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Ton Spek, Bijvoet Centre Utrecht University The Netherlands Bruker User Meeting, UCSD, La Jolla, March 22-24, 2012. CheckCIF Overview. Overview. Why Structure Validation Data Archival and Review before CIF The CIF Solution for Archival and Review The CIF Validation History
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Ton Spek, Bijvoet Centre Utrecht University The Netherlands Bruker User Meeting, UCSD, La Jolla, March 22-24, 2012 CheckCIF Overview
Overview • Why Structure Validation • Data Archival and Review before CIF • The CIF Solution for Archival and Review • The CIF Validation History • The Role of PLATON in IUCr checkCIF Validation • Validation Report, ALERT Levels A, B, C, G & Types • The Importance of FCF Validation • Two Case Studies • Talk #2 – PLATON Tools • Talk #3 - Validation/ALERT issues (Discussion) • Live Demo's (ADDSYM, Hooft etc.)
Why Automated Structure Validation • The large volume of new and routine structure reports submitted for publication. • The limited number experienced and available crystallographic referees for validation. • It should save time of authors, referees, journal editors and readers • Detection of errors due to the black box use of crystallography by less experienced analysts. • Setting some standards of quality and reliability. • Automated detection of unusual though not necessarily erroneous issues that need special attention • Sadly: The need to detect frauded structure reports.
Historic DevelopmentBefore CIF How it was when I started in crystallography as a student in 1966 at Utrecht University ...
Data Collection around 1966 Nonius AD3 Diffractometer One data set: weeks !
~1966, Electrologica X8 ALGOL60 ‘Mainframe’ (<1MHz) 16kW Operator Plotter Input Output Console Multiple Hours of computing time per structure
Flexowriter for the creation and editing of programs and data
Early Data Validation - The Cambridge Crystallographic Database. Data were typed from the publication and checked for internal consistency. Authors of an erroneous paper were approached to resolve unresolved issues. - The Journal 'Crystal Structure Communication' (1970's, Parma, Prof Nardelli) also checked coordinates with reported distances and angles for internal consistency after retyping the data from the submitted paper.
Problems Around 1990 • Multiple Data Storage Media (Often hardcopy on paper or microfilm only). I had a room full of card decks … and numerous magnetic tapes • No Standard Computer Readable Format for Archival and Data Exchange. • Data Entry of published data for follow-up calculations had to be done by Retyping. • No easy Numerical Checking or additional calculations by Referees etc. • Multiple typo’s and inconsistencies were common in the Published Data (as marked-up in the CSD) • Often incomplete information was reported.
The CIF Solution • CIF-Standard Proposal for data archival by S.R. Hall, F.H. Allen, I.D. Brown (1991). Acta Cryst. A47, 655-685. • Simple, Flexible and Free Format • First Implemented in the XTAL software package (Hall, Stewart et al.). • Adopted early (1992?) by the author of the nowadays most commonly used refinement program SHELXL (G.M.Sheldrick) • Adopted by the IUCr Journals (Syd Hall, Section Editor Acta Cryst. C)
CIF Constructs • data_name where name is the chosen identifier of the data • Data name and value associations e.g. _cell_length_a 16.6392(2) _ diffraction_radiation_source ‘sealed tube’ • Repetition (loop) loop_ __symmetry_equiv_pos_as_xyz ‘x, y, z’ ‘-x, y+1/2, -z’
Construct for Text • Text can be included between semi-columns • Used for Acta Cryst. Section C & E Abstract and Comment sections • Example _publ_section_comment ; This paper presents the first example of a very important compound. ;
CIF Completion • CIF Files are created by the refinement program (e.g. SHELXL, Crystals, JANA) • Missing Date can be added with a Text Editor, enCIFer (from the CCDC) etc.. • The CIF Syntax can be checked with a locally installed version of the program enCIFer (Freely Available: www.ccdc.cam.ac.uk)
PROGRAM enCIFer Missing Data
Note on Editing the CIF • The idea of editing the CIF is to add/update missing information to the CIF. • Unfortunately, some (Acta Cryst.) authors have been found to polish away less pleasing numerical values …. (including R-values e.g. 0.0975 => 0.0475) This of course leaves traces and is generally detected now (also in retrospect) by the validation software and is obviously not good for the career of the culprit…
The Acta Cryst Validation History • Structure Validation of data supplied in computer readable CIF format was pioneered in the 1990's by Syd Hall, the section editor of Acta Cryst. C at that time. • Initially the numerical checking of papers submitted to Acta Cryst. C in CIF format was done by the IUCr Chester staff. • Subsequently automated checking of the CIF for data consistency, data completeness and validity was introduced (checkCIF) (e.g. RFACR01 ALERT). • External PLATON facilities to check for Missed Symmetry and VOIDS were added soon after on Syd Halls Invitation. • This was followed by also including the numerous other PLATON based tests (PLATxxx) of the reported structure (currently more than 400). PLATON/checkCIF • Chester currently checks submitted papers for duplications. • Work is underway in Chester to also crosscheck geometrical data reported in the text with those in CIF format.
