Advanced Options
for FirstGlance in Jmol
These checkboxes apply to PDB Id's submitted from the form, and
also to the Gallery (when opened after a checkbox is changed).
The options checked below will be displayed at the bottom of the main page
in red. These options can also be
specified in links to FirstGlance.
Use the signed Jmol applet.
Check this to obtain PDB files that are problematic with the
default unsigned applet.
(Technical information.)
Use CIF.
Experimental use only. FirstGlance does NOT
work correctly with CIF files!
You will need to check Signed Applet above to access CIF
files from most FirstGlance installations.
By default, FirstGlance
uses atomic coordinate files of PDB format.
Checking this checkbox forces FirstGlance to use mmCIF
files from the Protein Data Bank
when a PDB identification code is specified.
Although the PDB format is
the most popular format among crystallographers, it has serious
limitations due to its age. The World Wide Protein Data Bank
(wwpdb.org) maintains
its primary and highest quality database in macromolecular crystallographic
information format (mmCIF), and there may be significant differences between
the mmCIF and PDB files. In particular, some inconsistencies or ambiguities
in PDB files may be corrected or resolved in mmCIF files.
Here are some preliminary observations on the
Behavior of CIF Files in FirstGlance.
(Embedded: The former option to embed FirstGlance in a table with top and left menus
has been discontinued. You can still try this option in
FirstGlance in Jmol 1.0.)
(Frames: The former option to use browser frames was discontinued in this version.
FirstGlance version 0.97
remains available for testing this option.)
Debugging Mode (for developers modifying or testing the
FirstGlance javascript). Sets debugscript on, opens the Jmol console,
and displays other debugging information. When checked, the query
parameter db=1 is passed to e.g. fg.htm, which then sets
top.debuggingFG to true.
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