Help:Jmol in EcoliWiki

About

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 and custom EcoliWiki templates.

What Types of Structures can I 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 (from PyMol) will not work.

"How To" Embed the Image

Text inserted by the Jmol_template

Setting the file name to the correct file

• 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 support, please contact us for help.

• When you upload your pdb file, put

{{subst:Jmol_template}} 

in the Description box. Click "Save" to save the page. The template will automatically load all the technical details necessary to make this work. 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.

• You will need to replace some text in your picture file. Click the "Edit" link again and there will be a lot more text than what you wrote (that's supposed to happen). In place of "REPLACE_WITH_FILENAME" (several lines from the top), insert the pdb file name (just XXXX.pdb). This will allow EcoliWiki to upload the file contents of the file.
  • If can add a short, useful title, replace "Text label", which is on the fourth line from the top, with the appropriate text. Explanations, links to the paper, or other comments go in the "Notes" section directly below the "Structure" and "Structure Figure" boxes.
• 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 display on the page.

Troubleshooting

• Biological vs crystallographic units: The coordinate files from the PDB are usually for the crystallographic asymmetric unit. This means that there may be multiple molecules in the same file, or that there may only be part of a multimer. The PDB provides a separate file for the biological unit in many cases. See this tutorial at the PDB.

Examples

• Image:1LMB.pdb shows the page you'll need to edit text on
• Image_talk:1LMB.pdb shows more images used on the main page
• lambda_repressor/N-domain is the interactive end product

See also

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

References

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