Transcript Crystallography Databases John C. Huffman IUMSC Crystallography Databases Data content Database availability Limitations Graphics and other “viewers”

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)
–
Crystallography Databases
Spectral
databases
JCPDS
– NIST
–
Crystallography Databases
Complete crystallographic analysis leads
to 3-dimensional structural data
Crystallography Databases
Coordinate
Systems
Crystallographic vs. Cartesian coordinates
Crystallographic Coordinates
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.
Crystallography Databases
Available Databases
–PDB
–ICSD
–CSD
–Metals Database
Protein Database (PDB)
http://www.rcsb.org/pdb/
Contains 16,433 Structures
Last Update: 30-Oct-2001
PDB
PDB
One Moment
Please………….
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
ICSD
ICSD
ICSD
ICSD
ICSD
ICSD
ICSD
ICSD
ICSD
ICSD
ICSD
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.
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-andstick, space filling, etc.)