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Crystallography Databases. John C. Huffman IUMSC. Crystallography Databases. Data content Database availability Limitations Graphics and other “viewers”. Crystallography Databases. Spectral databases Contain information on crystal properties (cell size, symmetry).

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Crystallography Databases

John C. Huffman

IUMSC


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Crystallography Databases

Data content

Database availability

Limitations

Graphics and other “viewers”


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Crystallography Databases

Spectral databases

Contain information on crystal properties (cell size, symmetry)


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Crystallography Databases

Spectral databases

JCPDS

NIST


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Crystallography Databases

Complete crystallographic analysis leads to 3-dimensional structural data


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Crystallography Databases

Coordinate Systems

Crystallographic vs. Cartesian coordinates



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Cartesian Coordinates

Cartesian coordinates in Angstroms, usually with first atom at 0,0,0; second atom at x,0,0, and third atom at x,y,0.


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Crystallography Databases

Available Databases

PDB

ICSD

CSD

Metals Database


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Protein Database (PDB)

http://www.rcsb.org/pdb/

Contains 16,433 Structures

Last Update: 30-Oct-2001





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ICSD

FIZ Karlsruhe

P.O. Box 2465

76012 Karlsruhe

Phone: (+49 7247) 808 555

Fax: (+49 7247) 808 131

Email: [email protected]

in cooperation with :

The National Institute of Standards and Technology

Gaithersburg, MD 20899













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ICSD

PDB formats can be viewed with a variety of viewers. CIF format viewers are being developed.

RasMol is one of the best viewers readily available at no charge.


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Suggested Exercises

Using a search engine, locate the “trial” version of the ICSD. Download and look for several simple structures.

Locate the PDB and look up snake toxins whose structures have been determined by X-ray crystallography. Save on or more of the .pdb files.

Download RasMol and use it to prepare figures of the snake toxins in a variety of formats (ball-and-stick, space filling, etc.)


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