Visualization software RasMol

Fig. 7.1 A general overview of the 3D fold of the extracellular region for one of the subunits in the human DPP-IV homodimer. The P-propeller domain is shown myellow whereas the o/(3-hydrolase domain is shown in green. The location of the active site is indicated by the red residues from the catalytic triad (Ser630, Asp708 and His740) and the fluoroolefin inhibitor (m cyan). This figure has been built with the PDB structure with 3C45 code [92] and with the molecular visualization software RasMol [208]...

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... 

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. 

RasMol V http //www.umass.edu/microbio/ rasmol/index2. htm Molecular visualization software. 

Due to the nature of MD simulations, one of the most productive forms of analysis of a simulation is to be able to visualize the trajectory of the molecules of interest. This is particularly useful since experimental techniques are not able to produce visual pictures of atomistic interactions and therefore it is something that only simulations (at this point) are able to provide. In order to visualize a simulation trajectory there are several different very powerful computer packages that are commonly used. These software packages include VMD (2009), PyMol (2010), RasMol (2008), and several others (Free Molecular Visualization Software 2008). O Figure 7-5 shows an example of the type of pictures that can be made using the visualization software. 

Free Molecular Visualization Software. (2008). http //www.umass.eduAnicrobio/rasmol/othersof. htm. Accessed 02 July 2011. 

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. 

Structural visualization Computer graphics is the most effective means for visualization and interactive manipulation of molecules and molecular systems. Numerous software programs (e.g., Cn3D, RasMol and KineMage, Chapter 4) are available for visualization, management, and manipulation of molecular structures. 

Protein explorer is one of the most widely used visualization tools for protein structures. Protein Explorer is free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. Protein explorer is easy to use, free, and widely used. It can be used be novice users as well as experts. The RasMol website has been visited by over 250,000people from 115 countries. 

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