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[Jmol-commits] CVS: Jmol-web/source/doc/demo/dots ddt.xyz.gz,NONE,1.1 index.html,NONE,1.1
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From: Michael T H. <mic...@us...> - 2003-10-16 19:10:23
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Update of /cvsroot/jmol/Jmol-web/source/doc/demo/dots
In directory sc8-pr-cvs1:/tmp/cvs-serv12784/source/doc/demo/dots
Added Files:
ddt.xyz.gz index.html
Log Message:
restructuring
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--- NEW FILE: index.html ---
<html>
<head><title>jmol applet atoms demo</title>
</head>
<body>
<table border="1">
<tr>
<td>
<h2>ddt</h2>
<applet name="jmol" code="JmolApplet" archive="JmolApplet.jar"
codebase="../jmol"
width="300" height="300" mayscript="true" >
<param name="emulate" value="chime" />
<param name="load" value="ddt.xyz.gz" />
</applet>
</td>
<td>
Jmol has the ability to show two types of 'dots' surfaces. The first is a
vanderWalls dots surface, where the dots are shown at the vanderWaals
radius for all atoms.<br />
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="dots on" />
<param name="target" value="jmol" />
<param name="script" value="dots on" />
</applet>
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="dots off" />
<param name="target" value="jmol" />
<param name="script" value="dots off" />
</applet><br />
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="cpk 25%" />
<param name="target" value="jmol" />
<param name="script" value="cpk 25%" />
</applet>
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="cpk 50%" />
<param name="target" value="jmol" />
<param name="script" value="cpk 50%" />
</applet><br />
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="cpk 95%" />
<param name="target" value="jmol" />
<param name="script" value="cpk 95%" />
</applet>
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="cpk off" />
<param name="target" value="jmol" />
<param name="script" value="cpk off" />
</applet><br />
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="wireframe on" />
<param name="target" value="jmol" />
<param name="script" value="wireframe on" />
</applet>
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="wireframe 0.1" />
<param name="target" value="jmol" />
<param name="script" value="wireframe 0.1" />
</applet><br />
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="wireframe 0.3" />
<param name="target" value="jmol" />
<param name="script" value="wireframe 0.3" />
</applet>
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="wireframe off" />
<param name="target" value="jmol" />
<param name="script" value="wireframe off" />
</applet><br />
The second type of dots surface you can display is a Connolly or
Solvent Accessible Surface. The model is that this is the surface which is
accessible by a probe sphere. This command interacts with the 'dots'
command.<br />
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="dots off; set solvent on; dots on" />
<param name="target" value="jmol" />
<param name="script" value="dots off; set solvent on; dots on" />
</applet>
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="dots off; set solvent off; dots on" />
<param name="target" value="jmol" />
<param name="script" value="dots off; set solvent off; dots on" />
</applet><br />
The default probe size is 1.2 Å, a probe size used for water.
So these first two buttons do the same thing. But you need to use
these in combination with the 'dots' buttons above. <br />
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="set solvent on" />
<param name="target" value="jmol" />
<param name="script" value="set solvent on" />
</applet>
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="set solvent 1.2" />
<param name="target" value="jmol" />
<param name="script" value="set solvent 1.2" />
</applet><br />
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="set solvent 2.0" />
<param name="target" value="jmol" />
<param name="script" value="set solvent 2.0" />
</applet>
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="set solvent off" />
<param name="target" value="jmol" />
<param name="script" value="set solvent off" />
</applet><br />
By default, convex dots on the outside of the atom spheres
inherit the color of the atom. Saddle dots are shown in blue.
There are explicit color commands for controlling dot color. <br />
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="color dots yellow" />
<param name="target" value="jmol" />
<param name="script" value="color dots yellow" />
</applet>
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="color dotsConvex cyan" />
<param name="target" value="jmol" />
<param name="script" value="color dotsConvex cyan" />
</applet><br />
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="color dotsSaddle hotpink" />
<param name="target" value="jmol" />
<param name="script" value="color dotsSaddle hotpink" />
</applet>
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="200" mayscript="true" >
<param name="type" value="button" />
<param name="label" value="color dots none" />
<param name="target" value="jmol" />
<param name="script" value="color dots none" />
</applet><br />
(Concave surfaces formed where three atoms come together are a problem
for me. If you are interested in this topic, please get in touch.
<b>mt...@mt...</b>) <br />
This button makes them pretty easy to see. They are the little spherical
triangles that do not have any dots. <br />
<applet code="JmolAppletControl" archive="JmolApplet.jar"
codebase="../jmol"
height="20" width="400" mayscript="true" >
<param name="type" value="button" />
<param name="label"
value="cpk 95%; color dots yellow; set solvent on; dots on" />
<param name="target" value="jmol" />
<param name="script"
value="cpk 95%; color dots yellow; set solvent on; dots on" />
</applet><br />
</td>
</tr>
</table>
</body>
</html>
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