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
available behind the new window.
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
colon (:) must be "escaped" to %3A. Thus, the link
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
"firstglance.jmol.org" (in the examples above) by your preferred mirror URL.
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:
The Jmol Java applet is requested with &JAVA (or &SIGNED).
JSmol (No Java) is requested with &NOJAVA (or &HTML5).
These query parameters override the preference setting within FirstGlance.
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.
Debugging mode is requested with &db=1&.
mmCIF format atomic coordinate files are requested with &cif=1&.
For example, to invoke FirstGlance
forcing JSmol (no Java) regardless of any preference setting,
in debugging mode, the hyperlink would be: