Chemistry with Jmol

UniWakka, starting from the 0.4.5 version, supports chemistry with the JmolApplet 

To insert a molecule just include between <chem></chem> the content of supported Jmol file formats.
The opening tag (<chem>) supports a number of parameters to controll the applet:

• width
• height
• style
• label
• bgcolor
• link
• wireframeRotation
• perspectiveDepth

It is also possible to use a jmol action.

Exemples

<chem link="false">
<molecule id="methanol">
<atomArray atomID="a1 a2 a3 a4 a5 a6"
elementType="C O H H H H"
x3="-0.748 0.558 -1.293 -1.263 -0.699 0.716"
y3="-0.015 0.420 0.202 0.754 -0.934 1.404"
z3="0.024 -0.278 -0.901 0.600 0.609 0.137"/>
</molecule>
</chem>
will produce:



<chem>
ATOM 1 N ALA 1 0.039 -0.028 0.000 1.00 0.00
ATOM 2 CA ALA 1 1.499 -0.043 0.000 1.00 0.00
ATOM 3 C ALA 1 2.055 1.361 0.000 1.00 0.00
ATOM 4 O ALA 1 1.321 2.356 0.011 1.00 0.00
ATOM 5 CB ALA 1 1.956 -0.866 -1.217 1.00 0.00
ATOM 6 1H ALA 1 -0.524 0.894 0.000 1.00 0.00
ATOM 7 2H ALA 1 -0.543 -0.938 0.000 1.00 0.00
ATOM 8 HA ALA 1 1.847 -0.534 0.928 1.00 0.00
ATOM 9 1HB ALA 1 3.058 -0.939 -1.274 1.00 0.00
ATOM 10 2HB ALA 1 1.571 -1.903 -1.181 1.00 0.00
ATOM 11 3HB ALA 1 1.610 -0.425 -2.172 1.00 0.00
ATOM 12 OC ALA 1 3.481 1.470 0.000 1.00 0.00
ATOM 13 HOC ALA 1 3.898 0.528 0.000 1.00 0.00
TER
</chem>
Will produce:

URL for retrieving molecule file is:
http://www.istitutocolli.org/uniwakka/ChemistrySupport/chem.cml?form=2

<chem bgcolor="black" width="100" height="100" link="true">
ATOM 1 N ALA 1 0.039 -0.028 0.000 1.00 0.00
ATOM 2 CA ALA 1 1.499 -0.043 0.000 1.00 0.00
ATOM 3 C ALA 1 2.055 1.361 0.000 1.00 0.00
ATOM 4 O ALA 1 1.321 2.356 0.011 1.00 0.00
ATOM 5 CB ALA 1 1.956 -0.866 -1.217 1.00 0.00
ATOM 6 1H ALA 1 -0.524 0.894 0.000 1.00 0.00
ATOM 7 2H ALA 1 -0.543 -0.938 0.000 1.00 0.00
ATOM 8 HA ALA 1 1.847 -0.534 0.928 1.00 0.00
ATOM 9 1HB ALA 1 3.058 -0.939 -1.274 1.00 0.00
ATOM 10 2HB ALA 1 1.571 -1.903 -1.181 1.00 0.00
ATOM 11 3HB ALA 1 1.610 -0.425 -2.172 1.00 0.00
ATOM 12 OC ALA 1 3.481 1.470 0.000 1.00 0.00
ATOM 13 HOC ALA 1 3.898 0.528 0.000 1.00 0.00
TER
</chem>

Will produce:

URL for retrieving molecule file is:
http://www.istitutocolli.org/uniwakka/ChemistrySupport/chem.cml?form=3