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   <title>Snapshot Gallery for FirstGlance in Jmol</title>
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<big><b>
Snapshot Gallery
<br>
for
<a href="index.htm">
<i>FirstGlance in Jmol</i></a>
</b>
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<br><br>
A look through these snapshots from <i>FirstGlance in Jmol</i>
will give you an overview
of what it can to.
Clicking on any of the
<a href="http://proteopedia.org/wiki/index.php/PDB_identification_code"
target="_blank"><b>four character PDB identification codes</b></a>
below
(such as 
<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>)
will enable you to explore that molecule in <i>FirstGlance</i>

<br><br>

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<script language='javascript'>

	writeTextInPinkBox(
'The snapshots below have not been updated since version 1.0 of \n\
<i>FirstGlance in Jmol</i>. They still give a somewhat useful \n\
impression. \n\
New capabilities not yet depicted: \n\
<ul> \n\
<li>FirstGlance defaults to non-Java mode that works on some mobile devices (iPads) and smart phones. The Java mode remains available for higher performance on computers.  \n\
<li>There are now 5 tabs for different control panels: Molecule Information, Views, Tools, Resources (external), and Preferences. \n\
<li>The <b>Molecule Information</b> tab provides a wealth of information about the model, \n\
including the title and publication abstract, and guidance for interpreting resolution \n\
and the reliability of the model (free R). \n\
<li><b>Missing residues</b> are marked in an obvious way with <i>empty baskets</i> and listed. \n\
<li>The <b>Quality</b> button removes the jagged edges that \n\
you see in some of the snapshots, and generally smoothes out the image. \n\
<li><b>Find, Hide</b>, and <b>Isolate</b> tools. <i>Find</i> can locate short sequences as well as many other things. \n\
<li>New tools to display <b>Disulfide Bonds, Crystal Contacts,</b> and the <b>Unit Cell</b>. \n\
<li>Easy access to external resources that construct and display (in FirstGlance) the <b>Biological Unit, Evolutionary Conservation, Lipid Bilayer Boundaries</b> (for integral membrane proteins). \n\
</ul> \n\
');

</script>

<br><br>

<hr noshade>
Each of the views in the next three tables is achieved with <b>one click</b> of the
mouse.
<br>
When actually using <i>FirstGlance</i>, the molecular
views are <b>much larger</b> .

<br><br>

<table cellpadding=5 border=1><tr>

	<td width=200 valign="top"><!---------------------------->
<center><img src="cartoon.gif"></center>
Initial view (<u>Cartoon</u> plus <u>Ligands+</u>)
of Gal4 transcriptional
regulator (DNA-binding domain only) bound
to DNA
(<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>).
Each chain is a different color.
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="rockets_1d66.gif"></center>
<u>Secondary Structure</u>
view of Gal4 with alpha helices
as "rockets"
(<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>).
Compare with another molecule below showing
a <a href="#table3">beta sheet</a>.

	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="rainbow.gif">
<br><img src="rainbow_key.gif"></center>
<u>N->C Rainbow</u> view of Gal4:DNA showing
<font color="blue"><b>Amino/5'</b></font>
and
<font color="red"><b>Carboxy/3'</b></font>
termini.
(<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>).
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="comp_1d66.gif"></center>
<u>Composition</u> view of Gal4:DNA indicating
<font color="#d0b060"><b>Protein</b></font>,
<font color="#ae00fe"><b>DNA</b></font>,
and
<font color="#3a79bc"><b>Water</b></font>
(<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>).
	</td>

</tr></table>

<br><a name="table2"><br></a><!--===================================-->

<table cellpadding=5 border=1><tr>

	<td width=200 valign="top"><!---------------------------->
<center><img src="phob_1d66.gif"></center>
<u>Hydrophobic/Polar</u> view of Gal4:DNA indicating
<font color="#a0a0a0"><b>Hydrophobic</b></font>
and
<font color="#d050d0"><b>Polar</b></font> residues on the surface.
(<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>).
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="charge_1d66.gif"></center>
<u>Charge</u> view of Gal4:DNA indicating
<font color="#a0a0a0"><b>Hydrophobic</b></font>,
<font color="#d050d0"><b>Polar uncharged</b></font>,
<font color="#3366ff"><b>Cationic (+)</b></font>,
<font color="#ff0000"><b>Anionic (-)</b></font>,
and
<font color="#b000b0"><b>Backbone atoms</b></font>
on the surface.
(<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>).
	</td>

