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Edumol user guide (V 2.0)

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Johannes Pernaa
Johannes Pernaa

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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Johannes Pernaa PhD, Beng Version 2.0 Edumol user guide 18.5.2017
Content ¡ñ Edumol history ¡ñ Architechture ¡ñ Basic tools, buttons & operations
Edumol history ¡ñ 2008¨C2010: ¡ñ Jmol-based site ¡ñ Java ¡ñ 2010¨C2014 ¡ñ iPads arrived ¡ñ Site continued via Jmol ¡ñ 2014 ¨C Edumol 1.0 ¡ñ JSmol had been developed ¡ñ Edumol changed its core to Jsmol ¡ñ 2017 ¨C Edumol inspired molecular modeling book was launched
Field of compu- tational chemistry
Edumol features
3D user interface Notice: Protein has to be reatrieved via PDB ID, like ¡±2mlt¡± returns melittin.
Base ¡ñ File ¡ñ Open & save file ¡ñ Export 3D to Blender or 3D printing ¡ñ Export Image ¡ñ Export mol to ChemSketch ¡ñ 3D canvas ¡ñ Height + width if needed ¡ñ Background color ¡ñ High resolution for fast web connection ¡ñ NIST search via chemical formula
Export 3D ¡ñ Works really fine. 3D-printing works really fine.
Move ¡ñ Rotate via 1 click ¡ñ Front, right, up ¡ñ X, Y, Z -axis ¡ñ Click atom and center molecule ¡ñ Spin ¡ñ Set high resolution on, if you wish ¡ñ to see the molecule rotating
Model & Biomodel ¡ñ Molecule models ¡ñ CPK ¡ñ Ball-and-stick ¡ñ Try all out ¡ñ Biomodel options ¡ñ Structures ¡ñ Colors ¡ñ Hydrogen bonds
Visualize ¡ñ MEP = Molecular electrostatic potential ¡ñ Charge distributions of molecules ¡ñ Charge related properties of molecules ¡ñ Shape and size ¡ñ Good article from Chemistry LibreTexts ¡ñ Atom labels ¡ñ Partial charge and dipole vector ¡ñ Atom numbers
Measure
Calculate ¡ñ Works only for geometrical optimization ¡ñ MMFF94 molecular mechanics calculations
2D editing FEATURES ¡ñ JSME 2D editing tools ¡ñ Intergrated to JSmol core ¡ñ Search structures from databases ¡ñ If NCI is down, 2D isn't working ¡ñ Note! Protein structures can't be edited in 2D side
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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Edumol user guide (V 2.0)

  • 1. Johannes Pernaa PhD, Beng Version 2.0 Edumol user guide 18.5.2017
  • 2. Content ¡ñ Edumol history ¡ñ Architechture ¡ñ Basic tools, buttons & operations
  • 3. Edumol history ¡ñ 2008¨C2010: ¡ñ Jmol-based site ¡ñ Java ¡ñ 2010¨C2014 ¡ñ iPads arrived ¡ñ Site continued via Jmol ¡ñ 2014 ¨C Edumol 1.0 ¡ñ JSmol had been developed ¡ñ Edumol changed its core to Jsmol ¡ñ 2017 ¨C Edumol inspired molecular modeling book was launched
  • 6. 3D user interface Notice: Protein has to be reatrieved via PDB ID, like ¡±2mlt¡± returns melittin.
  • 7. Base ¡ñ File ¡ñ Open & save file ¡ñ Export 3D to Blender or 3D printing ¡ñ Export Image ¡ñ Export mol to ChemSketch ¡ñ 3D canvas ¡ñ Height + width if needed ¡ñ Background color ¡ñ High resolution for fast web connection ¡ñ NIST search via chemical formula
  • 8. Export 3D ¡ñ Works really fine. 3D-printing works really fine.
  • 9. Move ¡ñ Rotate via 1 click ¡ñ Front, right, up ¡ñ X, Y, Z -axis ¡ñ Click atom and center molecule ¡ñ Spin ¡ñ Set high resolution on, if you wish ¡ñ to see the molecule rotating
  • 10. Model & Biomodel ¡ñ Molecule models ¡ñ CPK ¡ñ Ball-and-stick ¡ñ Try all out ¡ñ Biomodel options ¡ñ Structures ¡ñ Colors ¡ñ Hydrogen bonds
  • 11. Visualize ¡ñ MEP = Molecular electrostatic potential ¡ñ Charge distributions of molecules ¡ñ Charge related properties of molecules ¡ñ Shape and size ¡ñ Good article from Chemistry LibreTexts ¡ñ Atom labels ¡ñ Partial charge and dipole vector ¡ñ Atom numbers
  • 13. Calculate ¡ñ Works only for geometrical optimization ¡ñ MMFF94 molecular mechanics calculations
  • 14. 2D editing FEATURES ¡ñ JSME 2D editing tools ¡ñ Intergrated to JSmol core ¡ñ Search structures from databases ¡ñ If NCI is down, 2D isn't working ¡ñ 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.