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. Files can be found at the Protein Data Bank at http://www.pdb.org, as well as other sites.

"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, email us at ecoliwiki@gmail.com for help.
  • On the '"Upload File" page, select the file using the Choose File button in the Source Filename field. The Destination filename should automatically fill out, and you can change the filename here if needed. You do not need to enter any information in the Summary.
  • Upload file using the button at the bottom.

• When your file is uploaded, you will be redirected to your file's page. There will be no image, just a File History section. Use the edit tab at the top of the page, and on the Editing File: page enter

{{subst:Jmol_template}} 

in the description box. Click Save 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. There will not be an image yet.

• 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 you 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 back on the Gene Products page.)
• Click Save. Your picture should be visible 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 figures heading next to the Structure table, and click the edit link for Structure figures. Paste the image title into the text box and add 2 sets of curly brackets:

 {{File:1D9U.pdb}}  

• Click Save and the image should display on the page.
  • The Notes section on this page is the appropriate place for paper references, notes about the figure, etc.

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.