Tutorial 1 - running UnityMol from the editor

load share/caffeine.pdb
show game vs. scene windows
displace an atom manually in the editor
show inspector
change its size
generate a surface
- and modify its properties,
- delete it at the end
change the aspect of an atom, e.g. transform into a cube

Tutorial 2 - UnityMol Field lines

(Part 1)

load samples/fieldline/fieldlines.pdb
hide HyperBalls (Hide button)
show fieldlines menu (Electrostat. menu), customize options
- for ex. Speed=1, Density=1, Width=0.5, Length=0.9

(Part 2 : when running in Unity3D/editor)

explain project hierarchy menu
hide surface
edit field lines manually (delete unwanted)
re-display surface

(Part 3 : other visualizations of electrostatics)

close field lines by clicking on Field Lines button
select Volumetric Fields button
in Surface menu, toggle surface to hide
in Secondary Structures menu, enable sec. structures

(Part 4 : isosurface visualization)

hide volumetric fields by clicking the button again
Set both isosurface sliders to T: -5.0 and T: 5.0
Load Pos. and Load Neg.
Add molecule surface via Surface menu
Apply a nice texture to this surface
Apply a static cut to the surface to look inside

Tutorial 3 - UnityMol Sugar molecules

load share/Sugars/Case_9.pdb
explain complexity
change metaphor to licorice
add sugar planes as first identification (Sugar menu, option RingBlending)
show SugarRibbons and combinations
add sugar side-chains, hide hydrogens (deselect Hide option on the left, activate hide hydrogens in sugar submenu)
add oxygens (in the Tune submenu)
play with hyperballs coloring, e.g. by chain (Panel menu Chains option) or Sugar

Tutorial 4 - UnityMol GLIC visualization

load samples/3EI0.pdb or 3EAM.pdb
show chain coloring with hballs
look down channel
generate surface & color by chain
apply lit spheres texture to surface
generate B-factor surface @ 4.0
color by B-factor
superpose secondary structure
hide hyperballs

Tutorial 5 - UnityMol Guided Navigation

(see e.g. the following paper for more details: M. Trellet, N. Ferey, M. Baaden, P. Bourdot: "Content and Task Based Navigation for Structural Biology in 3D Environments". IEEE VR 2015, Arles)

Set up a compatible example system

load samples/3EI0.pdb
activate Guided Nav / Send
add a background through Advanced menu>BackGround=Yes
color by chain (Panel menu > Chains option)

Guided navigation functionalities

exploration around guides
- i toggles internal/external position
- arrow left/right up/down ;
automated exploration
- u/j automated pathway around the molecule ;
symmetry-exploited navigation
- jump monomer-monomer: m + arrows ;
spreading
- +/-/* or b/v/t for multi-level spreading ;
auto-generated path following
- Send to fly camera

Tutorial 6 - UnityMol Joypad Navigation

load adepth/1ay1.pdb
activate Advances/Ambient Occlusion
navigate, zoom, rotate with joypad
change viz mode

Tutorial 7 - Explore sweet (sugar) molecules

Sample data can be found in the share/Sugars/ directory.
All PDB files in that directory are sugar molecule pdb examples.
Just open any of the files in UnityMol and explore the numerous options in the Sugar menu and its submenus
Normally all Sugar menu functions should work on them.

File overview:

Case_9 is the most complex example of a sugar, with several chain, several units, and several sugar types.
Case_8 is an example with furanose and pyranose
Case_51 is a simple example with 3 glucose
Case_52 is a simple glucose helix
Case_53 is a double glucose helix
case_5 is an Arabose example (1 sugar)
case_32 is a beautifully simple example with 5 different sugars (with 5 different colors) and 2 chains (one ramification)

Todo:: Add a more complex protein-sugar complex sample PDB file to the share/Sugars directory.

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