How to Show a Molecule using FirstGlance in Jmol
from Your Website

How Specify a PDB Identification Code in a Hyperlink to FirstGlance

This help is for people who already know how to make a web page that includes hyperlinks.

Specify the PDB identification code in place of 1d66 in this example:

<a href="" target=_blank>View 1d66</a>
Try it: View 1d66

Using target=_blank is strongly recommended because it opens a new window or tab (depending on the browser and its configuration) for FirstGlance, leaving the page containing the link(s) to FirstGlance available behind the new window.

How to load a molecule from any server into FirstGlance

Replace the PDB identification code, in the above example, with the entire URL to the desired PDB file. For example, under Toxins in the Atlas of Macromolecules you can find a model for the heptamer of anthrax protective antigen, available from

This URL can be specified after ?mol= in the link to FirstGlance, but the colon (:) must be "escaped" to %3A. Thus, the link would be

<a href=""
target=_blank>Anthrax Protective Antigen Heptamer</a>
Try it: Anthrax Protective Antigen Heptamer

For more technical information, please see PDB Data File Access Methods Employed by FirstGlance.

Linking to a Mirror Site

If you are located outside the USA, and you get consistently faster display of the molecule from a FirstGlance Mirror Site, you can use the mirror URL for your links by replacing "" (in the examples above) by your preferred mirror URL.

Advanced Options/Query Parameters

By default, FirstGlance uses JSmol, which does not require Java. For large molecules or smoother rotation, use Java. Use of Java can be controlled with a preference setting within FirstGlance, or by adding these query parameters to the link URL: Generally, it is better to let the user choose whether to use Java with the preference setting in FirstGlance, since not all computers/devices can use Java. Also, after FirstGlance starts in default mode (JSmol), there is an option to run Java.

Advanced options (available from the main page with the Advanced Options link) can be specified in hyperlinks. These options should generally be unnecessary. If you think you need one of these options, please contact to discuss whether it is, indeed, necessary. For example, to invoke FirstGlance forcing JSmol (no Java) regardless of any preference setting, in debugging mode, the hyperlink would be:

<a href="" target=_blank>View
1d66 forcing no Java (using JSmol), in debugging mode</a>
Try it: View 1d66 forcing no Java (using JSmol), in debugging mode.

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