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<span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
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255); text-decoration: none; display: inline !important; float:
none;">Would you like to see an interactive virus capsid model
quickly and easily? Slab it or cut it in half? A clathrin coat? A
bacterial gas vesicle? The mysterious "vault" eukaryotic
nanocompartment?</span><span style="caret-color: rgb(34, 34, 34);
color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"> </span> <br
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<font size="2"><a
href="https://proteopedia.org/w/FirstGlance/Virus_Capsids_and_Other_Large_Assemblies"
target="_blank"
data-saferedirecturl="https://www.google.com/url?q=https://proteopedia.org/w/FirstGlance/Virus_Capsids_and_Other_Large_Assemblies&source=gmail&ust=1660865724783000&usg=AOvVaw03Laakz-jIT6KacDz1vTrd"
style="color: rgb(17, 85, 204); font-family: Arial, Helvetica,
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white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"
moz-do-not-send="true">https://proteopedia.org/w/<wbr>FirstGlance/Virus_Capsids_and_<wbr>Other_Large_Assemblies</a></font><br
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
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<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
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<span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">The views at the above link were obtained with Version 4.0
of</span><span style="caret-color: rgb(34, 34, 34); color: rgb(34,
34, 34); font-family: Arial, Helvetica, sans-serif; font-style:
normal; font-variant-caps: normal; font-weight: normal;
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text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"> </span><b
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; letter-spacing: normal; orphans: auto;
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text-decoration: none;">FirstGlance in Jmol</b><span
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
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normal; orphans: auto; text-align: start; text-indent: 0px;
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word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"> </span><span
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
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widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">released August 15, 2022 (free and open source; google
"firstglance" as one word, or</span><span style="caret-color:
rgb(34, 34, 34); color: rgb(34, 34, 34); font-family: Arial,
Helvetica, sans-serif; font-style: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal; orphans:
auto; text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
text-decoration: none;"> </span><font size="2"><a
href="http://firstglance.jmol.org/" target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://firstglance.jmol.org&source=gmail&ust=1660865724783000&usg=AOvVaw2TLsmKgjORCQtCOUxDBJMk"
style="color: rgb(17, 85, 204); font-family: Arial, Helvetica,
sans-serif; font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: auto;
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white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"
class="moz-txt-link-freetext" moz-do-not-send="true">http://firstglance.jmol.org</a></font><span
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">). Newly, it automatically constructs "biological
assemblies" and shows "biomolecule 1" in its initial view.
Exploring the asymmetric unit is then an option.</span><br
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<p><span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34,
34); font-family: Arial, Helvetica, sans-serif; font-size:
small; font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); text-decoration: none;
display: inline !important; float: none;">Very large* assemblies
are automatically simplified to alpha carbons, or a subset of
alpha carbons; see examples at the above link. What are such
simplified models good for? They can be measured, colored by
secondary structure, hydrophobic/polar, charge, amino-to-carboxy
rainbow, or evolutionary conservation (if pre-processed by the
ConSurf Server). Each group of sequence-identical chains can be
assigned a distinct color (under Solid in the Views tab).</span><span
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"> <br>
