Help:Jmol in EcoliWiki

Description

Jmol is a Java-based molecular visualization tool. Extensive documentation can be found on the Jmol website. This page describes how you can embed images and set scenes inside EcoliWiki using Jmol's MediaWiki extension.

What types of structures to Display

The structures that are most displayed are protein, nucleotide, inorganic and organic molecules, etc.

Selecting a Compatible File

There are several file formats compatible with the jmol viewer, such as .pdb, .mol. Other file formats such as .pse will not work.

Embedding the Image

• Click on the "Upload File" link toolbox to the left. EcoliWiki allows you to upload pdb files so you may display a picture of the structure on any page you wish. If you encounter a file format that EcoliWiki does not allow, please contact us for help.

• When you upload your pdb file, put {{subst:Jmol_template}} in the Description box. The template will automatically load all the technical details necessary to make this work. Click "Save" to save the page. This will put the viewer in a box on the right that allows text to wrap around it, add the Help link, set the background to white, and so on. The box will appear with a "1" in it.

• You will need to replace the one with your picture. Click the "Edit" link again and there will be a lot more text than what you wrote (that's suppose to happen). In place of the 1 (several lines from the top), insert the pdb file name. This will allow EcoliWiki to upload the file contents of the file. Click "Save." Your picture should replace the 1 and should be rotating around. Highlight and copy the title of the page (at the top) for the next step.

• Go to the gene product page where you want to embed the image. Scroll down to the Structure Heading, and click the edit link for the structure notes. Paste the Image title into the text box and add 2 sets of curly brackets. Example:{{Image: 1JFE.pdb}}. Click "Save" and the image should be on the page

Examples

• Image:1LMB.pdb
• Image_talk:1LMB.pdb
• lambda_repressor/N-domain

Jmol scripting

Is this Relevant still? We'll just cover a few commonly used commands. See below for links to more extensive documentation and tutorials.

Command	Notes	Examples
select [atom-expression]	You need to select things to work on them selectively. Atom expressions include: numbers for residues :chain_id for chains (subunits) backbone sidechains	select 1-10; selects residues 1-10 in all chains select *:A; selects all atoms in chain A select 84:A, 156:B; selects two residues, one in chain A and one in chain B.
spacefill (on/off/only) (synonym: cpk)	Shows atoms as VdW sized spheres
wireframe (on/off/only)	shows the bonds between atoms.
cartoon (on/off/only)	shows helices and sheets in cartoon form.
zoom (atom-expression) %zoom zoomto (atom-expression) %zoom	centers on atom-expression and zooms there to the specified percentage of the 100% default. The zoom factor can range from 5 to 20,000, where larger numbers are zoomed in.	zoomto (84:A) 500;
color [drawn-object] [RGB-color]	if drawn-object is ommitted, color uses whatever is selected. Colors can be: color names: white, blue, red, cyan, etc. special names monomer - gives a rainbow from N to C cpk amino - by aa type for proteins shapely - by base type for nucleic acids structure - helices and sheets chain - subunits hex values: [xRRGGBB] (brackets needed) RGB triples: [255,0,255]
edit table

See also

• Scripting on the Jmol wiki.
• Colors
• scripting commands

References

See Help:References for how to manage references in EcoliWiki.