Jmol Training
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.


Description:
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.
Click for Details and to AccessTopics Covered:
- Protein Structure
- Molecular Visualization
External Resources:
★ How to Access:
- Getting Started in Jmol
(Webpage) (PDF) - Finding Protein and Molecular Structures
(Webpage) (PDF) - Changing Colors and Display Formats
(Webpage) (PDF) - Saving and Reloading Your Work
(Webpage) (PDF) - The Select Command and Boolean Operators
(Webpage) (PDF) - Adding Sidechains to Your Structure
(Webpage) (PDF) - Bonds and Structural Supports
(Webpage) (PDF) - Working with Nucleic Acids
(Webpage) (PDF) - 3D Printing a Model Designed in Jmol
(Webpage) (PDF)


Description:
Jmol can be embedded directly into a web page, allowing for the creation of fully interactive molecular tutorials that run on any device, from smart phones and tablets to desktop and laptop computers. The Jmol Tutorial Creator lets you develop custom tutorials through a user-friendly online application.
Click for Details and to AccessExample Tutorials:
- Serotonin Transporter by Kendra Banks Roberta Halimi
- Collagen by Alverno College
- Penicillin Binding Protein Inhibition by Lactivicins by Nicole Bazan and Debra Kopydlowski
★ How to Access:
- Jmol Tutorial Creator (website)
Documentation:
Topics Covered:
- Protein Structure
- Molecular Visualization

CBM Blank Placemat Template - 8.5" x 11" (PowerPoint File)
This blank placemat template will give you and your students a simple starting point to begin designing a molecular visualization placemat.

CBM Blank Poster Template - 36" x 24" (PowerPoint File)
This blank poster template will give you and your students a simple starting point to begin designing a molecular visualization poster.

Storyboard Template (PDF)
This simple storyboard template will help you and your students clearly define the purpose, goals, flow and content of your placemat, poster, Jmol tutorial, video or animation.
Nitty Gritty of 3D Printing


- History of 3D printing
- What can they currently do?
- Parts and supplies of an FDM printer
Click for Details and to Access
FDM 3D Printing
- Overview of FDM Printing (PowerPoint File)
- Fused Deposition Modeling (FDM / FFF) by 3D Printing from Scratch (PDF)
- Short Video on FDM Printing Technology (YouTube)
Reviews of FDM Desktop 3D Printers and Supplies
- http://www.3ders.org/pricecompare/3dprinters/
- https://www.3dhubs.com/3d-printers
- http://directory.3dprintingindustry.com/category/3d-printer-manufacturers/
- http://3dprintingfromscratch.com/3dprinters-catalog/
- http://3dprintingfromscratch.com/3d-printer-filament-finder/
- https://www.3dhubs.com/materials
History of 3D Printing
- History of 3D Printing (PowerPoint File)
- History of 3D Printing: the Free Beginner’s Guide by 3D Printing Industry (PDF)
- History of 3D Printing by ZD Net (Webpage)
- Many 3D Printing Patents Are Expiring Soon: Here’s A Round Up & Overview of Them by 3D Printing Industry (Webpage)
- 3D Printing and Education by AJ Perez (PDF)
Overview of 3D Printing Technologies
- Types of 3D Printing Technology by 3D Printing From Scratch (Webpage)
- Continuous Liquid Interface Production (CLIP) Technology by the Washington Post (Webpage)
- Demonstration of Carbon 3D using CLIP Technology (YouTube)
Most Common Desktop 3D Printing Companies


- Leveling and preparing the platform
- Loading and changing materials
- Preparing the machine to build
Click for Details and to Access
Routine Maintenence
- Routine Maintenence (PDF)
- Nozzle Cleaning Tool(Webpage)
- Nozzle Cleaning Tutorial (YouTube)
Preparing the Machine to Print
- Preparing the Machine to Print (PowerPoint File)
- Preparing the Machine to Print (PDF)
- Suggested 3D Print Bed Materials by Richard Horne (Webpage)
- Clearing Nozzles by MakerBot 3D Printing Wiki (Webpage)
- The 3D Printing Essential Toolkit by 3D Printing For Beginners (Webpage)


