CREST Jmol Resources

Below is a collection of CREST Team Resources to help with CREST projects and materials development.

Through September of 2018, the CBM plans to use Jmol Version 14.15.3.

Jmol Version 14.15.3 (Mac or PC) (Single JAR file)

Note that you will need to have Java on your computer to run the desktop version of Jmol. Most computers will already have a Java installed, but if you do not, you can download it for free from https://java.com/en/download/.

Jmol is an open source molecular visualization program available to researchers, educators and students. Please note for CREST projects beginning August 24 and later, we will be using Jmol 14.4.4. The link above will provide you with that release. Later releases of Jmol are available, but have not been completely tested for compatibility with our 3D printers.


Digital Jmol Training Guide

These materials include and expand on the written Jmol Training materials (below) and will be replaced by the Jmol Training Guide Website (above) when it is complete.

Written Jmol Training

A PDF version of the Jmol Training Guide that leads users through downloading Jmol, visualizing proteins using the command line and creating Jmol models to be built using 3D Printing Technology.

The written Jmol Training Guide can also be downloaded as individual sections using the links below.

Jmol Quick Reference Sheet (pdf)
A double-sided Jmol Quick Reference Sheet that highlights key commands and useful resources for designing protein models in Jmol.

How to Morph a Protein (pdf)
Instructions on how to "morph" your protein (between two PDB files) using the Yale Morph Server.


Jmol Quick Links

Additional Jmol Notes


Guidelines for Submission

When submitting a model design for review, please include

The model should be reviewed by your instructor and/or research mentor for accuracy of displayed details; CBM staff will review the model for structural soundness.

Guidelines for submissions are provided below:

Model Design Parameters
This form will help you think through what features you might want to include in your model design.

Model Description Sheet
Each model that is built is accompanied with a Model Description Sheet that includes an abstract describing the molecular story as well as a key that describes the coloring scheme and displayed sidechains for the model. The Model Description helps to convey the molecular story of the model when you are not present to tell the story yourself.

Guidelines for Writing an Abstract
Recommended design guidelines for writing an abstract that will be included on your Model Description Sheet..

Model Design Review
Parameters to review to ensure your model is ready to build.

Guidelines for Designing a Poster
Recommended design guidelines for writing a CREST Team poster.

Jmol Images for Posters
Tricks for getting high resolution Jmol images

Sample Posters
A collection of sample posters that represent the good, the bad and the ugly.

Final Oral Presentations
Recommended guidelines and concepts for creating a CREST oral presentation.

 

Jmol Tutorials

Many CREST Teams develop interactive molecular tutorial web pages using the molecular visualization program Jmol. Two main applications, Proteopedia and the CBM's Jmol Tutorial Creator allow for quick and easy Jmol tutorial development.

David Canner's PowerPoint Presentation
Proteopedia is a free, collaborative 3D-encyclopedia of proteins & other molecules. This overview Powerpoint slideshow introduces Proteopedia and explains its basic functionality.

CBM Electronic Poster Creator
In this interactive envrionment, users can create interactive Jmol tutorials using a collection of simple buttons and controls. These tutorials can then be exported for future viewing or editing.

Viewing Small Molecules From the NIH Cactus Database: If you want to view a small molecule in the Electronic Poster Creator, enter ANY pdb file in the "Enter pdb file to be used here" box. (4ins is a small file that loads quickly.) Then, for the first command in the Jmol command box, enter:

load $filename

Some examples:

load $adenine

load $lysine

load $glucose

load $aspirin

NOTE: The CBM Electronic Poster Creator is hot off the press - and we are still troubleshooting. If you encounter difficulties, please contact Mark Hoelzer (hoelzer@msoe.edu). Please describe the issue as well as the browser you are using and, if possible, attach the in-progress Jmol tutorial or electronic poster being developed. We also welcome feedback on how you are using the tool!



The CREST Project is funded by NSF-DUE 1022793 and NSF-DUE 1323414.

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