Tutorial: Using Custom 3D Views for Showing Multiple Properties

Custom 3D views can be a powerful tool for showing different molecular properties on one picture. For example, we want to show molecular structure, its HOMO, LUMO and electrostatic potential. Instead of creating four separate pictures we shall include all properties in one 3D object.

First, we load corresponding Gaussian cubes in Jamberoo and create isosurfaces for the HOMO, LUMO and electrostatic potential of paddlane and then save molecular scene in VRML format.

Import VRML file into Adobe Acrobat

Our first (default) view will show only molecule without isosurfaces.

First, we toggle Model Tree.

The Model Tree appears in the navigation pane on the left side of the work area.

The Model Tree has three panes, each of which displays a specific type of information or controls. The topmost pane shows the tree structure of the 3D object. In our case, a 3D object depicting the molecular scene has separate groups of objects (called nodes) for the atoms, bonds, and isosurfaces.

In this pane, we can move through the hierarchy and select, isolate, or hide various parts. So, first we deselect all nodes for isosurfaces

and create the first view which shows only molecular structure

We shall make this view as a default one. To do so we select "Manage Views..." in Views Combo-box

and make our view as a default one in Manage Views dialog

Now we shall create three more views for electrostatic potential, HOMO and LUMO, correspondingly. Also, we shall make isosurfaces transparent (select corresponding node, right-button mouse click to activate a popup menu, and select Transparent).

Name each view

So, finally we have the following views

Now after activation of the 3D object in Acrobat Viewer the default view will be shown

after activation ->

What we don't like probably is the default 2D preview generated by Acrobat for our 3D object, so we substitute it with our own 2D picture (so-called poster image).

Creating Poster Image

First, we prepare our poster image in favorite graphics editor:

Original image is here

To replace the default 2D view with our poster image choose Select Object tool in the toolbar

select 3D object, right-button mouse click to activate a popup menu and select Properties

In Edit 3D dialog select Create poster from file radio-button and browse poster file

Now our poster image will be shown when 3D model isn’t activated.

The final 3D PDF document is here

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Send all questions, suggestions and comments to Vlad (vvv900@gmail.com)

Dr. Vladislav Vasilyev

Supercomputer Facility,

The Australian National University,

Canberra, ACT, 0200, Australia