</span></p>
<p><span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34,
34); font-family: Arial, Helvetica, sans-serif; font-style:
normal; font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"><font
size="2">To clear the old FirstGlance out of your browser
cache:</font></span></p>
<p><span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34,
34); font-family: Arial, Helvetica, sans-serif; font-style:
normal; font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"><font
size="2"><a class="moz-txt-link-freetext"
href="http://firstglance.jmol.org/fg.htm?mol=7mgp"
moz-do-not-send="true">http://firstglance.jmol.org/fg.htm?mol=7mgp</a></font></span></p>
<p><span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34,
34); font-family: Arial, Helvetica, sans-serif; font-style:
normal; font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"><font
size="2">Regardless of whether the molecule is displayed, hold
down the Shift key while clicking Reload. <b>Shift-Reload</b>
forces the browser to get all files from the server. In the
7mgp tab of FirstGlance, click on "Biological Unit 1" to find
out that the hexamer displayed has been constructed from a
single chain in the asymmetric unit.</font><br>
</span></p>
<span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">You can make an</span><b style="caret-color: rgb(34, 34,
34); color: rgb(34, 34, 34); font-family: Arial, Helvetica,
sans-serif; font-style: normal; font-variant-caps: normal;
letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"><span> </span><font
size="2">animation, ready to drop into a presentation slide</font></b><span
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">, from any view in FirstGlance. It takes just a few mouse
clicks. Examples in Google Slides:</span><br style="caret-color:
rgb(34, 34, 34); color: rgb(34, 34, 34); font-family: Arial,
Helvetica, sans-serif; font-style: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal; orphans:
auto; text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
text-decoration: none;">
<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<font size="2"><a href="http://tinyurl.com/movingmolecules"
target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://tinyurl.com/movingmolecules&source=gmail&ust=1660865724783000&usg=AOvVaw3gYgubr-UNOQjtA3NStBzg"
style="color: rgb(17, 85, 204); font-family: Arial, Helvetica,
sans-serif; font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"
moz-do-not-send="true">http://tinyurl.com/<wbr>movingmolecules</a></font><br
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">A small assembly, 2acz, has 4 chains in its asymmetric
unit, and 12 chains in its biomolecule 1. You will be offered the
option to simplify, so you can try it both ways. Even simplified
to alpha carbons, the</span><b style="caret-color: rgb(34, 34,
34); color: rgb(34, 34, 34); font-family: Arial, Helvetica,
sans-serif; font-style: normal; font-variant-caps: normal;
letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"><span> </span><font
size="2">transmembrane helices stand out</font></b><span
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"> </span><span
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">with the hydrophobic/polar and charge views. Its
construction can be understood by giving a</span><span
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"> </span><font
size="2"><b style="caret-color: rgb(34, 34, 34); color: rgb(34,
34, 34); font-family: Arial, Helvetica, sans-serif; font-style:
normal; font-variant-caps: normal; letter-spacing: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">distinct
color to each of the 4 sequence-distinct protein chains</b></font><span
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"> </span><span
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">(Solid in the Views tab).</span><br style="caret-color:
rgb(34, 34, 34); color: rgb(34, 34, 34); font-family: Arial,
Helvetica, sans-serif; font-style: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal; orphans:
auto; text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
text-decoration: none;">
<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<font size="2"><a href="http://firstglance.jmol.org/fg.htm?mol=2acz"
target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://firstglance.jmol.org/fg.htm?mol%3D2acz&source=gmail&ust=1660865724783000&usg=AOvVaw3BNq2JBw5xGorC2aN5dsn1"
style="color: rgb(17, 85, 204); font-family: Arial, Helvetica,
sans-serif; font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"
moz-do-not-send="true">http://firstglance.jmol.org/<wbr>fg.htm?mol=2acz</a></font><br
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">Structural biologists: With FirstGlance, you can't miss
(after clicking "Show more details") incomplete sidechains,
missing residues, alternate locations (can be animated), occupancy
< 1.0 (all exemplified in 1ijw). All salt bridges can be
displayed with one click (Tools tab), and a spreadsheet-ready list
is reported with one more click. A "Contacts & Non-Covalent
Interactions" tool makes it easy to visualize the interactions
with any moiety you specify. Protein crosslinks are automatically
detected and highlighted/zoomed with a few clicks: isopeptides,
thioesters, thioethers, his-tyr, lys-cys NOS as well as, of
course, disulfides. Step by step:</span><br style="caret-color:
rgb(34, 34, 34); color: rgb(34, 34, 34); font-family: Arial,
Helvetica, sans-serif; font-style: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal; orphans:
auto; text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
text-decoration: none;">
<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<font size="2"><a
href="https://proteopedia.org/w/FirstGlance/Evaluating_Protein_Crosslinks"
target="_blank"
data-saferedirecturl="https://www.google.com/url?q=https://proteopedia.org/w/FirstGlance/Evaluating_Protein_Crosslinks&source=gmail&ust=1660865724783000&usg=AOvVaw1cugdD_TiYKG43reDd9118"
style="color: rgb(17, 85, 204); font-family: Arial, Helvetica,
sans-serif; font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"
moz-do-not-send="true">https://proteopedia.org/w/<wbr>FirstGlance/Evaluating_<wbr>Protein_Crosslinks</a></font><br
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">Electron density maps (or EM density maps) can be displayed
for anything selected with the Find.. dialog, as well as
crosslinks and ends of chains. See examples from FirstGlance here:</span><br
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<font size="2"><a
href="https://proteopedia.org/w/Electron_density_maps"
target="_blank"
data-saferedirecturl="https://www.google.com/url?q=https://proteopedia.org/w/Electron_density_maps&source=gmail&ust=1660865724783000&usg=AOvVaw0gwjsm7XrSyxFJ7uPIPwMK"
style="color: rgb(17, 85, 204); font-family: Arial, Helvetica,
sans-serif; font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"
moz-do-not-send="true">https://proteopedia.org/w/<wbr>Electron_density_maps</a></font><br
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">New color schemes for simplified models:</span><br
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<font size="2"><a
href="http://firstglance.jmol.org/notes.htm#bucolors"
target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://firstglance.jmol.org/notes.htm%23bucolors&source=gmail&ust=1660865724783000&usg=AOvVaw2_kLnGC21kFOabiSr4kRoW"
style="color: rgb(17, 85, 204); font-family: Arial, Helvetica,
sans-serif; font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"
moz-do-not-send="true">http://firstglance.jmol.org/<wbr>notes.htm#bucolors</a></font><br
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">*"Very large" assemblies means >25,000 non-hydrogen
atoms. Only about 3% of entries in the World-Wide Protein Data
Bank have biological assemblies that large. However, these include
very important structures, such as virus capsids. Simplification
rules:</span><br style="caret-color: rgb(34, 34, 34); color:
rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<font size="2"><a
href="http://firstglance.jmol.org/notes.htm#simplification"
target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://firstglance.jmol.org/notes.htm%23simplification&source=gmail&ust=1660865724783000&usg=AOvVaw1sYWhWPAYeCAfkFlqgaW0x"
style="color: rgb(17, 85, 204); font-family: Arial, Helvetica,
sans-serif; font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"
moz-do-not-send="true">http://firstglance.jmol.org/<wbr>notes.htm#simplification</a></font><br
style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<br style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<span style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-size: small;
font-style: normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); text-decoration: none; display: inline !important; float:
none;">Hope you enjoy!</span>
<div style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34);