	<td width=200 valign="top"><!---------------------------->
		<center><table border=0><tr><td>
<center><img src="vines1.gif" border=1></center>
			</td><td>
<center><img src="vines2.gif" border=1>
<img src="vines3.gif" border=1></center>
		</td></tr></table></center>
Atomic detail is available in <u>Vines..</u> views.
The <u>Slab..</u> option (not pictured) hides
atoms distant from the point of interest.
(<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>).
	</td>

</tr></table>

<br><a name="table3"><br></a><!--===================================-->

<table cellpadding=5 border=1><tr>

	<td width=200 valign="top"><!---------------------------->
<center><img src="planks.gif"></center>
<u>Secondary Structure</u> view of <i>Streptococcal</i>
protein G
(<a href="../fg.htm?mol=1pgb" target=_blank>1PDB</a>)
indicating
<font color="#e08000"><b>beta-strands</b></font>,
<font color="#ff0080"><b>alpha-helices</b></font>
and
<font color="#6080ff"><b>turns</b></font>.
	</td>

</tr></table>

<br><br><!--===================================-->
<hr noshade>
<big><center>
	<a name="contacts">Begin <i>Contacts..</i> Section</a>
</center></big>
<hr noshade>

The <b><i>Contacts..</i></b> tool of <i>FirstGlance</i> produced
the following views.
<br>

The snapshots below are much smaller than
the actual views when using <i>FirstGlance</i>.

<br><br>
<table cellpadding=5 border=1><tr>

	<td width=200 valign="top"><!---------------------------->
<center><img src="contacts_1d66.gif"></center>
<u>Contacts..</u> enables you to see how the chains
(each a different color) touch each other.
(View obtained with 1 click.)
Optionally, you can select a target (by clicking on chains, groups, or atoms)
in order to display the putative non-covalent bonds to the target.
(<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>)
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="target.gif"></center>
Clicking on one protein chain (green) marks it as the target
with a black asterisk (magnified in inset) on each atom.
(View of 
<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>
obtained with 2 clicks.)
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="contacts2.gif"></center>
Only the atoms that contact the green target chain
are now shown. 

(View obtained with 3 clicks;
<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>).

These contacts can be shown in great
detail, in seven subsets of different kinds of
non-covalent bonds, as shown below.
	</td>

</tr></table>

<br><br><!--===================================-->

<table cellpadding=5 border=1><tr>

	<td width=306 valign="top"><!---------------------------->
<center><img src="1d66_cgg.gif"></center>
	</td>

	<td width=500 valign="top"><!---------------------------->
<u>Contacts 1:</u> non-water <b>hydrogen bonds</b>.
(<a href="../notes.htm#hbonds" target=_blank>Definition</a>.)
At left,
target Gal4 protein
atoms (larger balls, bottom, marked with white asterisks)
are shown within hydrogen-bonding
distances of DNA atoms (smaller balls, top).
These hydrogen bonds are to a specific sequence of bases.
The DNA sequence
recognized by Gal4, CGG (in chain E), can be visualized here.
Atoms represented as sticks are too distant from the protein to be
hydrogen-bonded, but are shown for context.
(View of
<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>
obtained with 6 clicks, plus additional double-clicks
for each distance measurement.)

<br><br>

Double-clicking atoms reports <b>distances or angles</b>.
<a href="../notes.htm#distances" target=_blank>More..</a>

<br>

In this view (and many views below), atoms are colored by element:


<center><br>
<table border=0 cellpadding=5 bgcolor='black'><tr>
<td><center><big><big><b>
<font face='sans-serif'>

<font color='#909090'>C</font>
<font color='#ffffff'>H</font>
<font color='#ff0d0d'>O</font>
<font color='#6070f8'>N</font>
<font color='#ffff30'>S</font>
<font color='#ff8000'>P</font>

</font></b></big></big><br>
(<a href='http://jmol.sourceforge.net/jscolors/'
target='coewin'><font color='c8c8ff'>more elements..</font></a>)
</center></td></tr></table></center>

