RasMol

Figure C2.5.1. The 3D native stmcture of haemoglobin visualized using RasMol 2.6 [8], The linear sequence of amino acids of haemoglobin is given below tire figure.

Figure C2.5.5. Native stmcture of acyl-coenzyme A binding protein (first NMR stmcture out of 29 deposited to PDB). The figure was created using RasMol 2.6 [8],...

Sayle R and Milner-White E J 1995 Rasmol Biomoleoular graphios for all Trends Biochem. Sci. 20 374-6... 

The temperature factor (together with the Cartesian coordinates) is the result of the rcfincincnt procedure as specified by the REMARK 3 record. High values of the temperature factor suggest cither disorder (the corresponding atom occupied different positions in different molecules in the crystal) or thermal motion (vibration). Many visualisation programs (e.g., RasMol [134] and Chime [155]) have a special color scheme designated to show this property. 

Name/ SymApps ChemBD ACD/3D MraMol Rasmol Molmol JMol chime Ortep III ViewerLite ... 

Name/ version SymApps Chem3D Ultra 7.0 ACD/3D View UltraMol 2003 Rasmol Molmol JMol chime 2.63 Ortep III VieiverLite... 

RasMol is open source and runs on every platform (Windows, Macintosh, UNIX). 

Figure 12 ModBase, a database of comparative protein stracture models. Screenshots of the following ModBase panels are shown A form for searching for the models of a given protein, summary of the search results, summary of the models of a given protein, details about a single model, alignment on which a given model was based, 3D model displayed by RASMOL [237], and a model evaluation by the Prosall profile [217],...

R Sayle, EJ Milner-White. RasMol Biomolecular graphics for all. Trends Biochem Sci 20 374, 1995. 

RasMol A free program that displays molecular strucmre. It is easy to use... 

Visualization software allows the user to display molecular structures imported from databases or other software programs. Chime, RasMol, and Protein Explorer programs are available at the websites listed below for Windows operating PCs and Macintosh PowerPC computers. 

One important technique that users should acquire is the ability to transform two-dimensional stereoviews into three dimensions. The stereoviews may be found in visualization software such as Chime and RasMol. They are also found in journal... 

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB at http //www.rcsb.org/pdb/) is the online source for X-ray and NMR structural data. Many software programs mentioned in Section 3.12 include the facility to visualize imported data however, two free software programs operate well in this regard. These are RasMol and Chime, described below. 

The free RasMol visualization program is available at http //www.umass.edu/ microbio/rasmol/ or http //www.ch.ic.ac.uk/. The latter is the Department of Chemistry site at Imperial College of Science, Technology and Medicine, London. 

Protein Explorer, a free RasMol and Chime derivative with extended capabilities, is available at http //www.umass.edu/microbio/chime/explorer/. The program allows the user to visualize macromolecular structure in relation to function. 

Fig. 2. An example of a complex multidomain protein that includes both domain concatenation and intercalation. (A) See color insert. RASMOL view of phosphotransferase pyruvate kinase (pdb entry lpkn) colored to show the three identifiable domains. Blue is the j3 barrel regulatory domain, orange is an eightfold a/fi barrel, the catalytic substrate binding domain, and green is a central /3, a/(B nucleotide binding domain. Not displayed is the leader subsequence composed of a random coil and short helix. (B) Linear order along the sequence of these components.

Rasmol It was one of the first Protein Databank (PDB) compatible viewers available as freeware. Upgrades have now been stopped, but the program is still widely available. Versions exist for both PC and Mac. 

Protein explorer This program is the expanded version of Rasmol and works very well. It is available at http //proteinexplorer.org and has better mouse control than Rasmol. 

Figure 10.4. The D. vulgaris Rbo dimer (Coehlo et al. 1997). Spheres, iron atoms in centers I and II. The model was generated via RASMOL (Sayle and MUner-White 1995) and coordinates from IDFX in the Protein Databank.

Figure 10.6. Structural features of D. vulgaris Rbr (deMare et al. 1996). A, Rbr subunit with protein backbone and iron atoms (spheres). B, Diiron-oxo site with amino acid side chain ligands. Models generated via RASMOL (Sayle and Milner-White 1995) and coordinates from IRYT in the Protein Databank.

One important visualization technique that users should acquire is the ability to transform two-dimensional stereoviews into three dimensions. The stereoviews may be found in visualization software such as MDL Chime and RasMol.They are also found in journal articles in Science or Nature and others, especially those describing new biomolecule X-ray crystallographic or NMR solution structures. The following hints for learning to transform the stereoviews come from the extremely helpful website http //www.usm.mame. edu/ rhodes/OHelp/StereoView.html. 

At the same time, the power and capabilities of standard PCs increased dramatically. The Richardsons (Richardson and Richardson, 1992) at Duke University developed molecular graphics programs to run on the Macintosh. In a dramatic development, the World Wide Web emerged. Roger Sayle created RasMol as part of his PhD dissertation at Oxford, and made the source code freely available on the web. This program allowed raster display of molecules on UNIX or PCs. The RasMol... 

Sayle, R. and Milner-White, E. J. (1995). RasMol biomolec-ular graphics for all. TIBS 20,374. 

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