Phase 1: The Modeling Project


This Year's Topic Model Design Resources Building a Model

This Year's Topic

We're delighted to announce that we will be exploring research from the lab of Dr. Christine Dunham, who has received the ASBMB Young Investigator Award. We’re excited about the opportunity to work with Dr. Dunham’s lab for a number of reasons:

  • Her research topic(s) range from core curricular topics (protein synthesis, antibiotic resistance) to more advanced topics (regulation of protein synthesis in response to various types of stress) – topics relevant for both early career and upper level undergraduates!
  • The lab employs a range of interdisciplinary approaches in structural biology, biochemistry and molecular biology
  • Dr. Dunham has LOTS of structures in the PDB from which to choose!!!
  • All of her publications are accessible from her website.
  • One of her graduate students (Ian Pavelich) worked in the CBM as an undergraduate and knows all things modeling!

Exploring the Ribosome

Check out this video in which Tim and Margaret explore various riobosome models.

Dr. Dunham talks about her research, her career path and more!

Check out the video that Dr. Dunham and Ian made here.

Suggested Approach

Start exploring background information to narrow your research focus!

Background Reading
  • You might want to start by exploring (comparing) information about translation from various textbooks (intro bio, genetics, cell biology, biochemistry)
  • To get a more in depth view of translation, you might tackle an article or two in Trends in Biochemical Sciences, August 2017, a special issue on ribosomes and translation.
  • It might be an interesting discussion to compare the depth of the “facts” in the textbook with those in current research articles!
  • Another discussion might involve comparing prokaryotic and eukaryotic processes – and why/whether it is of value to study prokaryotic systems
Digging Deeper
  • With this background information, you should be ready to tackle some of the Dunham lab articles. Some of the articles list the associated pdb files, either on the first or last page or in the figure legends. If you can’t find the pdb files listed in the article, search the Protein Databank for the first author. Structures are listed in order of deposit, with the most recent at the top. Look for the primary citation that matches your paper to find associated pdb files. Pick a topic that intrigues you and start exploring.
  • If you want to explore the stringent response (bacteria under stress), here’s a good review from Trends in Microbiology

For those of you who have worked with Jmol in the past, there will be a few twists and turns in this year's project. If your team chooses to work with a model of the ribosome, there will be a few extra steps in handling the large data files for such a large structure. It's an opportunity to expand your horizions and pick up a few more tools in your molecular visualization toolkit. Once you have narrowed down which PDB file you want to use, the molecular story you want to tell, and what you want to include in your model, please contact Margaret (franzen@msoe.edu) to set up a Zoom meeting with your team to discuss your model design.

Model Design Resources



Jmol is a free, open source molecular visualization program used by students, educators and researchers internationally. The Jmol Training Guide will provide the tools needed to create molecular renderings, physical models using 3-D printing technologies, as well as Jmol animations for online tutorials or electronic posters.

Through September of 2019, the CBM plans to use Jmol Version 14.15.3.

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 Quick Reference Sheet

This two-sided reference sheet is the perfect companion for any Jmol designer. Side one includes the most important Jmol commands and side two is a handy amino acid chart.



Jmol Training Guide

This collection of tutorials covers everything needed to design physical models of protein and molecular structures using Jmol. These tutorials are set up to learn as you go.



Additional Design Resources

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

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

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

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 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.



Useful External Resources

Building a Model

This section of the website provides resources for building a protein model on a 3D printer at your institution. After you design your model in Jmol, you'll have to go thorugh additional steps to communicate your design with your printer. Not all prnters are the same, but with a little time and practice, you'll be on your way! CBM staff stand ready to assist! If you have any questions about building a physical protein model on your 3D printer, contact Mark Hoelzer at: hoelzer@msoe.edu.

How to Create an .STL File of Your Jmol Design

Webpage Tutorial

PDF Tutorial



How to 3D Print Your .STL File

An Introduction to Desktop 3D Printing

  • History of 3D printing
  • What can they currently do?
  • Parts and supplies of an FDM printer

Click for Details and to Access
Preparing Your Printer

  • Leveling and preparing the platform
  • Loading and changing materials
  • Preparing the machine to build

Click for Details and to Access
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Routine Maintenence
Preparing the Machine to Print
"Slicing" Your Model and Sending it to Print

  • Loading .stl files into a slicer
  • Settings for your print
  • Starting the printer!

Click for Details and to Access
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Open Source Slicers
Slicers and 3D Printing
Trouble Shooting Problems

  • Trouble shooting
  • Discussion boards and resources
  • A role for this community of friends!

Click for Details and to Access
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General Trouble Shooting Discussion Boards and Forums
  • Soliforum - community-populated discussion board on a wide range of topics (Webpage)
  • 3Ders.org - community-populated discussion board on a wide range of topics (Webpage)
  • Toms Guide to 3D PRinting - a useful overview of 3D Printing (Webpage)
  • Toms Guide to 3D Printing Discussion Forums - community-populated discussion board on a wide range of topics (Webpage)
  • 3D Verkstan - a great trouble shooting resource for all types of common problems/errors (Webpage)
  • The 3D Printing Directory - A general resource for printer companies and organizations (Webpage)
  • 3Ders - a news and reviews website with tons of great articles published regularly (Webpage)
  • 3D Hubs - a useful way to find and connect with local printers (Webpage)
  • 3D Printing From Scratch - a news and reviews website with tons of great articles published regularly (Webpage)
  • Fargo 3D Printing - a supply and purchase site with reviews and product feedback (Webpage)
  • 3D Printing for Beginners - a news and reviews website with tons of great articles published regularly (Webpage)


Questions about the CREST Program? Contact Margaret Franzen at franzen@msoe.edu or 414-277-2806. We look forward to hearing from you!



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

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