CREST Workshop, 2014: Using Surfaces to Depict Contacts and Interactions Bob Hanson St. Olaf College, Northfield, MN Center for Biomolecular Modeling Milwaukee School of Engineering Milwaukee, WI 6/2/2014
Rendering in Jmol Many rendering options, including cartoons,
Rendering in Jmol Many rendering options, including cartoons, transparency,
Rendering in Jmol Many rendering options, including cartoons, transparency, fog-like shading
Rendering in Jmol Many rendering options, including cartoons, transparency, fog-like shading 3D Ramachandron plots and Ramachandran angles
Jmol Sources on the Web
Jmol Sources on the Web Load “” FILTER “biomolecule 1”
Jmol Sources on the Web contact {ligand} surface
Jmol Sources on the Web write PNGJ “?myfile.png”
Jmol Sources on the Web script " gotoLigand "1eve" "e20"
Jmol Sources on the Web script " gotoLigand "1eve" "e20" function gotoLigand(xxxx,ligandAtoms) { // load with hydrogens (13.3.9_2013_11_13c) if (!ligandAtoms) { return } if (xxxx) { filter "addhydrogens" } else { isosurface delete; contact delete; } if (ligandAtoms.type == "string" && !ligandAtoms.find("[")) { ligandAtoms = "[" + ligandAtoms + "]" } ligandAtoms = {selected}[1] ligandAtoms = {within(group, ligandAtoms)} // contact surface //isosurface select {ligandAtoms} only vdw //isosurface slab 60 fullylit contact ID "surf" {ligandAtoms} surface contact slab 60 fullylit …
Surfaces: Van der Waals isosurface VDW or isosurface select {xxx} only VDW load :morphine or load $morphine (PubChem) (NCI Resolver)
Surfaces: Van der Waals isosurface VDW translucent 0.3
Surfaces: Van der Waals isosurface VDW frontonly translucent 0.3
Surfaces: Van der Waals isosurface VDW map MEP frontonly translucent 0.3
Surfaces: Solvent-excluded isosurface select {protein} only solvent
Surfaces: Solvent-excluded isosurface select {protein} only solvent -- most sophisticated surface -- requires some time -- can be CACHED for PNGJ
Surfaces: Solvent-accessible isosurface select {protein} only SASURFACE
Observations: Numerical data can be mapped onto atoms and surfaces for visualization
Surfaces: Numerical data can be mapped onto surfaces for visualization load =1crn isosurface solvent map property temperature isosurface colorscheme "bwr"
Surfaces: Numerical data can be mapped onto surfaces for visualization, or used to change atom properties, such as displayed atom radius load =1crn color property temperature “bwr” {*}.radius = {*}.temperature.all.div(20)
Surfaces: Cavities and Pockets load =1eve isosurface select {protein} only cavity
Surfaces: Cavities and Pockets load =1eve isosurface select {protein} only pocket cavity
Surfaces: Cavities and Pockets load =1eve isosurface select {protein} only pocket cavity isosurface slab none slab within 7.5 {e20} select protein wireframe -0.2 center e20 zoom {e20} 0 background black set zshade set zshadepower 3
Clipped Isosurfaces Idea: There are many more ways to clip an isosurface than just “within some distance of a set of atoms.”
Example: Static Mapped Surface Backdrop Isosurface slab off slab 50
Example: Dynamically Clipped Surfaces
Contacts Using Jmol, we have been experimenting with different ways of creating and using surfaces.
Contact Mapping Idea: Map a Van der Waals surface with data representing proximity to another surface. Color data red to indicate overlap of Van der Waals surface. Color data blue to indicate atoms far from contact.
Contact Mapping contact {ligand} SURFACE
Contact Mapping contact {ligand} TRIM
Contact Mapping contact {ligand} TRIM
Contact Mapping contact {ligand} HBOND
Contact Mapping contact … CONNECT
Contact Mapping contact … CONNECT
Contact Mapping
Surfaces: Electron Density Mesh
Surfaces: Electron Density Mesh load =1eve; display e20; zoomto {e20} 0
Surfaces: Electron Density Mesh isosurface “=1eve”
Surfaces: Electron Density Mesh isosurface “=1eve” isosurface display within 2.5 {e20}
Dynamic Volume Data Rendering Idea: Show actual crystallographic electron density data, and allow for dynamic clipping based on sigma values.
Dynamic Volume Data Rendering Idea: Show actual crystallographic electron density data, and allow for dynamic clipping based on sigma values.
Dynamic Volume Data Rendering Idea: Show actual crystallographic electron density data, and allow for dynamic clipping based on sigma values.
Dynamic Volume Data Rendering Idea: Show actual crystallographic electron density data, and allow for dynamic clipping based on sigma values.