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Table 10.5. Programs for viewing protein molecules
Viewer		Web location		Features
Chime	http://www.umass.edu/microbio/chime/	A Web browser plug-in that can be used to display and manipulate structures inside a Web page. There are many mouse-driven controls. Excellent for lecture presentations.
Cn3da	http://www.ncbi.nlm.nih.gov/Structure/ (Hogue 1997)	Provides viewing of three-dimensional structures from Entrez and MMDB.a Cn3D runs on Windows, MacOS, and UNIX; simultaneously displays structural and sequence alignments; can show multiple superimposed images from NMR studies.
MAGE	http://kinemage.biochem.duke.edu (see Richardson and Richardson 1994)	Standard molecular viewing features with animation and kaleidoscope effects.
Rasmolb	http://www.umass.edu/microbio/rasmol/ (Sayle and Milner-White 1995)	Most commonly used viewer for Windows, MacOS, UNIX, and VMS operating systems. Performs many functions.
Swiss 3D viewer, Spdbv	http://www.expasy.ch/spdbv/mainpage.html (Guex and Peitsch 1997)	Protein models can be built by structural alignments; calculates atomic angles and distances, threading, energy minimation, and interacts with the Swiss Model server.
Additional viewers are accessible from the referenced Web sites. Viewer functions usually include wireframe of Cα backbone, ribbon of secondary structures, space-filling displays, color schemes to illustrate features such as residues, structures, temperature, mouse-drag rotation; several views including stereo and zooming; and exporting to graphic file formats. Assistance with these viewers is provided at the following Web sites for obtaining molecular coordinates: Molecules R Us at NIH, http://molbio.info.nih.gov/cgi-bin/pdb, and NCBI, http://www.ncbi.nlm.nih.gov/Structure/. A large list of available graphics viewers may be found at http://www.csb.yale.edu/userguides/graphics/csb_hm_graph.html.     a The NCBI structure group has established a new format for databases called ASN.1 (see Chapter 2). The PDB files have been converted into this format to create another database MMDB (Molecular Modelling DataBase) that is highly suitable for structural alignments by vector methods described below. Ambiguities in PDB entries have been made explicit in the MMDB database (Hogue and Bryant 1998a,b; http://www.ncbi.nlm.nih.gov/Structure/).     b Rasmol and other viewers as well have many features in the molecular viewing window in addition to those described above. These additional features are accessible through a command line window that appears when the program is running.