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.