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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.
Jmol Training Guide
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.

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Topics Covered:
  • Protein Structure
  • Molecular Visualization
External Resources:
★ How to Access:
Jmol Tutorial Creator
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.

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Example Tutorials:
★ How to Access:
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

Section 1

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

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Section 2

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

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Routine Maintenence
Preparing the Machine to Print
Section 3

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

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Open Source Slicers
Slicers and 3D Printing
Section 4

  • Removing models and struts
  • Smoothing, painting and gluing

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Section 5

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

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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)
Trouble Shooting Overview
User Manuals and Official Support
Discussion Boards and Forums

Molecular Stories

Aquaporin and the Movement of Water
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.

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Potassium Channels and Action Potentials
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.

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Nic Volker and XIAP
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.

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The Twenty Standard Amino Acids
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!

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Topics Covered:
  • Protein Structure
  • Basic Principles of Chemistry
STL Files:
Additional Resources:
DNA and Nucleotides
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.

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Topics Covered:
  • DNA Structure
  • Basic Principles of Chemistry
  • Flow of Genetic Information
Documentation:
STL Files:


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.