font-family: Arial, Helvetica, sans-serif; font-style: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; text-decoration: none;"><br>
<div><font size="1"><span style="color: rgb(0, 0, 0); font-size:
medium;">Eric Martz, Professor Emeritus, Dept Microbiology
(he/him/his)</span><br style="color: rgb(0, 0, 0);">
</font><font size="2"><font size="1"><span style="color: rgb(0,
0, 0); font-size: medium;">Univ. Massachusetts, Amherst</span></font></font><font
size="2"><font size="1"><span style="color: rgb(0, 0, 0);
font-family: -webkit-standard; font-size: medium;"> -- </span><a
href="http://martz.molviz.org/" target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://martz.molviz.org/&source=gmail&ust=1660865724783000&usg=AOvVaw2nqiKVuCqSmFsnAvJ1MGZv"
style="color: rgb(17, 85, 204);" moz-do-not-send="true">Martz.MolviZ.Org</a></font><span
style="color: rgb(0, 0, 0); font-family: -webkit-standard;
font-size: medium;"></span></font>
<ul style="color: rgb(0, 0, 0);">
<li style="margin-left: 15px;"><font size="2">Guided
Exploration of Macromolecules with Powerpoint-Ready
Animations: <a href="http://firstglance.jmol.org/"
target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://firstglance.jmol.org/&source=gmail&ust=1660865724783000&usg=AOvVaw2TMFPywJ4BqH-kH72zlAvx"
style="color: rgb(17, 85, 204);" moz-do-not-send="true">FirstGlance.Jmol.<wbr>Org</a></font></li>
<li style="margin-left: 15px;"><font size="2">Make Custom
Interactive Molecular Scenes EASILY: <a
href="http://proteopedia.org/" target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://proteopedia.org/&source=gmail&ust=1660865724783000&usg=AOvVaw1t0utrgDCvTojqh0KitWiD"
style="color: rgb(17, 85, 204);" moz-do-not-send="true">Proteopedia.Org</a></font></li>
<li style="margin-left: 15px;"><font size="2">DNA, Hemoglobin,
etc. Tutorials: <a href="http://molviz.org/"
target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://molviz.org/&source=gmail&ust=1660865724783000&usg=AOvVaw1-dIrSRqJSWqJZbir_m8oL"
style="color: rgb(17, 85, 204);" moz-do-not-send="true">MolviZ.Org</a></font></li>
<li style="margin-left: 15px;"><font size="2">Find Functional
Patches in Proteins with <a
href="http://consurf.tau.ac.il/" target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://consurf.tau.ac.il/&source=gmail&ust=1660865724783000&usg=AOvVaw3om2qQsvLlMN6onHgKKkyU"
style="color: rgb(17, 85, 204);" moz-do-not-send="true">ConSurf</a></font></li>
<li style="margin-left: 15px;"><font size="2">Atlas of
Macromolecules: <a href="http://atlas.molviz.org/"
target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://atlas.molviz.org/&source=gmail&ust=1660865724783000&usg=AOvVaw0msfYOfQLbVg_p3P_4I2XB"
style="color: rgb(17, 85, 204);" moz-do-not-send="true">Atlas.MolviZ.<wbr>Org</a></font></li>
<li style="margin-left: 15px;"><font size="2">See multiple
protein sequence alignments clearly: <a
href="http://msareveal.org/" target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://msareveal.org/&source=gmail&ust=1660865724783000&usg=AOvVaw2EuD7Bn4w3DZ6hByzK2J5a"
style="color: rgb(17, 85, 204);" moz-do-not-send="true">MSAReveal.Org</a></font></li>
<li style="margin-left: 15px;"><font size="2">Pockets And
Cavities Using Pseudoatoms in Proteins: <a
href="http://molviz.org/pacupp" target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://molviz.org/pacupp&source=gmail&ust=1660865724783000&usg=AOvVaw0B1HteAH5w52HxmfZUX4uW"
style="color: rgb(17, 85, 204);" moz-do-not-send="true">PACUPP</a></font></li>
<li style="margin-left: 15px;"><font size="2">Interactive
Molecules in Architectural Spaces: <a
href="http://molecularplayground.org/" target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://molecularplayground.org/&source=gmail&ust=1660865724783000&usg=AOvVaw2ugRMkQBgNLTQ44srcxG7K"
style="color: rgb(17, 85, 204);" moz-do-not-send="true">MolecularPlayground.<wbr>Org</a></font></li>
<li style="margin-left: 15px;"><font size="2">Teaching Plans: <a
href="http://workshops.molviz.org/" target="_blank"
data-saferedirecturl="https://www.google.com/url?q=http://workshops.molviz.org/&source=gmail&ust=1660865724783000&usg=AOvVaw11bDfvXlnp3Ar4YT_RHfs_"
style="color: rgb(17, 85, 204);" moz-do-not-send="true">Workshops.MolviZ.Org</a></font></li>
</ul>
</div>
<font size="2"> </font></div>
<font size="2"> <br class="Apple-interchange-newline">
</font><wbr style="caret-color: rgb(34, 34, 34); color: rgb(34, 34,
34); font-family: Arial, Helvetica, sans-serif; font-style:
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