Chimera is the sucessor of MidasPlus, but is a completely new design. Chimera is available for Unix and Windows.
Compared with Pymol, Chimera has a larger feature-set, and a better integrated GUI but as many other programs mentioned here, is only free for academic and non-profit use.
The GUI, which apparently has been written in Tk, consists of a single large window with a pulldown-menu, from which the user can access submenus and non-modal dialogues to interact with the program and several plugins and wrappers for external tools (see below).
Maybe it is me, but I found the selection-principle of Chimera a bit counter-intuitive (still nothing beats Rasmol), but probable one simply has to get used to it.
There are better sollutions for this, like in WebLab Viewer Lite.
On the other hand, Chimera has a nice plugin-interface, which allows extending the annalysis, display and editing capabilities of Chimera with external programs (see below).
Taken from the Chimera-homepage
- Advanced Display
- ** solid and mesh surfaces
- stick, ball-and-stick, CPK, and ribbon representations that can be combined with surfaces
- interactive rotatability of all display types
- interactive color editing in various color spaces (RGB, CMYK, etc.) including transparency
- movable lenses in which the display differs from the surroundings
- ability to save high-resolution image files for presentation and publication
- Basic Manipulations
- ** highly intuitive translation, scaling, and "spaceball" rotation with the mouse
- Side View tool for adjusting clipping planes and scaling
- significant functionality available through menus
- a rich set of commands, including most of those used in Midas and several new commands
- easy specification of entire chains and handling of multiple models within a single PDB file
- Chemical Knowledge
- ** determination of atom types in arbitrary molecules (not just standard residues)
- selection of atoms and bonds for further operations according to element, atom type, functional group, and amino acid category
- hydrogen addition
- hydrogen bond identification
- ** full online manuals: User's Guide and Programmer's Guide
- extensive help, both "balloon" help and display of HTML manual pages
- Extensions: Some Examples
- ** viewing 3D data sets as solid or mesh contours or transparent solids (Volume Viewer)
- protein structural superposition (MinRMS and AlignPlot)
- viewing multiple sequence alignments along with structural alignments ( Multalign Viewer and MSF Viewer)
- convenient examination of docked molecules output by DOCK (ViewDock)
- capability for sharing modeling sessions among distant researchers