The information provided here is intended primarily for members of the Department of Chemistry.
For assistance and questions, please contact
Prof. Bernhard Spingler
Office: 38 G 12
Tel: 54656
E-Mail: Bernhard Spingler
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On-line documentation for searching the CSD
Go to X-ray User Info
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How to access the Cambridge Structural Database (CSD) and start a basic search:
Software for accessing the CSD
The University of Zurich has a site license for the CSD and its related software. The best solution, offering the user the greatest flexibility, is to install the entire CSD System, which includes the software and database, on your own computer (Mac, Windows and Linux are supported). However, the CSD System cannot be downloaded directly by users. Please contact Prof. Spingler (contact details above) and he will make the relevant installers available to you and provide the license key. Installation can require about 20 GB of storage.
Once installed, the software and database update automatically three or four times during the year. At the end of each year, the entire next version of the CSD System must be obtained and installed.
WebCSD is an online alternative to the CSD search software ConQuest, but has less functionality. It is ideal for relatively straightforward searches. You can access WebCSD from anywhere in the UZH network, including via a VPN connection.
Mercury is a the structure visualisation and analysis program, which has a license-free standalone version that can be installed in the absence of the CSD System. The free version has some functionality disabled, but these functions can be activated by applying the license key obtainable from Prof. Spingler(contact details above).
Starting a search
The ConQuest graphical interface is quite intuitive. If you try the various options, you should quickly learn how to construct queries, perform searches and analyse the results. Interactive help and tutorials are available and the on-line manuals should be consulted for detailed information.
The structure drawing tool is similar to that of ChemDraw, but one key difference is that H-atoms are not implied. If you do not define H-atoms for a particular parent atom, structures with all possible substitutions at that site will be found. This is advantageous when looking for structures with a similar fragment or backbone, but might give too many hits when looking for a single specific compound.
Detailed on-line documentation is available. Help is also available during a search, as each window has a HELP menu or button.
If the manuals do not resolve a question, Prof. Spingler is available to assist you. He can also help with any questions that you might have about search strategies.
When using a local installation of the database, double-click on the ConQuest icon to start the software.
Some information will be displayed in a small window and then the main window will apppear. From the list of buttons on the left side select the Draw option to sketch a molecule and a new window will be displayed, while the other options allow you to enter various text or numerical information to search on.
In the Draw window, the ADD-3D option can be used to define geometrical tests for the search, so that these features can be analysed, or used later in the structure analysis program Vista. When drawing a fragment, remember that H-atoms are not implicit and you must define them to complete an atom's valency if you do not wish to find all structures with ANY substituent at the incomplete site(s).
Several questions can be built up before starting the search. Search questions do not have to be based solely on structural fragments. Text and numeric strings, such as authors' names, compound names, formula and year are a few examples of possible options. If you wish to develop multiple queries, choose the Store option after creating each individual query (choosing the Search option will start a search directly using the current query only). Multiple questions can be combined using the Combine Queries tab in the main window, e.g. with AND, OR, NOT, etc. You may also specify various options, such as to display only error-free data, or only structures for which atomic coordinates are available, or only organic structures, etc.
Further information is available in the comprehensive on-line documentation.
The search results
During a search with ConQuest, hits will be displayed in a list and you can select any hit and examine it in more detail while the rest of the search is running. Many options are available, including on-screen rotations of a 3D view of the structure and the ability to find bond lengths, angles and torsion angles just by clicking on the relevant atoms. Right-click in the 3D window to activate a menu. To reject any hit, click on the green tick in the list. A question that is too general could give a very large number of hits and the question may need to be defined more restrictively.
Search results will not be saved unless this is specifically requested (you will be warned if you attempt to exit without saving anything). Under the File-menu, a summary PDF file of the search results can be saved. If you want to work further with the atomic coordinates, use the "Export Entries As..." option of the File menu in ConQuest and the primary crystallographic data and atomic coordinates can be exported in CIF or several other formats.
Geometrical analysis of the search results
The program Mercury can be used to analyse the structures you saved during the search, provided some geometrical tests (e.g. bond lengths, angles, torsion angles, etc.) were defined with the ADD-3D button in the DRAW window of ConQuest during the building of the search question. Start Mercury from within ConQuest under the File-menu: "View in Mercury".
It is then possible to get a graphical analysis for various geometrical features, or to graphically look at the information available individually for each entry in the same way that the hits could be viewed during the original search. Thus it is possible to view the molecule in 3D and to rotate it on the screen, as well as look at individual bonding parameters. The full bibliographic data can also be viewed on the 1D screen.
Views of the molecules located during the search
The program Mercury can be used to view, rotate, draw and analyse the structures you saved during the search. This is similar to the 3D viewer available during the search itself, but may be faster when used locally. Mercury for the Mac or Windows PC can be downloaded freely from the CCDC web site. We have a site license to activate some additional features in Mercury. If you want full functionality, please ask Prof. Spingler for the license key (contact details above).
