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PDB category

This category (namespace) is a space for the PDB files. You can read the PDB files from any pages using Jmol plugin in the Symplus Wiki. You can place the molecular model by Jmol applet easily. This page demostrates how to use the Jmol applet with the DokuWiki jmol plugin.

1. Uploading of PDB file

<jmol ala.pdb.gz 150 150></jmol>

The PDB file of alanine, ala.pdb.gz was uploaded to this namespace.

You can display a link for the file by the follwing code like this.

  *{{pdb:ala.pdb.gz|Ala.pdb.gz}}

 {{file name|displaying name}}

The code above will display the following. Visitors can download the file by this link.

About compression by gzip

You can get raw PDB files from RCSB PDB page. Since they are plain text format, compress them by using gzip. Plain .pdb file format is prohibited in this DokuWiki.

2. Display molecules !

You can use 'jmol' tag for displaying Jmol applets.

<jmol (PDB file name) (width) (height) (button)>

// javascripts for Jmol. You can use jmol.js library.

</jmol>

The plugin requires 'PDB file name'. Other items are not neccesary.

2-1 The simplest code

First of all, write the simplest code.

The sipmlest
Just place the file name.

<jmol arg.pdb.gz></jmol>

<jmol arg.pdb.gz></jmol>

2-2 Simpler code

One might want to change the size of applet.
You can use the two properties, width and height.

Simpler code

<jmol tyr.pdb.gz 500 160></jmol>

<jmol tyr.pdb.gz 500 160></jmol>

2-3 Button for late loading

If the PDB file is large, it would take a long time to load the page. And, if there are many Jmol applets in the page, it also would take a long time.
In the such cases, you can place the loading button so that the visitor won't be waited.

Button

<jmol ile.pdb.gz 200 200 true></jmol>

<jmol ile.pdb.gz 200 200 true></jmol>

2-4 Advanced

Advanced users of Jmol may want to adjust the parameters or utilize 'jmol.js' codes. You can code the scripts within 'jmol' tag.

Using jmol.js

<jmol pro.pdb.gz 200 200 true>
   jmolBr();
   jmolRadioGroup([
       "spacefill off",
       "spacefill 20%",
		["spacefill 95%", null, "checked"]
       ], "<br />");
	jmolBr();
</jmol>

<jmol pro.pdb.gz 200 200 true>

 jmolBr();
 jmolRadioGroup([
     "spacefill off",
     "spacefill 20%",
	["spacefill 95%", null, "checked"]
     ], "<br />");
jmolBr();

</jmol>

Pages containing Jmol

See pages with 'Jmol' tag.

Links

Acknowledgment

The web page 'An Introduction to Jmol Scripting' by Nathan Silva and David Marcey was greatly helpful to write Jmol script codes.