KinImmerse 0.5 – Translate Kinemage Files into Software for Virtual Environment

KinImmerse 0.5

:: DESCRIPTION

KinImmerse translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE.

In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Linux

:: DOWNLOAD

KinImmerse

:: MORE INFORMATION

For a detailed description see KinImmerse: Macromolecular VR for NMR ensembles.

KinImmerse is free software available under the terms of its own BSD-style license.

Prekin 6.51 – Prepares Kinemages Files from PDB-format Files

Prekin 6.51

:: DESCRIPTION

Prekin prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files, using either a choice of built-in scripts or a flexible user specification of options. Prekin can be run in either an interactive mode with option selection from dialog panes; or, it can be run in command-line fashion with all options specified at program invocation.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

Prekin

:: MORE INFORMATION

Prekin is free software available under the terms of its own BSD-style license.

Mage 6.47 – Kinemage File 3D Display

Mage 6.47

:: DESCRIPTION

Mage is a 3D vector display program which shows “kinemage” graphics. Used in both teaching and research, in applications ranging from estuary ecology to X-ray crystallography model quality assessments, Mage displays the 3D relationships between data in an interactive environment which facilitates both open-ended exploration and structured presentation. It includes many tools for on-screen measurement, construction, and editing of the display objects; it can write either kinemage output or various types of 2D image output.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux / Silicon Graphics

:: DOWNLOAD

  Mage

:: MORE INFORMATION

Mage is free software available under the terms of its own BSD-style license.

PovChem 2.1.1 – Chemical Visualization & Illustration & POV File Converter

PovChem 2.1.1

:: DESCRIPTION

PovChem is a chemical visualization and illustration program with a new graphic interface. It takes molecules in the PDB format, lets you to set up a picture with fine control over details of the illustration – colors, atom and bond radii, view orientation, etc. It will even calculate and display hydrogen bonds.

PovChem can export the picture in POV-Ray format, which allows you to render the image with a state-of-the-art raytracer, giving high-quality images at any resolution, for anything from web page thumbnails to full-size high-resolution images for journal covers, advertisements, posters, anything!

::DEVELOPER

Paul A. Thiessen

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PovChem

:: MORE INFORMATION

PovChem is now free!Use this key to register your copy of PovChem:
APyUrblJnYZr

WPDB 2.2 – The Protein Data Bank Through Windows

WPDB 2.2

:: DESCRIPTION

WPDB is a Microsoft Windows based program for browsing and interrogating native and derived structural features of biological macromolecules using data obtained from the Protein Data Bank (PDB). Major features of WPDB are a 20-fold compression of PDB files and query and analysis tools. The latter permit the geometric and sequence properties of structures to be analyzed individually or through comparative analysis. The object oriented software design provides a high level of interaction between display windows which facilitates information discovery.

WPDB is useful for detailed analysis of a single structure or comparative analysis of two or more structures. It comes with a variety of databases. Alternatively, you can build your own database from PDB files with the WPDB Loader (WPDBL).

WPDBL Used to build a WPDB database from PDB files for access by the WPDB program. Prebuilt databases of a complete PDB distribution are available already built in the ../ directory.

::DEVELOPER

Ilya Shindyalov and Phil Bourne

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

WPDB ; WPDBL

:: MORE INFORMATION

Those using WPDB should cite:
I.N.Shindyalov and P.E.Bourne J. App. Cryst. 1995, 28(6) 847-852. WPDB A PC-based Tool for Analyzing Protein Structure. [Postscript]

ANTHEPROT 3D 1.0.162- Molecule Viewer to look at PDB files

ANTHEPROT 3D 1.0.162

:: DESCRIPTION

Antheprot 3D is a molecular graphics program intended for the visualisation of proteins, nucleic acids from RCSB archive. The program is aimed at display, teaching and generation of publication quality images.

The program reads in a molecule coordinate file (PDB format) and interactively displays the molecule on the screen in a variety of color schemes and molecule representations. Currently available representations include wireframes, sticks, spheres, ball and stick, atom labels and distances. PDB files that are available either locally (Ctrl+O or File=>Open) or distantly at “POLE Bioinformatique Lyonnais” (Ctrl+I) or File=> PBIL URL can be loaded directly into AntheProt3D.