	</td>

</tr></table>

<br><br><!--===================================-->

<table cellpadding=5 border=1><tr>

	<td width=200 valign="top"><!---------------------------->
<center><img src="water.gif"></center>
<u>Contacts 2</u> view of <a href="../fg.htm?mol=1d66" target=_blank>1D66</a>:
putative hydrogen bonds to
<font color="magenta"><b>water</b></font>.
(<a href="../notes.htm#hbonds" target=_blank>Definition</a>.)
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="waterbridge.jpg"></center>
<u>Contacts 3</u> view of <a href="../fg.htm?mol=1d66" target=_blank>1D66</a>:
putative
<b><font color="magenta">water</font>
bridges</b>, a subset of hydrogen bonds to water.
One putative bridge from 1D66 is shown above.
(<a href="../notes.htm#waterbridges" target=_blank>Definition</a>.)
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="ident.gif"></center>
Clicking on any atom reports its <b>identity</b> to the lower left
of the molecule, as shown above. ("NH2" means Nitrogen, Eta2.
<a href="../notes.htm#ident" target=_blank>More..</a>)
	</td>

</tr></table>

<br><br><!--===================================-->

<table cellpadding=5 border=1><tr>

	<td width=250 valign="top"><!---------------------------->
<center><img src="cont_vdw.gif"></center>
<u>Contacts 4</u> view of <a href="../fg.htm?mol=1d66" target=_blank>1D66</a>:
van der Waals (<b>hydrophobic</b>) interactions.
(<a href="../notes.htm#hphob" target=_blank>Definition</a>.)
Here, the target chain atoms are spacefilled to van der Waals
radii, while the contacting atoms are small balls.
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="cont_sb.gif"></center>
<u>Contacts 5</u>: <b>protein salt bridges</b>.
(<a href="../notes.htm#saltbr" target=_blank>Definition</a>.)
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="cont_catpi.gif"></center>
<u>Contacts 6</u> view of <a href="../fg.htm?mol=1bl8" target=_blank>1BL8</a>:
<b>protein cation-pi orbital interactions</b>.
(<a href="../notes.htm#catpi" target=_blank>Definition</a>.)
	</td>

</tr></table>

<br><br><!--===================================-->

<table cellpadding=5 border=1><tr>

	<td width=200 valign="top"><!---------------------------->
<center><img src="hb3.gif"></center>
	</td>

	<td width=200 valign="top"><!---------------------------->

<u>Contacts 7</u>: <b>metal and misc. interactions</b>.
Here the interactions of
<b><font color="#e06633">iron</font></b>
in heme are shown (from 
<a href="../fg.htm?mol=2hhd" target=_blank>2HHD</a>).

(<a href="../notes.htm#memi" target=_blank>Definitions</a>.)

	</td>

</tr></table>

<br><br><!--===================================-->

<hr noshade>
<big><center>Begin <i>Hide.., Find..</i> Section</center></big>
<hr noshade>

<br><br><!--===================================-->

<table cellpadding=5 border=1><tr>

	<td width=200 valign="top"><!---------------------------->
<center><img src="1bl8_1.gif"></center>
This potassium channel
(<a href="../fg.htm?mol=1bl8" target=_blank>1BL8</a>)
is a homotetramer (four identical chains).
This view is obtained with one click on <i>Contacts..</i>.
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="1bl8_2.gif"></center>
Here, the <i><b>Hide..</b></i> dialog of <i>FirstGlance</i> has been
used to hide the front two chains (3 more clicks). Now we can see three potassium
ions, and one water molecule.
(View of <a href="../fg.htm?mol=1bl8" target=_blank>1BL8</a>).
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="1bl8_3.gif"></center>
<i><b>Hydrophobic/Polar</b></i> shows that most of the surface of this
molecule is hydrophobic (gray), consistent with its transmembrane
location.
(View of
<a href="../fg.htm?mol=1bl8" target=_blank>1BL8</a>
obtained with 1 click.)
Compare with the
<a href="#table2">
same view for Gal4</a>.
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="1bl8_4.gif"></center>
The <i><b>Find..</b></i> dialog of <i>FirstGlance</i> was
used to locate all tryptophan residues (yellow clouds). Clearly,
they sit at the lipid-water boundaries.
(View of
<a href="../fg.htm?mol=1bl8" target=_blank>1BL8</a>
obtained with 2 clicks plus typing "TRP".)
	</td>

</tr></table>

<br><br><!--===================================-->

<hr noshade>
<big><center>Begin <i>Structural Bioinformatics Resources</i> Section</center></big>
<hr noshade>

<br><!--===================================-->

<i>FirstGlance</i> has numerous links to structural bioinformatics
servers and resources.
<br>
One of the most important is the link to
Probable Quaternary Structure:

<br><br>
<table cellpadding=5 border=1><tr>

	<td width=282 valign="top"><!---------------------------->
<center><img src="1k28.gif"></center>
Here is
<a href="../fg.htm?mol=1k28" target=_blank>1K28</a>
Notice the implausible folding of the left end,
which suggests that some of the chains are missing in this model,
(the asymmetric unit).
(View obtained with 1 click.)
	</td>

	<td width=200 valign="top"><!---------------------------->
Might this molecule have formed <b>specific oligomers</b>, with more chains,
in the protein crystal? The answer is provided by a visit to
the <b><i>Probable Quaternary Structure</i> (PQS)</b> server of the <i>European
Bioinformatics Institute</i>.

