14 Analysis of Initial Solution Examine peak heights Higher peaks Not significant Peak height relative to electron density Weaker peaks may not be real Look for sharp break Sucrose: C 12 H 22 O 11 14

15 Graphical Editing Editors allow for easy analysis of results Direct Methods solution of sucrose structure. 15

16 Molecular Editor/Visualization Please tell us about your favorites. What software packages do you use most frequently? XSHELL ShelXle XP Olex2 X-Seed WinGX Use the polling section on your screen to select your choices. Multiple selections are allowed. 16

17 Graphical Editing Trim away spurious peaks Desired structure is readily evident Direct Methods solution of sucrose structure. 17

18 Structure Refinement Assign atom types and numbering Model disorder, if present Add H atoms Refine with anisotropic displacement parameters Completed refinement of sucrose structure. 18

19 Return to APEX2 Add any final SHELX instructions Adjust WGHT if necessary Check for finish Completed refinement of sucrose structure. 19

20 Return to APEX2 Add any final SHELX instructions Adjust WGHT if necessary Check for finish Proper assignments No significant residual density Sensible numbering Sorted Converged 20

21 Final Refinement End of results file Completed refinement of sucrose structure. 21

22 Final Refinement End of results file R1 WGHT HTAB instructions Difference map peaks Completed refinement of sucrose structure. 22

23 SHELX.lst File Summary of everything done by XL during last execution Completed refinement of sucrose structure. 23

24 SHELX.lst File Last cycle: wr2 GooF Shifts correlation 24

25 SHELX.lst File Last difference map: Highest peak Deepest hole 25

26 Checking CIF File Select Open Report 26

27 Checking CIF File PLATON CIF validation is launched Summary check Summary check Listing of alerts Explanation Listing of alerts Explanation 27

28 Structure Refinement with APEX2 Structure refinement plug-in Reads results from Structure Solution plug-in Intrinsic Phasing Direct Methods Patterson method Dual-space Versatile interface to SHEXL-2013 Direct links to graphical editors Quick check of refinement through PLATON 28

29 Report Generation with APEX2

30 The Role of Reports The information that drives the business success of the laboratory is contained in reports These reports, numbering from dozens to hundreds, are typically generated in a manual fashion by crystallographers While the role of analyzing data is vital and might best be left for human beings, the role of generating reports is an activity that should be automated 30

31 The Need for Automated Reports Increased throughput Better instrumentation Automation in hardware and software More and more papers on automation, robotics, hi-throughput Diversified distribution channels Data exchange formats (e.g. CIF and mmcif) World Wide Web (e.g. Reciprocal Net) Laboratory Information Management Systems Reports needed in different formats and for various purposes High-throughput molecular assembler C&E News, Dec 2003 Make the crystallographer s life easier 31

32 Report Purposes and File Formats Publication (e.g. CIF, mmcif) Deposition (e.g. CRT (Reciprocal Net) CSD) Presentation (e.g. HTML, RTF, Word, PowerPoint) Audit 32

33 Audit Trail Preserve all the required information Experimental data and analytical results Tools (hardware and software) Metadata (user name, date and time, etc.) Context 33

34 Audit Trail Handled by a relational database Data storage and retrieval system Data items relate to each other, thus building a hierarchy reducing redundancy increasing consistency Access privileges prevent tampering with data items Examples for relational databases SQL databases (Oracle, Microsoft, MySQL, PostgreSQL) mmcif files 34

35 Example 8 7 6a 6b P3 1 P3 2 5a b 35

36 Preserving the Context Link (unit cell) 6a Process Process 5a Indexing 4 3 Process 2 5b input 7 6b P3output 1 Link P3 2 Link (images) input input output Integration Data Collection 1 output output manual 8 (images) Link Link 36

37 Selecting the Target for a Report 8 7 6a 6b P3 1 P3 2 5a b 37

38 Templates Retrieve data from the database Use retrieved data for output to the report calculations (e.g. unit cell volume from lengths and angles) turning sections of the report on and off Format data (e.g. number of decimals, ESDs) Define defaults for missing data Take care of file format specific syntax and limitations CIF text blocks, maximum line length, loops HTML tags 38

39 Template Snippet A %(_exptl_crystal.colour)s %(_exptl_crystal.description)s of %(_chemical_formula.sum)s, approximate dimensions %(_exptl_crystal.size_min).2f mm x %(_exptl_crystal.size_mid).2f mm x %(_exptl_crystal.size_max).2f mm, was used for the X-ray crystallographic analysis. A clear colorless irregular block of C6 H8 O6, approximate dimensions 0.02 mm x 0.08 mm x 0.12 mm, was used for the X-ray crystallographic analysis. 39

40 Implementation Manual input of sample information 40

41 Implementation Representation in report 41

42 Report Generation Choose template Control template sections Load additional information from local.pcf files 42

43 Implementation Tabs for Report Atoms Bond lengths Bond angles Torsion angles Export of miscellaneous items into.pcf files 43

44 Cif Report Load cif template Add additional information in appropriate tabs Load additional information from.pcf files 44

45 Cif Report - Editing Edit miscellaneous fields like software versions Experimental parameters Provides drop down boxes with cif approved items Export and import to and from pcf files Add or remove authors Change position Export and import authors 45

46 Sample HTML Report 46

47 Finishing with publcif Edit and add information WYSIWYG input Templates for Acta C, Acta E,Acta B Generic template 47

48 Validation with checkcif Syntax and content checking at IUCr Report required for publication in most chemistry journals 48

49 Report Generation with APEX2 Easy to use Report Generation Plug-in Fairly automated report generation Data base audit trail preserves all relevant information Reports as CIF or HTML 49

50 18 TH ANNUAL BRUKER/MIT SYMPOSIUM MODERN APPROACHES IN CRYSTAL STRUCTURE SOLUTION Friday, February 21 st to Sunday, February 23 rd

51 A Crystallographer s Guide to SHELXL Edited by Peter Müller, Principal Research Scientist, Massachusetts Institute of Technology, and founder of The Structure Factory. Thorough descriptions of advanced topics of structure refinement, including Disorder Pseudosymmetry Twinning Much more Companion CD-ROM with examples from the book to be used as exercises for the reader. 51

52 Questions and Answers Any questions? Please type any questions you may have for our speakers in the Q&A panel and click Send. How did we do? When you exit the webinar, please fill out our evaluation survey to let us know. We appreciate your feedback. Thank you! 52

53 Copyright Bruker Corporation. All rights reserved. Innovation with Integrity