UCSF Chimera offers 3-D visualization of molecular structures and related data, including density maps, super molecular assemblies, molecular dynamics trajectories, and multiple sequence alignments. The user can also create images and animations for publication and presentation. Besides supporting core visualization, the software is specifically designed for extensibility, to allow outside developers to incorporate new desirable functions. UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. High-quality images and animations can be generated. Chimera includes complete documentation and is free of charge for academic, government, nonprofit, and personal use. Chimera development was supported by the National Institutes of Health.

Advantages

• Rich set of features accessible through both commands and graphical interfaces

• Visualization of molecular data on all scales, including large molecular assemblies

• Integrated sequence and structure views

• Production of high-quality images and movies for publication and presentation

• Designed to accommodate outside development of software extensions

• Broad use for academic and industry researchers, educators, and students

Uses

• automatic identification of atom

• hydrogen addition and partial charge assignment

• high-quality hydrogen bond, contact, and clash detection

• measurements include distances, angles, surface area, volume

• calculation of centroids, axes, planes and associated measurements

• amino acid rotamer libraries, protein Ramachandran plot, protein contact map

• structure building and bond rotation

• molecular dynamics trajectory playback (many formats), distance and angle plots

• morphing between conformations of a protein or even different proteins

• display of attributes (B-factor, hydrophobicity, etc.) with colors, radii

• easy creation of custom attributes with simple text file inputs

• ViewDock tool to facilitate interactive screening of docking results

• rich set of commands, powerful specification syntax

• many formats read, PDB and Mol2 written

• Web and fetch from Protein Data Bank, CATH or SCOP (domains), EDS (density maps), EMDB (density maps), ModBase (comparative models), CASTp (protein pocket measurements), Pub3D (small molecule structures), VIPERdb (icosahedral virus capsids), UniProt (protein sequences with feature annotations)

Working

Loading a structure into Chimera

Two methods can be used to load a structure into Chimera. 1) If the structure file is present in the user's computer, choose the menu item “File/Open”. Then select “name_of_file.pdb” and click “Open”.

The structure might also be fetched from a database, when available. Choose the menu item “File/Fetch by ID”. Choose the PDB databank and type the PDB code “name_of_file”. Then click “Fetch”.

Once the structure has been loaded, all macromolecule's bonds should appear in the “wire” representation, which is Chimera's default.

Moving / zooming

Macromolecule can be rotated by clicking the left button and dragging the cursor over Chimera's window. The translation is obtained similarly, but using the central mouse button.

Most of Chimera functionalities can be accessed by typing a given command in the “Command line”, which is situated at the bottom of the Chimera window. If the command line is not present, display it using “Favorites/Command Line”. A line precededby “Command” will appear on the lower part of the principal window.

Ribbon representation The   secondary   structure   elements   can   be  shown using   the  ribbon   representation.   This   can   be accessed through the “Actions/Ribbon” submenu.

One convenient feature of Chimera is its ability to detach 

submenus so that one can use them many times without the need to go again through the different menus. For instance, choose the “Actions/Ribbon” menu item, and click on the dotted line at the top of this submenu. The submenu will be detached and freely movable.

The ribbon representation of the secondary structure elements can be switched on by choosing “show” in the “Ribbon” menu. Three variants are available: “flat”, “edged” and “rounded”.

The ribbon can be colored according to the secondary structure element, i.e. strand, helix or loop. Open the Model Panel by choosing the “Tools/Depiction/ Color Secondary Structure” menu item. This will open the “Color Secondary Structure” window.