Protein Data Bank and RasMol.

The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are freely accessible on the internet. The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.

The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as the NIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. For example, both SCOP and CATH categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.
To know more about PDB, have a stop at PDB.

Lexa on RasMol

RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 90s.

Historically, it was an important tool for molecular biologists since the extremely optimized program allowed the software to run on (then) modestly powerful personal computers. Before RasMol, visualization software ran on graphics workstations that, due to their expense, were less accessible to scholars. RasMol has become an important educational tool as well as continuing to be an important tool for research in structural biology.

RasMol has a complex version history. Starting with the series of 2.7 versions, RasMol is licensed under a dual license (GPL or custom licenseRASLIC).

RasMol includes a language (for selecting certain protein chains, or changing colors etc). Jmol and Sirius has incorporated the RasMol scripting language into its commands.

Protein Databank (PDB) files can be downloaded for visualization from the Research Collaboratory for Structural Bioinformatics (RCSB) bank. These have been uploaded by researchers who have characterized the structure of molecules usually by X-ray crystallography or NMR spectroscopy.

For more information on RasMol, please visit RasMol.

RasMol Version and its Features.

Version	Features
RasMol 2.7.1	The ability to automatically mark non bonded atoms in wireframe and stick displays. The ability to use a proportionally spaced font and to draw labels with heavier strokes.  The ability to auto-recognize PDB vs. CIF and mmCIF datasets. Extensive updating to the manual. Updating the canvas title with the PDB ID code and EXPDTA information, so models will be clearly distinguished from experimental data. The ability to report coordinates. Additions to the list of pre-defined colours. Improved accuracy of coordinates in pseudo-PDB output. Fixes to the centring logic.
RasMol 2.7.1.1	Introduction of a multilingual structure for RasMol. Population of messages and menu lists for English and Spanish. Upgrade of some of the Windows printer logic. Correction of coordinate handling for Mol2 and XYZ coordinates. Fix to the parsing of D2O.
RasMol 2.7.2	RasMol may have difficulty in allocating colours for molecules after the first. The fix for this interacts with some other pending changes, and should be ready for the next release. As has been true for all recent versions, the stereo mode defaults to cross-eyed, which is inconvenient for many users. Printing under windows is not working for many modern systems.  The fixes for several of the bugs reported against RasMol 2.7.1 have not been incorporated into RasMol 2.7.2 yet.
RasMol 2.7.2.1	Adaption of the multilingual mods from RasMol 2.7.1.1 into Rasmol 2.7.2.1. Rewrite of the mouse handling and rotation logic to correct the problems in 2.7.2 and make the feel of 2.7.2.1 closer to that of RasMol 2.7.1. Addition of French menus and messages. Addition of Italian menus and messages. Adoption of picking for selection of atoms, groups or chains from RasTop 1.3. Adoption of backclipping from RasTop 1.3. Adoption of shadepower command for glassy surfaces from RasTop 1.3 Change of the menu stereo option to rotate cross-wall-none Allow longer atom names (12 characters) in CIFs.
RasMol 2.7.3	Adjustment to the mouse handling for a better, more natural feel. Our thanks to C. Chigbo for the suggestion. Correction to cif.c for blanks after an initial quote mark.  Correction to mswin31.c to restore lost initializations of ZRange and DialValue[8..9].  Correction to vector.c for nested bond rotations. Modifications by Mamoru Yamanishi to Imakefile and rasmol.c to use xforms for GUI file open. This patch needs the opens source xforms 1.0.90 library by Steve Lamont. Correction to molecule.c to correct input of xyz files. Revision to CPK colors by C. Chigbo. The new colors are called CPKNEW. The current CPK colors remain available as CPK.  Correction to negative torsion angle monitors and to imprecise distance and angle monitors by C. Chigbo.  This patch corrects the display of negative torsion angles caused by use of the unsigned short type, and correctys imprecise distance and angle displays. This extends the original patch which was just for torsion angles (torsion.patch). A side effect of this change is to limit the available range for distance monitors to approximately 327 Ångstroms. Initial code for display of solid Lee-Richards molecular surfaces. This patch adds the basic code for display of Lee-Richards surfaces with a new Molecular Surface menu item, and surface molecule <probe radius> and surface solvent <probe radius> commands. Two other, related, major patches are pending that depend upon this one: code by P. Zhivkov to simulate surfaces efficiently by blurring and code to display surfaces using OpenGL. Corrections of ribbons 0, etc. commands by R. Chachra. With this patch, the wireframe 0, ribbon 0, cartoon 0, backbone 0, strands 0 and trace 0 commands work the same as these command with off instead of 0.
RasMol 2.7.4	Extended language support. Messages and menus in Bulgarian, Chinese, English, Italian, Japanese, Russian and Spanish are now supported on systems with appropriate fonts. Support for maps. On systems with sufficient memory, RasMol now can read maps in CCP4 and CBF map formats and can write maps in CBF map format. Maps of density from pseudo-Gaussian atoms can be generated. Support is provided for generation of surfaces for SAXS bead models. An MS windows installer was proposed by G. A. Pozhvanov, and reimplemented on the open source base of NSIS-2.21. A unix installer script, rasmol_install.sh, and a matching script to select an appropropriate binary version to run under unix, rasmol_run.sh have been added by H. J. Bernstein.