Phase 1: The Modeling Project


This Year's Protein Model Design Resources Building a Model

This Year's Protein

This year’s topic will focus on the work of Gerald Hart – the 2017 Herbert Tabor Award winner. Dr. Hart established a whole new field of research when he reported in the 1980’s that many cytosolic and nuclear proteins contained Ser and Thr amino acids that were modified by N-acetylglucosamine. Over the years, Dr. Hart and his colleagues have shown that this modification rivals phosphorylation as a fundamental mechanism whereby protein structure and function is regulated in our cells. This O-GlcNAcylation (yes... this is a word – pronounced "OH-Gluck-Nack–illation") has been shown to regulate all kinds of cellular processes including transcription, protein turnover, neurodegenerative diseases, cellular stress responses and cancer.

Once you get your team registered, you will have access to all the modeling resources that will allow you to explore this topic. . .

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 2018, 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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