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Edumol user guide (V 2.0)

Edumol user guide (V 2.0)

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This slide set is a small user guide for Edumol.fi web application.

Edumol is JSmol-JSme-based molecular modelling site. It's chemistry and educational functions are optimized for all school levels. Please enjoy.

Learn more about molecular modeling in chemistry education through this book: http://bit.ly/immice. All exercises are done via Edumol.

This slide set is a small user guide for Edumol.fi web application.

Edumol is JSmol-JSme-based molecular modelling site. It's chemistry and educational functions are optimized for all school levels. Please enjoy.

Learn more about molecular modeling in chemistry education through this book: http://bit.ly/immice. All exercises are done via Edumol.

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Edumol user guide (V 2.0)

  1. 1. Johannes Pernaa PhD, Beng Version 2.0 Edumol user guide 18.5.2017
  2. 2. Content ● Edumol history ● Architechture ● Basic tools, buttons & operations
  3. 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. 4. Field of compu- tational chemistry
  5. 5. Edumol features
  6. 6. 3D user interface Notice: Protein has to be reatrieved via PDB ID, like ”2mlt” returns melittin.
  7. 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. 8. Export 3D ● Works really fine. 3D-printing works really fine.
  9. 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. 10. Model & Biomodel ● Molecule models ● CPK ● Ball-and-stick ● Try all out ● Biomodel options ● Structures ● Colors ● Hydrogen bonds
  11. 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. 12. Measure
  13. 13. Calculate ● Works only for geometrical optimization ● MMFF94 molecular mechanics calculations
  14. 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. 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.

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