What is the website for compound structure?

3D model

The Model menu contains some general functions for the 3D model.

Reset

This function sets the model position, zoom and rotation back to default.

Representation

You can choose from a list of different molecule representations including; ball and stick, stick, van der Waals spheres, wireframe and lines. Macromolecules are automatically drawn using ribbons.

Background

You can switch between a black, gray or white background. The default background is black (exported images from GLmol or ChemDoodle have a transparent background)

Engines

You can choose from three different render engines: GLmol, Jmol and ChemDoodle. GLmol is used as default render engine. GLmol and ChemDoodle are based on WebGL, a browser technology to support 3D graphics. If WebGL is not available in your browser, Jmol will be used for all rendering.

MolView automatically switches to:

1. Jmol if you execute functions from the Jmol menu
2. GLmol if you load macromolecules (due to significant higher performance)
3. ChemDoodle if you load a crystal structure (GLmol cannot render crystal structures)

You might want to switch back to GLmol when you do no longer need Jmol or ChemDoodle since GLmol has a better performance.

Note that macromolecules are drawn slightly different in each engine. ChemDoodle provides the finest display. You should, however, avoid using ChemDoodle for very large macromolecules.

Model transformation

You can rotate, pan and zoom the 3D model. Use the right button for rotation, the middle button for translation (except for ChemDoodle) and the scrollwheel for zooming. On touch devices, you can rotate the model with one finger and scale the model using two fingers.

Crystallography

You can load an array of crystal cells (2x2x2 or 1x3x3) or a single unit cell when viewing crystal structures.

Fog and clipping

When you are viewing large structures, like proteins, it can be useful to hide a certain part using fog or a clipping plane. GLmol offers a few options to do this.

1. Fog: you can move the fog forward by dragging the mouse up while holding CTRL + SHIFT (drag in the opposite direction to move the fog backward)
2. Clipping plane: you can move a frontal clipping plane into the structure by dragging the mouse to the left while holding CTRL + SHIFT (drag in the opposite direction to move the clipping plane back)

We are working on a new version of ChemSpider – if you want to try the new interface go to

– if you want to try the new interface go to beta.chemspider