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 tab/page containing the link(s) to FirstGlance available.

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 DNA in the Atlas of Macromolecules you can find a theoretical (idealized) model for B form DNA with 36 base pairs. It is 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

< href=""
target="_blank">DNA Double Helix</a>
Try it: DNA Double Helix

Advanced Options/Query Parameters

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. Example 1: The SV40 capsid protein 1sva defaults to biological unit 1 with 360 simplified chains. After that is displayed, if you click on Biological Unit, you are offered the option of displaying the asymmetric unit. If you wish to skip showing the complete capsid and start with the asymmetric unit, use &au=1:

<a href="" target="_blank">View
the asymmetric unit of the SV40 capsid protein</a>
Try it: View the asymmetric unit of 1sva.

Example 2: Birnavirus capsid 1wce has a molecular weight of 37 million Da with ~332,000 alpha carbons. By default, FirstGlance shows every 14th alpha carbon (~24,000 atoms), offering the option of showing every 4th if you are willing to be patient while the ~83,000 alpha carbons are processed. An interesting surface pattern is discernable if you look closely. If you want to see how it looks with all ~332,000 alpha carbons loaded, and if you are willing to wait several minutes while it is processed by FirstGlance, use the query parameter &bbonly=1:

<a href="" target="_blank">View
all ~332,000 alpha carbons of the birnavirus capsid protein</a>
Try it: View all ~332,000 alpha carbons of the birnavirus capsid protein.

Browser Spoofing: These options are obsolete in 2022, but the code remains. For test purposes, FirstGlance can be told to behave as if a specified browser were in use, regardless of the actual browser employed. This is done with a "&spoof=browsername" query parameter, where browsername is one of chrome, edge, ie, firefox, opera, safari, or maxthon. These query parameters do not cause the browser to behave like a different browser -- they affect only FirstGlance. Links that use these query parameters to display 1d66 are provided in the Updated section for version 2.4 in versions.htm.

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