Marvin and MarvinSpace Developer's Guide

Version 4.1.1

MarvinSketch

  1. Parameters
    1. Applet only parameters

MarvinView

  1. Parameters
    1. Applet only parameters
    2. 3D and animation
    3. Molecule tables
      1. layoutn
      2. paramn
      3. celln
  2. Troubleshooting - MView and JMView tables

MarvinSpace

Marvin General documentation

Marvin Sketch/View Applets

Platform dependence

MarvinSketch Applet Examples

  1. Simple sketcher
    1. The <applet> tag; preparing for different browsers; the ARCHIVE option
    2. Colors
    3. Alternative look
    4. My Templates
  2. Query atoms, extra bond types, disallowing elements, extra templates
  3. Visualization, loading molecules
    1. Loading a molecule and starting in visualization mode; the magnification
    2. Inline, compressed molfiles
    3. Triggering molfile download from JavaScript, naming the applet
    4. Import/export of built-in and user defined molecule formats in JavaScript; preloading modules
    5. Pure visualization mode; detaching the sketcher from the web page
    6. Opening a sketcher window from visualization mode
  4. Workaround for browsers without Java - JavaScript communication
    1. Retrieve a structure
    2. Import/export a structure

MarvinSpace Applet Examples

  1. Draw types in MarvinSpace illustrated with NAPAP
  2. Draw types and Color types in MarvinSpace illustrated with HLA
  3. Multiple view and control of a protein with 4 cells

MarvinView Applet Examples

  1. Viewing a molecule
    1. The <applet> tag
    2. Compression, color, magnification, atom size, hydrogen labels
  2. Molecule tables
    1. Making a molecule table
    2. Labels, buttons, images, scrolling, header row
    3. Fine-tuning the layout
    4. Checkboxes, JavaScripting, CGI scripting
    5. Background colors, 3D, rotation
    6. Displaying an SD file
  3. 3D viewer
    1. Viewing a 3D molecule
    2. XYZ animations
  4. Editable table, selection, templates
  5. Changing contents, selecting atoms
  6. Coloring atom and bond sets
  7. Visualizing configurations

 

Some applications developed by our users

User's Guide

 

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