Searches on the Inorganic Crystal Structure Database (ICSD)
The structural details of inorganic compounds (i.e. compounds not containing at least one carbon atom) are not stored in the Cambridge Structural Database, but in a separate database known as the Inorganic Crystal Structure Database. The ICSD can be searched with a web browser from anywhere in the UZH network, including via a VPN connection.
Searches on the Protein Databank (PDB)
The structural details of proteins larger than 24 residues are not stored in the Cambridge Structural Database, but in a separate database known as the Protein Databank. The PDB can be searched with a web browser.
Searches on the Nucleic Acids Database (NDB)
The structural details of nucleic acids larger than trinucleotides are not stored in the Cambridge Structural Database, but in a separate database known as the Nucleic Acid Database. The NDB contains structures of oligonucleotides and nucleic acids and can be searched with a web browser. This site also has links to databases containing the structural details of DNA-binding proteins and the structures of nucleic acids determined by NMR.
FAQs
What is the Cambridge database in computer science? ›
The Cambridge Structural Database (CSD) is the world repository of small molecule organic and metal-organic crystal structures.
Is the Cambridge Structural Database free? ›Structural Database (CSD) for free through Access Structures.
How do I download CIF files? ›CIF files for many compounds can be downloaded from the American Mineralogist Crystal Structure Database (AMSD), or from the Crystallography Open Database (COD), for instance. A file in the CIF format may contain the positions of atoms, as well as the symmetry group that the compound belongs to.
Which type of information can be retrieved from Cambridge database? ›The Cambridge Structural Database (CSD) is both a repository and a validated and curated resource for the three-dimensional structural data of molecules generally containing at least carbon and hydrogen, comprising a wide range of organic, metal-organic and organometallic molecules.
How hard is Cambridge Computer Science? ›Computer Science is one of the most competitive courses at Cambridge and requires you to perform well in multiple stages to be in with a chance of securing an offer.
Is Cambridge Computer Science good? ›It is taught very well and fundamentally. In fact, I would go as far as to say that I enjoy my Computer Science courses terribly more than I enjoy my Natural Science courses and, mind you, Cambridge is renowned for its Natural Sciences.
How can I use database for free? ›- ClickUp. ClickUp is one of the highest-rated project management software in the world, loved by super-productive teams from startups to large corporations. ...
- MySQL. Via MySQL. ...
- Microsoft SQL Server. Via Microsoft SQL Server. ...
- Airtable. Via Airtable. ...
- MongoDB. Via MongoDB. ...
- PostgreSQL. ...
- Amazon RDS. ...
- RazorSQL.
You can log into this database using your student portal password. Cambridge University Press publishes a prestigious list of scholarly journals, ranging across the humanities, social sciences and STM disciplines, made available electronically through Cambridge Core.
When was Cambridge Structural Database launched? ›The ongoing stewardship of the Cambridge Structural Database (CSD) has been the core activity of the Cambridge Crystallographic Data Centre (CCDC) since its inception in 1965.
How do I convert CIF to excel? ›- In Excel, choose File Open and select the CIF file. ...
- Select Delimited and click Next.
- Select Comma as the delimiter and quote (") as the text qualifier. ...
- Click Next.
- Select all columns in the Data preview pane (Shift-click), select Text as the column data format, and click Finish.
How do I open a CIF file in Windows 10? ›
The CIF files are just text files, so, you can open it with any text file editor (nano, vi, emac, notepad, even Microsoft Word).
What programs view CIF files? ›- General STAR File utilities.
- CIF validation.
- Software libraries.
- File manipulation programs.
- coreCIF applications.
- pdCIF and msCIF applications.
- mmCIF applications.
- imgCIF/CBF applications.
Structured data is data that has been organized into a formatted repository, typically a database. This is done so the data's elements can be made addressable for more effective processing and analysis. The data resides in a fixed field within a record or file.
Which database is used for retrieving protein structure data? ›The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids.
What is structure database in bioinformatics with example? ›Other structural databases
Examples include: MMDB: Experimentally determined three-dimensional structures of biomolecules derived from Protein Data Bank (PDB). Nucleic acid Data Base (NDB): Experimentally determined information about nucleic acids (DNA, RNA).
Frequently Asked Questions About Computer Science
For students with no programming experience, learning their first programming language can be the most challenging aspect of computer science. Additionally, data structures, algorithms and discrete mathematics can prove difficult.
Computer Science
However, it remains one of the hardest college majors. Students enrolled in a computer science degree program will need to learn popular programming languages and challenging theoretical concepts. Coding assignments can be tricky, especially when it comes to finding small errors in a program.
