Blender

Introduction

Some introductory material to Blender 3D.

Theory

Add ons

• Align tool
• The animation of paths is easy with AnimAll plugin. Enable it at Preferences.
• TextFx animoitua kirjoituskonetekstiä.

Modifiers

• Array

• Bevel

• Curve

Shader Editor

Rusty metal

Metallic, red

Rendered metallic red

Add Bump (Strength: 0.5), ColorRamp (to Bump/Height), NoiseTexture (Scale: 1.5, Detail: 16), Mapping and Texture Coordinate.

Also a second Bump (to Bump/Normal), NoiceTexture (Scale: 50, Detail: 16) and NoiceTexture (Scale: 20, Detail: 16).

Wood

ColorRamp (brown, orange--brown), NoiseTexture (Roughness: 0.75, Detail: 4, Distortion: 0.7), Ctrl - T (if Node Wrangler Add On is enabled) pops Mapping (Scale X, Y or Z: 7) and Texture Coordinate (Object -> Vector).

Bump (to Principled BSDF/ Normal). NoiseTexture to Bump/ Height (Strength: 0.01).

Wood.

Wood rendered.

Molecular Visualization

ChimeraX

Sciencevis.org

Metrics https://book.bionumbers.org/ cellPACK mMaya

• Diffusion rates
• Concentrations
• Reaction rates
• Dissociation constants

Principles and practices https://www.youtube.com/watch?v=G5FxPdBMUHE&list=PLcKSD7d0T-HBKMOGoghGk3weyrGmA2Re3&index=8

• What ideas will this molecular visualization communicate: learning objectives + what else
• Molecular structure. Structure defines functions. Structural and dynamic information should be both considered.
  • Simple shape: graphical, 2d
  • Arbitrary shape: misleading structural data, possible to use data if available
  • Data-driven base: PDB protein Data Bank
  • Atomic style: Conveys scale, complexity; shows atom types; no chains; visually complex
  • Ribbon style: highlights intermediate structure, functional components, domains and linkers; however Volume is not clear
  • Coarse/ tight surface style:
• What is dynamic realism; experimental data vs photorealism. MD & CG modelling.
  • Crowded messines.
• Principles of molecular visualization (for your consideration)
  1. Molecules move by Brownian motion
  2. Proteins exhibit a range of flexibility
  3. Unproductive collisions are frequent
  4. Many instances of molecules and events exists
• Gravity, friction, light, color, inertia, texture are meanles.
• Use available attention cuing and communication strategies
  • Depth of field, color, saturation, staging, cinematography

Blender for Scientist - Making Any molecule

Blender for Scientist - How to make protein in Blender

• Avogadro; import (or download) from PDB (eg. 1crn.pdb)
  • Cartoon; use settings to
  • Export to VRML
• Import X3D Extensible 3d (.x3d/wrl) and delete the extra camera.
• Tab into edit mode
  • M(erge) By Distance
  • Convert triangles to quads (gives better results). F3 mesh.tris_convert_to_quads -> tris to quads
• Small problems due to Avogadro: Areas of higher vertices density
  • Add modifier: Subdivision surface
  • Add modifier: Weld
  • Apply All; or if not possible Apply both.
• Shade smooth
• Into Edit mode
  • Edge -> UnSubdivide; if not smooth enough, go to Object Mode -> Add Modifier -> Subdivision
  • Edge select: Choose the ring at the end of the molecule. If more ends: Shift G: Amount of Faces Around an Edge. F to fill those. [Check that the scale is one 1; Ctrl+A Scale.] Edit mode; Ctrl+B to bevel and hold shift and drag.
• Change the origin
  • Right click: Set Origin -> Origin to geometry. Alt+G
• Make a copy in Edit mode; Choose the other (by hitting L while mouse on top), make new material and press Assign.

References

• https://www.youtube.com/watch?v=G5FxPdBMUHE&list=PLcKSD7d0T-HBKMOGoghGk3weyrGmA2Re3&index=8
• https://www.youtube.com/playlist?list=PLYWq6N3TyBgw472RwfniSqcGna0szGpLT

References

Blender - Procedural Rust in Blender 2.8 Nodes

Blender Just Made Creating Wood So Easy in Blender 2.9!!