- Loading .stl files into a slicer
- Settings for your print
- Starting the printer!
Click for Details and to Access
Open Source Slicers
- Cura Slicer Download (Webpage)
- Skeinforge Slicer Download (Webpage)
- Skeinforge Slicer Wiki Page (Webpage)
Slicers and 3D Printing
- Slicers and Slicer Settings (PowerPoint File)
- Trouble-shooting Slicer Settings (PDF)
- Overview of Slicers and User Interfaces for 3D Printing by EduTech Wiki (Webpage)


- Removing models and struts
- Smoothing, painting and gluing
Click for Details and to Access
Gluing Parts
- Loctite Super Glues
- StickFast Super Glues
- Great Planes Instant Glue Activator (Webpage)
- Merging ABS Plastic Parts Using Acetone (YouTube)
- Guide to Gluing ABS Parts by Stratysus (Webpage)
Painting and Sealing Your Parts
- Golden Brand Fluid Acrylic Paints (Webpage)
- Testors Enamel Paints (Webpage)
- Smooth-on Epoxy Coatings (Webpage)
- The "Ultimate Guide" to Finishing 3D Printed Parts by Dave Evans (Webpage)
- Sanding, Cleaning and Painting 3D Printed Parts by Instructables(Webpage)
Overview of Post Processing
- Overview of Post Processing (PowerPoint File)
Dissolvable Filament and Removing Supports
- Using Limolene to Remove HIPS Support Material (PDF)
- Using Water to Remove PVA Support Material (PDF)
- WaveWash Support Cleaning System (Webpage)
Smoothing and Polishing Models
- Using Acetone to Smooth ABS Plastic Parts (PDF)
- Using XTC-3D to Smooth Rough Parts (PDF)
- Smoothing ABS Parts with Acetone by Hack-a-Day (Webpage)
- Building a Basic Acetone Evaporation Chamber by Sink Hacks (Webpage)
- Smoothing ABS Parts with Acetone (YouTube)
- Low Heat Acetone Smoothing Wash for ABS Parts (Webpage)
- Advanced Smoothing Techniques Using Ultrasonic Vapor Polisher (Webpage)
- MagicBox Commercial Smoother for ABS or PLA Parts (Webpage)


- Trouble shooting
- Discussion boards and resources
- A role for this community of friends!
Click for Details and to Access
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)
Trouble Shooting Overview
- Discussion Boards and Trouble Shooting (PowerPoint File)
- The Problem with 3D Printing. . . (PDF)
User Manuals and Official Support
- Rep Rap Printer Trouble Shooting Guide (Webpage)
- Lulzbot Printer Support Documents (Webpage)
- Ultimaker Printer Trouble Shooting Guide (Webpage)
- Stratysus Mojo Printer Customer Documents (Webpage)
- 3D System Cube Printer Tutorials (Webpage)
- MakerBot Printer Support Documents (Webpage)
- Afinia Printer Manuals (Webpage)
- Afinia Printer Frequently Asked Questions (Webpage)
Discussion Boards and Forums
- Rep Rap Printer Forum (Webpage)
- Lulzbot Printer Forum (Webpage)
- Ultimaker Printer Forum (Webpage)
- 3D Systems Cube Printer Forum (Webpage)
- 3dPrintBoard.com MakerBot Printer Forum (Webpage)
- Tested.com MakerBot Printer Forum (Webpage)
Molecular Stories


Description:
Water molecules rapidly flow through the membrane-spanning protein aquaporin. Its structure consists of 6 alpha helices and 2 half alpha helices that form an hourglass shape through which water molecules move one at a time. A variety of engaging stories can be explored related to this amazing structure and the scientists that discovered it.
Click for Details and to AccessTopics Covered:
- Protein Structure
- The Process of Science
- Osmosis
STL Files:
- Aquaporin STL File Overview (PDF)
- Aquaporin STL Files (ZIP)
- Aquaporin PDB Files (ZIP)
External Resources:
★ How to Access:
- Borrow from the Lending Library
- Purchase Mini Model from 3D Molecular Designs
- Purchase Phospholipid Membrane Transport Kit from 3D Molecular Designs
Additional Resources:
- Subangstrom Resolution X-Ray Structure Details Aquaporin-Water Interactions (PDF)
- A Tale of Two Channels (PDF)
- The 2003 Nobel Prize in Chemistry (PDF)
- Appearance of Water Channels in Xenopus Oocytes Expressing Red Cell CHIP28 Protein (PDF)
- The Aquaporin Water Channels by Peter Agre (PDF)
- Watch Water Flow (PDF)


