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.
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
(use http not https):
<
href="http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/atlas/pdb/dna_b_form.pdb.gz"
target="_blank">DNA Double Helix</a>
Try it:
DNA Double Helix
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.
&bu=N, where N is an integer, specifies that Biological Unit N
(biomolecule N) should be loaded.
&au=1 forces loading of the asymmetric unit or deposited model when
the default is biological unit 1.
&bbonly=1 forces loading of
backbone atoms only. The "=1"
means to load all backbone atoms (not a subset).
This occurs automatically
when appropriate for a specified PDB code. When the number of backbone atoms exceeds
, FirstGlance does not
offer to load ALL alpha carbons because of the performance penalty.
When a user-provided PDB file is loaded,
automatic simplification does not occur. This query parameter is provided for such cases.
&bbonly=N forces loading of the subset of only every Nth backbone atom.
This is useful for user-provided PDB files when
the number of backbone atoms is large enough to degrade performance of FirstGlance.
This could also be used when you want to load a smaller or larger group than the two sets
that FirstGlance offers (in the
Molecule Information Tab)
for
simplified models:
the default subset, and one group larger than default subset.
&bbmax allows up to
backbone atoms. Without this, when backbone atoms exceed
,
a subset of backbone atoms will be loaded, such as every 2nd, every 5th, etc.
in order to keep the number loaded from exceeding
.
This query parameter is used when the user clicks the link in the
Molecule Information Tab,
just after "SIMPLIFIED", that offers
to show more backbone atoms than the default limit of
.
Even with &bbmax=1, a subset of backbone atoms will be loaded if the number of
backbone atoms exceeds
.
See &bbonly=1 above to force loading of ALL backbone atoms regardless of the performance penalty.
&nosimp prevents any simplification other than excluding hydrogen atoms.
Reporting of elapsed times and all scripts is turned on with &eltim=1.
This is applied automatically by selecting the Report checkbox after clicking "Advanced Options"
at the bottom of the
main entrance.
&editanim opens JSmol's state script in a form so you can edit it before submitting
it for generation, on the server, of an animated multi-GIF. This was added to help with debugging
the program firstglancegif on the server.
Debugging mode is turned on with &db=1
This is applied automatically by selecting the debug checkbox after clicking "Advanced Options"
at the bottom of the
main entrance.
mmCIF format atomic coordinate files are requested with &cif=1
(FirstGlance has not yet been adapted to work with cif files).
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
(and use http not https):
<a href="http://firstglance.jmol.org/fg.htm?mol=1sva&au=1"
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
(and use http not https):