In previous years, this has been around 75% of Home applicants. Not everyone interviewed will be offered a place but everyone who is made an offer will have been interviewed. Interviews usually take place in December. In 2022-23, most shortlisted applicants were interviewed virtually.
Is MIT better than Cambridge? ›Massachusetts Institute of Technology (MIT) is the world's best university, followed by the University of Cambridge, Stanford University, Oxford, and Harvard. This classification is according to the QS World University Ranking 2023, which features 1418 institutions worldwide, and was released this week.
Is Cambridge as good as Harvard? ›Harvard is ideal for computer science and business- and medicine-related majors. Most of its graduates end up in the finance and healthcare industries. Meanwhile, many Cambridge graduates wind up in academia, research and public service. Many apply to it for its social sciences and engineering courses.
Which Ivy League has good computer science? ›
Ivy League university Cornell ranked #5 in the US News and World Report 2022-23 rankings for Computer Science. Within that it ranked #3 for Programming Languages, #5 for Theory, #7 for Cybersecurity and Data Analytics/science, and #8 for Artificial Intelligence.
Which database is best for beginners? ›Microsoft SQL Server is used as the fundamental tool in universities for Web applications and software. SQLite, a powerful Relational Database Management System (RDBMS), is also very easy to learn and to practice simple queries. It is very essential to become familiar with the basics of the most popular SQL Databases.
Can I use Excel as a database? ›As a spreadsheet program, Excel can store large amounts of data in workbooks that contain one or more worksheets. However, instead of serving as a database management system, such as Access, Excel is optimized for data analysis and calculation.
What is the easiest database software to use? ›MySQL and PostgreSQL come without any limitation to RAM and database. MySQL and SQL Server are easy to use. MySQL can be used for high volume websites, packaged software, and business-critical systems. Oracle works for Windows and Linux platform.
What are the 4 databases? ›There are four kinds of this database: document databases, key-value stores, column-oriented databases, and graph databases.
How do I search in Cambridge core? ›- Click on the search bar in the centre of Cambridge Core or Click on the search bar in the top right hand corner of any other Cambridge Core website.
- Enter your search term and click on the magnifying glass icon or press the enter key.
- The search results will display on the following screen.
The Cambridge Curriculum consists of four stages and gives students a clear path for educational success from age five to 19. These four stages of the Cambridge Curriculum are Cambridge Primary, Cambridge Lower Secondary, Cambridge IGCSE and Cambridge International AS & A Levels.
Who discovered CSD? ›Established in 1965 by the Cambridge Crystallographic Data Centre (CCDC), the Cambridge Structural Database (CSD) is the world's repository for small-molecule organic and metal-organic crystal structures.
When did the Cambridge Structural Database and Protein data Bank launch? ›It began in 1970's at Brookhaven National Laboratory under the leadership of Walter Hamilton and now it is the largest worldwide repository for the processing and distribution of three-dimensional structural data of proteins and nucleic acids.
What is the small-molecule structure database? ›SMPDB (The Small Molecule Pathway Database) is an interactive, visual database containing more than 30 000 small molecule pathways found in humans only. The majority of these pathways are not found in any other pathway database.
What is equivalent to CIF? ›
Buyers and sellers wishing to use CIF for air shipments can substitute CIF for CIP, which stands for carriage insurance paid to the destination. With this Incoterm, the seller must insure the cargo to the defined destination.
How to calculate CIF? ›- Cost of goods (as per the sale agreement between the seller and the buyer)
- Insurance of the shipment until it reaches the destination port.
- Freight incurred to send the shipment until the destination port.
In cell B2, type =PROPER(A2), then press Enter. This formula converts the name in cell A2 from uppercase to proper case. To convert the text to lowercase, type =LOWER(A2) instead. Use =UPPER(A2) in cases where you need to convert text to uppercase, replacing A2 with the appropriate cell reference.
How do I access CIFS on Windows? ›- From Windows search, right click File Explorer.
- Click Map Network Drive (at top). ...
- In the Drive list, select an available drive.
- In the Folder box, do the following: ...
- Click to select the Connect using different credentials check box.
- Click Finish.
STEP 1 :Access Control Panel. Then, select Programs. STEP 2 : Locate Programs and Features and click Turn Windows features on or off. STEP 3 : Find SMB 1.0/CIFS File Sharing Support in the list and enable all three functions belong to it.
How to convert XLSX to CIF? ›- Save the Excel file as a comma-separated values (CSV) file.
- Open the file in Notepad and remove all extra commas at the end of each line. Note: When you open the CSV file, all the lines contain extra commas at the end. ...
- Save the CSV file as a CIF file (. ...
- Upload the CIF file.
A well-established standard file structure for the archiving and distribution of crystallographic information, CIF is in regular use for reporting crystal structure determinations to Acta Crystallographica and other journals.
How do you see what files are being accessed by a program? ›- Open Process Explorer. Running as administrator.
