DS Visualizer

From MarcsHomepage

Introduction

DS (Discovery Studio) Visualizer is a cut-down version of a commercial viewer/editor-program sold by Accelrys. DS Viewer comes as a Windows or Linux binary and the Windows version can also be downloaded as an ActiveX control usable for integration into other programs.

To download the binary you have to register at the Accelrys Website.

User Interface

Dsview1.jpg

DS Visualizer is a Windows app, which has been ported to Linux, it´s interface sticks to the Microsoft Style guide, and it makes extensive use of right-button-menu´s and quickhelp.

Contrary to the older WebLab Viewer, DS Visualizer has a pane-and-tab interface with an explorer like tree view on the left side and a graphics window on the right side. The tree view can be used to browse projects and directories and history of opened documents. It is also possible to activate further panes which -like in WebLab Viewer- allow browsing of a tree representation of the loaded structure and to show a data table with further annotations, which is a very usefull feature of the program.

Features

Below you will find a complete list of features, derived from Accelrys web page

Building/Sketching Molecules

  • Manipulate atom coordinates.
  • Manipulate torsions.
  • Automatically add/remove hydrogens.

File Import and Export

  • Import PDB (pdb, ent), MDL (mol/sd), Insight II (car), CSD(csd, fdat), Sybyl (mol2), Quanta (msf), Cerius 2 (msi), Catalyst (cpd), XYZ, ISIS (skc).
  • Convert 2D sketches (ISISDraw and ChemDraw) to 3D upon import.
  • Automatically add Hydrogens upon import.
  • Calculate charges on import.
  • Display crystal unit cells upon import.
  • Automatically assign secondary structure from pdb files.
  • Export MDL (mol, sd), PDB (pdb), VRML, JPEG, GIF.
  • Print to standard printers.

Display Options

  • Utilize high resolution GL graphics.
  • Display molecules using Stick, Ball and Stick CPK and Polyhedron styles.
  • Rotate using track ball and track surface rotation.
  • Speed up manipulation through fast rendering when moving.
  • Display models full screen.
  • Continuously spin the molecule.
  • Display side-by-side stereo molecules.
  • Display in orthographic or perspective projection.
  • Color molecules by properties - element, parent color, charge.

Internet and Data Communications

  • Cut and paste from ChemDraw.
  • Cut and paste from IsisDraw.
  • Utilize Active Document Support.
  • Utilize OLE2 to embed molecules within documents from other desktop applica-tions.
  • Configure WebLab ViewerPro as helper application.
  • Open files using http and ftp protocols.

Computation Features

  • Monitor distances, angles, and torsions.
  • Monitor hydrogen bonds and bumps -contacts between non-bonded atoms.
  • Label chirality.
  • Assign partial and formal charges.
  • Permit manual editing/assignment of partial and formal charge.
  • Calculate volumes.
  • Compute surface areas.

Surface Display

  • Display soft surfaces.
  • Display solvent accessible surfaces.

Crystal Cells

  • Visualize organic and inorganic crystal structures in a variety of display styles.

Protein Structures

  • Display proteins using C-alpha Wire, C-alpha stick, Line Ribbon, Flat Ribbon, Solid Ribbon, Tube and Schematic display styles.
  • Color by Amino Acid, Amino Acid chain, pKa, hydrophobicity, secondary type.

Annotation

  • Label molecules, atoms and bonds.
  • Assign font and color properties to annotations.

Selection Features

  • Select cells, amino acids, atoms and bonds.
  • Context sensitive selection of amino acid and amino acid chain.
  • Context sensitive property listing of selection.
  • Create named groups of atoms.