Description:
Help your students better visualize and understanding ionic interactions and protein channel selectivity of the potassium channel. A variety of engaging stories can be explored related to this amazing structure and the scientists that discovered it.
Click for Details and to AccessTopics Covered:
- Protein Structure
- The Process of Science
- Action Potential
STL Files:
★ How to Access:
- Borrow from the Lending Library
- Purchase Mini Model from 3D Molecular Designs
- Purchase Phospholipid Membrane Transport Kit from 3D Molecular Designs
Additional Resources:


Description:
This amazing genetic story takes you from undiagnosable symptoms and a dying child to gene sequencing and an eventual cure. Nic Volker's rare genetic disorder, effecting his XIAP protein involved in cell apoptosis, can be used to to discuss gene sequencing, protein structure/function, the flow of genetic information, and personalized medicine.
Click for Details and to AccessTopics Covered:
- Protein Structure
- The Process of Science
- Gene Sequencing
- Personalized Medicine
STL Files:
- XIAP STL File Overview (PDF)
- XIAP STL Files (ZIP)
- XIAP PDB Files (ZIP)
Additional Resources:
- Nic Volker and XIAP Placemat(PDF)
- Nic Volker and XIAP Presentation (PowerPoint File)
- The Role of XIAP in the Mammal Apoptosis Pathway (PDF)
- Nic Volker and XIAP Learning Module from the 2012 Science Olympiad Protein Modeling Event (Webpage)
- Nic Volker and XIAP Jmol Tutorial (Webpage)
- Milwaukee Journal Sentinal Story on Nic Volker (Webpage)
- One in a Billion: The Story of Nic Volker and the Dawn of Genomic Medicine (Book)


Description:
The twenty standard amino acids make up all of the proteins in our bodies. They are linked together in unique sequences, based on the genetic code inherited in our DNA, to form complex 3-dimensional machines. They are also excellent structures for 3D printing!
Click for Details and to AccessTopics Covered:
- Protein Structure
- Basic Principles of Chemistry
STL Files:
- Amino Acid STL File Overview (PDF)
- Amino Acid STL Files (ZIP)
- Amino Acid PDB Files (ZIP)
Additional Resources:
- Protein Structure Jmol Tutorials
- Primary Structure (Webpage)
- Secondary Structure (Webpage)
- Tertiary Structure (Webpage)
- Quaternary Structure (Webpage)
- Amino Acid Starter Kit from 3D Molecular Designs (Kit)
- What is a Protein? from the RCSD Protein DataBank (PDF)
- Amino Acid Sidechain Chart (PDF)


Description:
DNA Contains the hereditary information needed to create every different protein in our bodies. Encoded with the four standard bases (Guanine, Adenosine, Cytosine, and Thimine) and read by ribosomes three bases at a time, this genetic code in large part makes us who we are.
Click for Details and to AccessTopics Covered:
- DNA Structure
- Basic Principles of Chemistry
- Flow of Genetic Information
Documentation:
- Hydrogen Bonding in DNA Base Pairs Jmol Tutorial (Webpage)
- DNA Discovery Kit from 3D Molecular Designs (Kit)
- DNA Starter Kit from 3D Molecular Designs (Kit)
STL Files:
- Nucleic STL Files (ZIP)
- Nucleic PDB Files (ZIP)
Miscellaneous Resources

MSOE Center for BioMolecular Modeling
Fact Sheet

3D Molecular Designs
Product Catalog

The Three Dimensions
of the Next Generation Science Standards

Rethinking Outreach
Teaching the Process of Science Through Modeling
Our work is supported by grants from the NIH National Center for Research Resources SEPA program, the NSF CCLI program, the Department of Education Institute for Educational Sciences and the Howard Hughes Medical Institute.