Tag: Molecule

Kin2Dcont 1.8 & Kin3Dcont 1.12 – Produce Molecule Contour Map

Kin2Dcont 1.8 & Kin3Dcont 1.12

:: DESCRIPTION

Kin2Dcont and Kin3Dcont read value/coordinate lists to produce contour maps in kinemage format. Both scattered data and uniformly sampled data can be contoured. Kin2Dcont can also be used to produce contours in PostScript format.

They are used to generate 2D or 3D contour maps in kinemage format. The programs kin2Dcont and kin3Dcont produce contour plots from tables of values and their 2-D or 3-D coordinates. If the data is scattered in space, the programs can smooth it and produce what is essentially a histogram in two or three dimensions. Evenly sampled data values can also be contoured, as well as data which is periodic, for example when the dimensions are angles with 360 deg the same as 0 deg.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux/ MacOsX/SGI-irix/Sun-SPARC

:: DOWNLOAD

Kin2Dcont  & Kin3Dcont

:: MORE INFORMATION

Citation:

A Decomposable Algorithm for Contour Surface Display Generation, Michael J. Zyda, ACM Transactions on Graphics, Vol. 7, No. 2, April 1988, Pages 129-148.

Kin2Dcont  & Kin3Dcont are free softwares available under the terms of its own BSD-style license.

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