<br><br>
In <i>FirstGlance</i>, simply click on

<center><br>
<img src="../pqs.gif" border=1></center>
	</td>

	<td width=281 valign="top"><!---------------------------->
<center><img src="1k28_mmol.gif"></center>
Indeed, PQS reports that the molecule existed in the crystal as a hexamer,
rather than a dimer. The hexamer is formed from three dimers by symmetry
operations. A link to <i>FirstGlance</i> at PQS displays the above
specific oligomer.
	</td></tr><tr><td colspan=3 width=762>

What is this amazing molecular machine? To find out,
view
<a href="../fg.htm?mol=1k28" target=_blank>1K28</a>
in <i>FirstGlance</i>,
and click on either 
<img src="../pdb.gif" align="center" border=1>
or
<img src="../oca.gif" align="center" border=1>.

<br><br>
Crystallographic models often have portions missing -- regions where the molecule
was disordered ("blurry") in the crystal.

To find out,
in <i>FirstGlance</i>,
click on
<img src="../gaps2.gif" border=1 align="center">.

Nearly 50 amino acids are missing from the asymmetric unit (so nearly
150 from the specific hexamer)!

<br><br>

In addition to the structural bioinformatics resources mentioned above,
<i>FirstGlance</i> offers links, under 
<b><i>More Views..</i></b>, to:
<ul>
<li>Assessment of model quality by <b>All Atom Contact Analysis</b>
at the <b>MolProbity</b> server

<li>List of energetically significant cation-pi orbital interactions
at the <b>CaPTURE</b> server.

<li>The <b>Jmol console and command language</b>.

<li><b>Protein Explorer</b>: more information for beginners, and more power
for advanced users, compared to <i>FirstGlance in Jmol</i>.

<li>Visualize evolutionary conservation with the <b>ConSurf</b> server.

<li>And more.

</ul>


	</td>
</tr></table>

<br><br><!--===================================-->

<hr noshade>
<big><center>Begin <i>More Views..</i> Section</center></big>
<hr noshade>

<br><br><!--===================================-->

<table cellpadding=5 border=1><tr>

	<td width=200 valign="top"><!---------------------------->
<center><img src="all_saltbr.gif"></center>
Within <i>FirstGlance, <b>More Views..</b></i> offers a display of all <b>protein salt bridges</b>
throughout the molecule. Here, all salt bridges in an SH3 domain
<a href="../fg.htm?mol=1b07" target=_blank>1B07</a>
are shown. (View obtained with 2 clicks.)
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="all_saltbr_c.gif"></center>
When the same view is colored by chain, it is easy to see
that one of the salt bridges is between two chains.
(View obtained with 1 additional click.)
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="all_catpi.gif"></center>
The same dialog displays all <b>protein cation-pi orbital</b> interactions
throughout the molecule.
(View obtained with 2 clicks.)
	</td>

</tr></table>

<br><br><!--===================================-->

<table cellpadding=5 border=1><tr>

	<td width=200 valign="top"><!---------------------------->
<center><img src="nonstd.gif"></center>
<i><b>More Views..</b></i> has a checkbox to
highlight (as ball and stick) non-standard amino acids
or nucleotides. Here, phospho-serine (SEP) is indicated in
<a href="../fg.htm?mol=1bkx" target=_blank>1BKX</a>
(View obtained with 2 clicks.)
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="temperature.gif"></center>
<i><b>More Views..</b></i> also offers to 
color the molecule by <b>uncertainty</b> (crystallographic "<b>temperature</b>" or "<b>B factor</b>").
The positions of the red atoms in Gal4:DNA model above have the least
certainty.
(View of
<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>
obtained with 3 clicks.)
	</td>

	<td width=200 valign="top"><!---------------------------->
<center><img src="unitcell.gif"></center>
<i><b>More Views..</b></i> also offers to show the atomic coordinate
axes, the unit cell, or the boundbox (in any combination).
Above, all three are shown for Gal4:DNA
(<a href="../fg.htm?mol=1d66" target=_blank>1D66</a>).
(View obtained with 4 clicks.)
	</td>

</tr></table>

</div>

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