The program is made of 3 different windows:

  • A 3D view window which allows the user to interactively move the molecule
  • A group selection panel for group selection
  • A text window for provinding the user the list of clicked atoms, information (F2) and PHI, PSI values

A Ramachandran interactive plot is also available

Features

  • Alpha trace, wireframe, space filled,Balla nd Sticks, Sticks and surface mode.
  • Full support of clipping (“molecule slicing”)
  • Full support of stereo (side by side, anaglyph or quad buffer stereo)
  • Interactive Ramachandran plot
  • Hydrogen addition or removal by reduce
  • Selection of amino acids by group, chain or within a sphere
  • Surface viewer for MSMS files (Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996).Biopolymers, 38 (3), 305-320.
  • Ribbon or cylinder mode from Molscript program (P. J. Kraulis, (1991) Journal of Applied Crystallography 24, pp 946-950.)
  • Support for Delphi electrostatic potential Rocchia, W.; Alexov, E.; Honig, B. (2001) J Phys. Chem. 105, 6507-6514

::DEVELOPER

Pr Gilbert Deléage at France Institute of Biology and Chemistry of Proteins

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ANTHEPROT 3D 1.0.162

:: MORE INFORMATION

ANTHEPROT3D album

If you use ANTHEPROT on PC, please cite one of the following references :

Deleage G, Combet C, Blanchet C, Geourjon, C
ANTHEPROT: An integrated protein sequence analysis software with client/server capabilities?
(2001) COMPUTERS IN BIOLOGY AND MEDICINE 31 (4): 259-267

Chemis3D 2.89b – Java 3D Molecular Viewer Applet

Chemis3D 2.89b

:: DESCRIPTION

Chemis3D is a Java Applet which renders virtual 3D molecular models within a Web document. It is specially designed for open interactive molecular visualization on the Internet or via an intranet. Molecular structures can be manipulated in real-time and rendered in various styles and appearances.

Chemis3D is a small applet running well on any Java-enabled browser and requiring no specialized plug-in nor professional applications.

Features

  • Real-time manipulation and fast 3D rendering.
  • Wide variety of molecular representations including special styles and color coding schemes for proteins and nucleic acids .
  • Enhanced interface using popumenu and key shortcuts .
  • Multi-models display and molecular animation capabilities.
  • Measuring and analysing tools.
  • Support of the most popular molecular data formats :Brookhaven Protein DataBank (*.pdb).MSC XMol files (*.xyz).MDL molfiles (*.mol).

::DEVELOPER

Didier COLLOMB

:: SCREENSHOTS

:: REQUIREMENTS

  • Java-enabled browser

:: DOWNLOAD

Chemis3D 2.89b

:: MORE INFORMATION

Chemis3D MAY BE FREELY USED FOR PERSONNAL, ACADEMIC AND NON-COMMERCIAL PURPOSES, IN AGREEMENT WITH THE FOLLOWING RESTRICTIONS.

RasTop 2.2 – Molecular Visualization Software Adapted for Rasmol

RasTop 2.2

:: DESCRIPTION

RasTop is a molecular visualization software adapted from the program RasMol, which was initially developed by Roger Sayle. RasTop is particularly adapted for educational purposes and for the rapid analysis of macromolecules at the bench.  RasTop wraps a user-friendly graphical interface around the “RasMol molecular engine”. There is no need to type on the command line; each command in the menu generates its own script. Through an extended menu and a command panel, users can manipulate numerous molecules rapidly and learn about them. Work sessions are saved in script format and are fully regenerated with a simple mouse click.

::DEVELOPER

Philippe Valadon

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Linux with Wine
  • Mac with Virtual PC

:: DOWNLOAD

RasTop 2.2Version Francaise

:: MORE INFORMATION

RasTop 2.2 is distributed both under the GPL license ad the Rasmol license.  Certain conditions apply to users and to developers to ensure that RasTop remain open source. Please, consult the license.txt and raslic.txt file in the package.