The Role of PLATON in IUCr/checkCIF Validation - PLATON includes a collection of structure analysis tools (geometry, absolute structure, twinning etc.) - A default run of PLATON loops automatically over most of the available (analyze) tools in the program - 'On-the-fly' ALERT messages are send to a file. The content of this file is analyzed subsequently on the basis of validation criteria detailed in an external text file 'check.def'. The result is a validation report on a file name.chk. - The IUCr PLATON/checkCIF combines the Chester ALERTS with PLATON ALERTS into a single report.
WHAT ARE THE VALIDATION QUESTIONS ? Single Crystal Structure Validation addresses three simple but important questions: 1 – Is the reported information complete? 2 – What is the quality of the analysis? 3 – Is the Structure Correct?
ALERT LEVELS CheckCif Reports in terms of a list of ALERTS • ALERT A – Could Indicate a Serious Problem – Consider Carefully (Action: Correct or tell convincingly why Correct) • ALERT B – Might Indicate a Potentially Serious Problem • ALERT C – Check to Ensure it is O.K. & Not because of an oversight. • ALERT G – General Info. Check that it is not something Unexpected.
ALERT TYPES 1 - CIF Construction/Syntax errors, Missing or Inconsistent Data. 2 - Indicators that the Structure Model may be Wrong or Deficient. 3 - Indicators that the quality of the results may be low. 4 - Cosmetic Improvements, Queries and Suggestions.
Which Key Issues are Addressed • Missed symmetry (“being Marshed”) • Wrong chemistry (Mis-assigned atom types) • Too many, too few or misplaced H-atoms • Missed solvent accessible voids in the structure • Missed Twinning • Absolute structure issues • Data quality and completeness Issues
FCF Validation • Printed Fo/Fc listings were required in the past for most publications and journals for deposition. • Fo/Fc reflection file deposition and archival in CIF format (FCF) was made mandatory early on for Acta Cryst. papers. • FCF's are useful for subsequent analysis of possibly unique data. • CIF + FCF checking was added in 2010 into the IUCr PLATON/CheckCIF suite in response to fraud. • Major chemical journals now require CIF deposition and validation reports but (not yet) the deposition of reflection data. (There appears to be a strong opposition – too complicated for chemists ?) • The CCDC now accepts FCF's for deposition.
Validation with standalone PLATON - Details: www.platonsoft.nl/platon • Driven by the file check.def with criteria, ALERT messages and advice. • Use (UNIX/MAC-OSX): platon –u structure.cif • Result on file: structure.chk and structure.ckf • Applicable on CIF’s (Including CCDC generated) • MS-Windows (Louis Farrugia) from the Toolbar
ADVISE • Validation should not be postponed to the publication phase. Most validation issues are best taken care of during the analysis with the crystals still available. • Everything unusual in a structure is potentially suspect, mostly incorrect (artifact) and should be investigated and discussed in great detail and supported by additional independent evidence. - The CSD can be a very helpful tool when looking for possible precedents (but be careful)
Systematic Fraud • A massive fraud was detected in late 2009 of structures mainly published around 2007 in Acta Cryst. E. (Soon 200 retractions !) • Nobody was prepared for serious and systematic fraud in this not competitive field of routine structures before 2010. • Many deviations from the expected results can often be explained away as errors, inexperience or due to poor data. • Several Acta Cryst. retractions before 2010 might in hindsight concern frauded structures and not just errors. • Ongoing testing of our validation software on the archived data for structures published in Acta E often indicated suspect structures needing a more detailed investigation. • It was only by following up on a particularly strange structure report with an analysis of all structures published by the authors of that paper that an extensive fraud pattern emerged. • Among others, it was found that the same data set was used to publish a series if invented isomorphous structures.
BogusVariations (with Hirshfeld ALERTS) on the Published Structure 2-hydroxy-3,5-nitrobenzoic acid (ZAJGUM) OH=>NH2 NO2=>COOH OH => F H2O => NH3
Error and Fraud Detection Tools • Generalized Hirshfeld Rigid Bond Test. • CIF versus FCF data checking. • Scatter Plots of the reflection data of the same or related structure(s). • Look in Difference Maps for unusual features. • SHELXL re-refinement using the supplied CIF & FCF data. • Check in the CSD for related structures. • Next:Two case studies that illustrate the use of the above validation and analysis tools follow.
Example 1: Structure I Submitted to Acta Cryst. (2011)
RELATED STRUCTURE FROM THE CSD Structure II
Analysis • Structure (II) has no validation issues. • C-CH3 distance in (II) of 1.50 Ang. as expected. • ‘C-F’ distance in (I) is 1.50 Ang. and not the expected 1.35 Ang. • Conclusion: Structure (I) is the CH3 variety and not F. • Data sets of (I) & (II) are not identical (see next). • Data set (I) likely based on CH3 compound. • Fraud or Error ? DIFABS file Error ? • Authors of (I) confirmed Error believing external chemists proposal. Paper was retracted.
Conclusion ? • Structure now O.K. after an erratum ? • Search for similar (isomorphous) structures in the CSD • Yes, there is an isomorphous Mn complex published by a different set of authors from a different university. • Let us compare both structures.
