Chimera

From MarcsHomepage

Introduction

Chimera is the sucessor of MidasPlus, but is a completely new design. Chimera is available for Unix and Windows.

Like Pymol it uses Python as it's extension-language, which makes it very easy to program.

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.

User Interface

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.

Another feature is the overwhelming amount of popup-windows, which like in VMD and XTalView tend to clutter the desktop a lot.

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).

Chimera also integrates a complete Python-environment complete with Idle for editing scripts.

Features

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
• Documentation
• ** 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