Rasmol and Swiss-PDB viewer are molecular visualization tools that allow users to view and analyze protein structures. Rasmol can display molecules in various representations like wireframe, cylinders, or ribbons. It supports common file formats like PDB and can rotate, zoom, and translate structures. Swiss-PDB viewer is tightly integrated with homology modeling and allows users to build models, compare structures, and view electron density maps. It utilizes template structures from the PDB to generate models and assess their quality. Both tools provide publication-quality images and interactive visualization of biomolecular structures.

1. Introduction:
 The software used to examine and display structure information of biomolecules like
amino acids and protein are called structure visualization tools.
Examples: pyMOL, RasMol, Ribbons, Swiss-PDB viewer etc.
Rasmol
 Rasmol is a Protein structure visualization tool.
 This site was established in mid-September 2000 to provide a home for developers of
Open Source versions of RasMol.
 RasMol is an important scientific tool for visualisation of molecules created by Roger
Sayle in 1992. RasMol is used by hundreds of thousands of users world-wide to view
macromolecules and to prepare publication-quality images.
 RasMol is a molecular graphics program proposed for the visualization of proteins,
nucleic acids and small molecules.
 The program is aimed at display, teaching and generation of publication quality images.
 The program reads in molecular coordinate files and interactively displays the molecule
on the screen in a variety of representations and colour schemes.
 RasMol runs on wide range of architectures and operating systems including Microsoft
Windows, Apple Macintosh, UNIX and VMS systems.
Supported input file formats:
 Protein Data Bank (PDB)
 Mol2 formats
 Molecular Design Limited's (MDL) Mol file format
 Minnesota Supercomputer Center's (MSC) XYZ (XMol) format
 CHARMm format CIF format and mmCIF format files.
The loaded molecule (or Results) can be shown as:
 Wireframe bonds
 Cylinder 'dreiding' stick bonds
 Alpha-carbon trace
 Space-filling (CPK) spheres
 Macromolecular ribbons (either smooth shaded solid ribbons or parallel strands)
 Hydrogen bonding
 Dot surface representations.
 Atoms may also be labelled with uninformed text strings.

2.  Alternate conformers and multiple NMR models may be specially coloured and
identified in atom labels.
 Different parts of the molecule may be represented and coloured independently of
the rest of the molecule or displayed in several representations simultaneously.
 The displayed molecule may be rotated, translated, zoomed and z-clipped (slabbed)
interactively using either the mouse, the scroll bars, the command line or an
attached dial box.
 RasMol can read a prepared list of commands from a 'script' file (or via inter-process
communication) to allow a given image or viewpoint to be restored quickly.
 RasMol can also create a script file containing the commands required to regenerate the
current image.
 Finally, the purified image may be written out in a variety of formats including either
raster or vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a
MolScript input script or Kinemage.
 This software is freely available.Download
link: http://www.openrasmol.org/#Software
RasMol Features:
 The ability to automatically mark non bonded atoms in wireframe and stick displays.
 The ability to report coordinates.

3.  Additions to the list of pre-defined colours.
 Improved accuracy of coordinates in pseudo-PDB output.
 Updating the picture title with the PDB ID code and EXPDTA information, so models
will be clearly distinguished from experimental data.
 Introduction of a multilingual structure for RasMol.
 Population of messages and menu lists for English and Spanish.
 Correction of coordinate handling for Mol2 and XYZ coordinates
 An attempt to fix some of the chirality reversals in some of the output modes.
Swiss-PdbViewer
SWISS-MODEL is a structural bioinformatics web-server dedicated to homology modeling of
protein 3D structures. Swiss-PdbViewer has been developed since 1994 by Nicolas Guex.
 Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology
modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the
Structural Bioinformatics Group at the Biozentrum in Basel.
 Swiss-PdbViewer is an application that provides a user friendly interface allowing to
analyze several proteins.
 The proteins can be superimposed in order to deduce structural alignments
 It is used to compare their active sites or any other relevant parts.
 Amino acid mutations, H-bonds, angles and distances between atoms are easy to
visualize.
 Swiss-PdbViewer can also read electron density maps, and provides various tools to
build into the density.
 Various modeling tools are integrated and residues can be mutated.

4. Homology modeling is currently the most accurate method to generate reliable three-
dimensional protein structure models.
Homology (or comparative) modelling methods make use of experimental protein structures
("templates") to build models for evolutionary related proteins ("targets").
Today, SWISS-MODEL consists of three tightly integrated components:
(1) The SWISS-MODEL pipeline - a suite of software tools and databases for automated
protein structure modelling
(2) The SWISS-MODEL Workspace - a web-based graphical user workbench,
(3) The SWISS-MODEL Repository - a continuously updated database of homology models
for a set of model organism proteomes of high biomedical interest.
The Pipeline
SWISS-MODEL pipeline comprises the four main steps that are involved in building a
homology model of a given protein structure:
 Identification of structural template(s). BLAST and HHblits are used to identify
templates.
 The templates are stored in the SWISS-MODEL Template Library (SMTL), which is
derived from PDB.
 Alignment of target sequence and template structure(s).
 Model building and energy minimization.
 Assessment of the model's quality using QMEAN, a statistical potential of mean force.
The Workspace
.In this mode the input is a project file that can be generated by the DeepView (Swiss Pdb
Viewer) visualization and structural analysis tool, to allow the user to examine and manipulate
the target-template alignment in its structural context.
In all three cases the output is a PDB file with atom coordinates of the model or a DeepView
project file.
The four main steps of homology modelling may be repeated iteratively until a satisfactory
model is achieved.
The SWISS-MODEL Workspace is accessible via the ExPASy web server, or it can be used as
part of the program DeepView (Swiss Pdb-Viewer).
The Repository:
The SWISS-MODEL Repository provides access to an up-to-date collection of annotated
three-dimensional protein models for a set of model organisms of high general interest. SWISS-
MODEL Repository is integrated with several external resources, such as UniProt, InterPro,
STRING, and Nature PSI SBKB.
New developments of the SWISS-MODEL expert system feature
(1) automated modelling of homo-oligomeric assemblies

5. (2) modelling of essential metal ions and biologically relevant ligands in protein structures
(3) local (per-residue) model reliability estimates based on the QMEAN local score function
(4) mapping of UniProt features to models.