WebLab Viewer Lite

From MarcsHomepage

Introduction

WebLabViewer has been a cut-down version of a commercial viewer/editor-program now sold by Accelrys. Apparently Accelrys has discontinued the free version of what has now become DS Viewer Pro. Therefore all further information on this page might be of little use because you can't get the software anymore, there's only a 30-day trial version available (at least I couldn't find anything else on their site).

There will be no further updates to this page.

There is another tool from Accelry, called DS Visualizer, which looks suspiciously like the successor of WebLab Viewer Lite and comes as a freely downloadable binary for Windows and x86 Linux, see DS Visualizer for a review.

If you prefer the old version, there are downloads from third-party sites like http://www.scalacs.org/TeacherResources (thanks to Helmut Esenwein for pointing this out to me).

User Interface

Wlview1.jpg

WebLabViewer was a native Windows-application, it´s interface stuck to the Microsoft Style guide, and it made extensive use of right-button-menu´s and quickhelp. An interesting feature was the hierarchy-window, in which you got a tree-view of all molecules, residues, and atoms in one dataset. You could select certain objects from this list by simply clicking on them (they got highlighted in the viewing-window. No need for a command-language. This approach was quite similar to that of SwissPDBViewer, but imho even a bit more evolved (SwisPDBViewer gives you only a list of residues without a hierarchical structure). The disadvantage of this approach was, that it might be a little bit inflexible, concerning selection of a group of atoms which share some common features but are not connected (like charge or some sort of combined selection (e.g. all alpha-carbons from hydrophobic groups which are buried inside the molecule)). Despite of this small drawback, WebLabViewer provided a very easy-to-use, user-friendly approach for molecule-display. The output could be saved in different formats (molecular datasets or pictures), and you could even generate VRML-output for online-viewing (if you couldn´t use Chime which is light years faster. Unfortunately, a Povray-output-option (or something similar) wasn´t available, so that you had to stick to the quality of the realtime-display (which was quite good, due to the fact, that it used OpenGL for online-rendering). Another disadvantage was the fact that you couldn´t load two independent molecules in one single window (similar to Rasmol which also isn´t able to do this). A very interesting feature was, that you could incorporate WebLabViewer-objects into other Windows-applications as OLE-objects, which means, you could manipulate them from within -let´s say a Word-document. This might have been interesting for tutorials or online-documents based on Windows-technology.

Features

The list of features is more or less similar to that of the two other viewing-packages (Rasmol and Chime), in addition, WebLabViewer could generate and display surfaces and features a very easy to use interface (compared to the command-language used in Rasmol). To me it seems that MSI wanted to release a product to show it´s abilities in molecular modelling without giving too much for free, otherwise I can not understand why some of the limitations (only one molecule, no manipulation-options) are there. It´s a nice program though.

Contrary to that Accelrys seems to be confident, that people buy their commercial-only software and have discontinued their free edition of DS Viewer. There's a 30-day trail version for download on their site though.

Below you will find a complete list of features, derived from MSI´s 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.
  • Select using lasso and box.
  • Context sensitive selection of amino acid and amino acid chain.
  • Context sensitive property listing of selection.
  • Create named groups of atoms.