How to get a
on your website
slides.com/mbrgr/how-to-molecule
Melanie Burger
Let's start with demos
Lab3D
Lysome mechanism
Method 1
ChemDoodle Web Components
Method 2
ePMV or mMaya, and
Verold (or Unity?)
+
...a challenge!
Google Doc
Method 1
ChemDoodle Web Components
A Javascript library for chemical graphics & cheminformatics
18 components
Specialized <canvas> classes
var molecule = ChemDoodle.readPDB(PDBfileContentFromServer);
var component = new ChemDoodle.ViewerCanvas('component', 100, 100);
component.loadMolecule(molecule);Add script where you want the component to appear
Customize appearance
"Chemically intelligent"
I'm Alexa Fluor 488
Method 2
ePMV or mMaya, and
Verold (or Unity?)
Molecular graphics plugins for 3D graphics software
3D content web
publishing platform
Retrieve structures from PDB
Customize molecule appearance through UI
Drag-and-drop 3D assets
Handles mesh and animation optimization
Customize scene through UI
Attach event handlers
Create custom functionality with three.js
Method 1
ChemDoodle Web Components
Method 2
ePMV or mMaya, and
Verold (or Unity?)
Pros
- Chem. intelligent
- Faster for simple molecule display
- Well-documented
- More complex scenes
- Custom animations
- No coding required
Con
- Limited to chemical files
- Little community support
- ePMV/mMaya/Maya ~buggy
- Cannot use sim data for animations
Use ChemDoodle to do chemistry,
and ePMV/mMaya + Verold for everything else
one more thing...
...how to get molecular data?
$0
- Install iBabel
and ChemSpotlight - Look up structure and copy descriptor:
- PubChem
- eMolecule
- iBabel > Viewer > CIR (paste identifier) > import
- iBabel > Convert, (choose file, choose PDB output file type, check "generate 3D") > Convert
$
ChemDoodle desktop app
(also ChemDraw?)
$$
Molecular modelling software, e.g. Spartan, Gaussian, Maestro
melanie.brgr@gmail.com
@melaniebrgr
slides.com/mbrgr/how-to-molecule