- On the toolbar, find the gunsight icon on the right.
- Drag the icon and drop it on the open file or folder that is locked.
- The executable that is using the file will be highlighted in the Process Explorer main display list.
A CIF can be compared with an essay; both contain information expressed in a language in which rules of syntax link the lexical words whose meaning is defined in a dictionary. Both are also able to convey a wide range of information.
What are the three 3 different types of database structures? ›- hierarchical database systems.
- network database systems.
- object-oriented database systems.
What are the three types of structured data? ›
Graph data structures are used to represent relationships — physical, social, and abstract.
What are the two structural databases? ›The examples of structural database are MMDB,PDB etc.
What's the name of the database of all solved protein structures? ›The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules.
Which database is extensively used for protein structures? ›The Protein Data Bank (PDB) was established in 1971 as the central archive of all experimentally determined protein structure data. Today the PDB is maintained by an international consortia collectively known as the Worldwide Protein Data Bank (wwPDB).
Why do we need structural database? ›INTRODUCTION: • Structural databases are the essential tools for all crystallographic works. They are used in the process of producing, solving ,refining and publishing the structure of a new material.
What is the difference between bioinformatics and structural bioinformatics? ›Structural bioinformatics is the branch of bioinformatics which is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA.
What are the three main structures database systems use to organize data? ›- Hierarchical Structure.
- Network Structure.
- Relational Structure.
Biological databases can be broadly classified as sequence and structure databases. Structure databases are for protein structures, while sequence databases are for nucleic acid and protein sequences.
What is a database used for Computer Science? ›A database is an organized collection of structured information, or data, typically stored electronically in a computer system. A database is usually controlled by a database management system (DBMS).
Where is Cambridge Computer Science? ›The William Gates Building is located on JJ Thomson Avenue at the West Cambridge site.
Who is famous for Computer Science from Cambridge? ›
Alan Turing (King's College, 1934)
In fact, Alan Turing was also a pioneer of theoretical computer science, as well as of artificial intelligence. Nowadays, Turing is one of the most famous alumni of King's College.
Some examples of popular database software or DBMSs include MySQL, Microsoft Access, Microsoft SQL Server, FileMaker Pro, Oracle Database, and dBASE.
What are 5 examples of database in computer? ›MySQL, SQL Server, MongoDB, Oracle Database, PostgreSQL, Informix, Sybase, etc. are all examples of different databases. These modern databases are managed by DBMS. Structured Query Language, or SQL as it is more widely known, is used to operate on the data in a database.
What are the 4 types of database? ›There are four kinds of this database: document databases, key-value stores, column-oriented databases, and graph databases.
Is database important in computer science? ›Databases support good data access because: Large volumes of data can be stored in one place. Multiple users can read and modify the data at the same time. Databases are searchable and sortable, so the data you need can be found quick and easily.
What is special about Computer Science at Cambridge? ›Our course is broad and deep – giving you the skills to create future technology. All aspects of modern computer science are covered, along with the underlying theory and foundations in economics, law and business.
How many people apply for Cambridge Computer Science? ›| BA/MSci Natural Sciences | 3070 |
|---|---|
| MEng Engineering | 2759 |
| MB,BChir Medicine | 2022 |
| BA Law | 1870 |
| BSc Computer Science | 1658 |
Churchill College takes on about 35 NatSci Students every year, meaning it'll be easier to meet subject peers and people with similar interests. Churchill College is also the biggest college for Computer Sciences.
Is Mark Zuckerberg a Computer Science? ›He studied psychology and computer science and belonged to Alpha Epsilon Pi and Kirkland House. In his sophomore year, he wrote a program that he called CourseMatch, which allowed users to make class selection decisions based on the choices of other students and also to help them form study groups.
Did Mark Zuckerberg study Computer Science? ›Mark Zuckerberg, the founder of one of the largest social networking websites, 'Facebook' was originally a Psychology and Computer Science major, but took mostly computer science classes.
Who is the best computer scientists in the world? ›
- Tim Berners-Lee.
- Ray Tomlinson.
- John McCarthy.
- James Gosling.
- Margaret Hamilton.
- Alan Turing.
- Barbara Liskov.
- Ada Lovelace.
- Online encyclopedias (Wikipedia)
- Social media websites (Facebook)
- CRM systems (Salesforce)
- Email systems (Gmail)
- E-commerce websites (Amazon)
Your grocery store, bank, restaurant, online shopping sites, hospital, favorite clothing store and mobile service provider, for instance all use databases to keep track of customer, inventory, employee and accounting information.
What are four real life example of database? ›Dropbox, Google Drive, Microsoft OneDrive, and iCloud are just some examples of personal cloud storage services available to you. All of them use complex data models and powerful data warehouses to ensure your data is stored securely and is available to be called upon at a moment's notice, regardless of where you are.