The document is a user guide for the Edumol software, detailing its history, features, and tools for molecular modeling and visualization. It outlines functionalities such as 3D interface operations, file management, export options, and molecular visualization techniques. Additionally, it promotes a book designed to aid in the implementation of molecular modeling in chemistry education using the Edumol application.

1. Johannes Pernaa
PhD, Beng
Version 2.0
Edumol user guide
18.5.2017

2. Content
● Edumol history
● Architechture
● Basic tools, buttons & operations

3. Edumol history
● 2008–2010:
● Jmol-based site
● Java
● 2010–2014
● iPads arrived
● Site continued via Jmol
● 2014 – Edumol 1.0
● JSmol had been developed
● Edumol changed its core to Jsmol
● 2017 – Edumol inspired molecular modeling book was launched

4. Field of
compu-
tational
chemistry

5. Edumol
features

6. 3D user interface
Notice: Protein has to be reatrieved via PDB ID, like ”2mlt” returns melittin.

7. Base
● File
● Open & save file
● Export 3D to Blender or 3D printing
● Export Image
● Export mol to ChemSketch
● 3D canvas
● Height + width if needed
● Background color
● High resolution for fast web connection
● NIST search via chemical formula

8. Export 3D
● Works really fine.
3D-printing works really fine.

9. Move
● Rotate via 1 click
● Front, right, up
● X, Y, Z -axis
● Click atom and center molecule
● Spin
● Set high resolution on, if you wish
● to see the molecule rotating

10. Model & Biomodel
● Molecule models
● CPK
● Ball-and-stick
● Try all out
● Biomodel options
● Structures
● Colors
● Hydrogen bonds

11. Visualize
● MEP = Molecular electrostatic potential
● Charge distributions of molecules
● Charge related properties of molecules
● Shape and size
● Good article from Chemistry LibreTexts
● Atom labels
● Partial charge and dipole vector
● Atom numbers

12. Measure

13. Calculate
● Works only for geometrical optimization
● MMFF94 molecular mechanics calculations

14. 2D editing
FEATURES
● JSME 2D editing tools
● Intergrated to JSmol core
● Search structures
from databases
● If NCI is down, 2D isn't
working
● Note! Protein structures can't
be edited in 2D side

15. Learn molecular modeling
Introduction to Molecular Modeling in Chemistry Education
This book offers theoretical
insights and hands-on modeling
activities. The goal is to learn how
to implement molecular modeling
in chemistry teaching.
The exercises are performed using
Edumol.fi web application, which is
a free JSmol-JSME-based
molecular modeling and
visualization service.
Order the book.