Ruđer Bošković Institute

Cambridge Structural Database Workshop

 

Ruđer Bošković Institute, Zagreb, Croatia

March, 3rd and 4th, 2010

 

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Zagreb, March, 8th, 2010, POST FESTUM

 

Dear participants,

 

Let me take this opportunity to thank you all for your interest, attendance and active participation to the Cambridge Structural Database Workshop, held at the Ruđer Bošković Institute in Zagreb, March, 3rd and 4th, 2010. The lecturers, Gary Battle and Tracy Allgood gave us a comprehensive overview of the Cambridge Structural Database by presenting the CCDC, the database itself, as well as the powerful software distributed by the CCDC to its users, which enables a detailed insight into the enormous body of knowledge accumulated in this remarkable database. The intensive afternoon hands-on sessions gave us the opportunity to try, ourselves, the features that were presented during the morning demonstrations. First day was dedicated to the basics of the CSD system, and the second day was dedicated to more advanced uses of the database and the corresponding software tools. Thus, the workshop was, in my opinion, useful to both those of you having previous experience with the CSD, as well as to those who encountered this database for the first time. I strongly believe that the results will be both spreading the use of the CSD throughout of the academic community in the region, as well as enhanced use of the advanced features by those who already are using the CSD in their labs.

I believe that I speak on behalf of all the participants, when saying that the presentations, demonstrations and hands-on sessions were well prepared and delivered, and that the database and its huge potential were presented in an efficient and easily understandable manner. The feedback that I have received so far both through the survey forms that have been distributed to the participants, and their e-mails, is extremely encouraging, and motivates me to think about the emerging idea to make this workshop a regular event in the future.

We had alltogether 30 participants, out of which 19 from Croatia, 4 from Slovenia, 4 from Serbia, 2 from Bosnia and Herzegovina, and one participant from Macedonia. Most of the participants were graduate and PhD students. Unfortunately, two students cancelled their attendance in the last moment due to private reasons. However, as the workshop was held at the Ruđer Bošković Institute where we have a large community of structural chemists, we were pleased to welcome few "unofficial" participants that shared our enthousiasm, and contributed to the success of the workshop by their attendance, questions and comments.

I thank you again, wish you all a very successful career, and hope to see you soon, maybe at the next CSD workshop, somewhere in Croatia.

 

Yours faithfully,

Aleksandar Višnjevac

 


 

 

The Cambridge Structural Database Workshop is organized jointly by The National Foundation for Science, Higher Education and Technological Development of the Republic of Croatia, Ruđer Bošković Institute and Cambridge Crystallographic Data Centre (CCDC). It is intended primarily to the postgraduate and PhD students from the universities and public institutes in the Republic of Croatia and other SEE countries. Its aim is to get the students acquainted with the Cambridge Structural Database (CSD), by far the largest and most important database of the crystal structures in the world, as well to exemplify more advanced use of the tools and software for the database search. By the decisions of their respective faculty councils, the workshop is included into the ECTS system of two postgraduate courses at the Faculty of Science, and at the Faculty of Chemical Engineering and Technology of the University of Zagreb.

 

 


 

The workshop will take place at the Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia (Building 1, lecture room at the ground floor) over two days (March, 3rd and 4th, 2010). The official language of the workshop is English. The organizer will provide computers for the practical sessions for all participants on the "work in pairs" principle.  

 


 

ABOUT THE CCDC

The CCDC is a non-profit, charitable institution whose objectives are the general advancement and promotion of the science of chemistry and crystallography for the public benefit. It is located on the Chemistry Campus of the University of Cambridge, and serves the scientific community through the acquisition, evaluation, dissemination and use of the world's output of small molecule crystal structures by:

  • Compiling the Cambridge Structural Database (CSD) - the world repository of small-molecule crystal structures

  • Developing scientific products and services - structural knowledge bases and applications software for the life sciences and crystallography

  • Maximizing worldwide accessibility to the CSD academic and industrial scientists

  • Performing and supporting fundamental research using CSD information and CCDC products

  • Promoting and supporting applications of crystal structure information in academia and industry

The CCDC also sponsors international scientific awards for younger scientists. CCDC Prizes are awarded for original research in chemical crystallography and applications of small-molecule crystallographic information in, e.g., structural chemistry, molecular modelling, materials design, structural biology or chemical informatics.

 

ABOUT THE CAMBRIDGE STRUCTURAL DATABASE (CSD)

 

The Cambridge Structural Database (CSD) is the principal product of the CCDC and contains the results of X-ray and neutron diffraction analyses of almost half a million small molecule organic and metal-organic crystal structures. The CSD is fully retrospective of the published literature and also contains directly deposited data that are not available elsewhere.  The 3D structure, bibliographic and crystallographic information provided in the CIF are thoroughly validated and are supplemented with additional data abstracted from the publication citing the structure. The Cambridge Structural Database System (CSDS) includes the database in addition to software components that enable search, analysis and exploration of the data.  These components and their functions are listed below:

 

  • PreQuest, build proprietary databases that are searchable alongside or independently of the CSD.

  • ConQuest, the primary search interface to the CSD. Perform textual, bibliographic, numeric or chemical searches on any of the data fields stored in the CSD.  Search for 2D or 3D substructures, monitor or constrain bonds, angles or torsions of interest or perform searches for inter and/or intra-molecular interactions.

  • Vista, for interactive data analysis.  Use Vista to analyse user-defined geometric parameter data or other numerical data retrieved from the CSD using ConQuest.

  • Mercury, crystal structure visualisation and analysis made easy.  Pack single or multiple unit cells; display symmetry elements, voids, H-bond and other short range non-bonded interactions; calculate planes and centroids, BFDH morphology, simulated powder patterns, structure overlay, graph sets; validate inter- and intra-molecular interactions; carry out theoretical calculations using MOPAC.  Use the Materials module to compare packing patterns of structures and quantify similarity between them, identify regions of structural similarity, search sets of structures for specific interactions motifs or general packing features and compare geometries.

  • Mogul, pre-computed library of molecular geometry.  Input a query molecule and select atoms to rapidly retrieve a histogram and descriptive statistics for the selected geometric parameter(s).  Hyperlinking enables inspection of the underlying data.

  • IsoStar, a pre-computed library of inter-molecular interactions.  Instantly display visual plots illustrating the distribution of a contact group around a central functional group.  Contour plots at user-defined contour levels to highlight interaction hotspots.

  • WebCSD, browser-based access to the CSD.  Make use of either on-site or CCDC-hosted versions of the software, subject to your licence agreement.


The page was updated on 11.03.2010