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CREST Workshop, 2014: Using Surfaces to Depict Contacts and Interactions. Bob Hanson St. Olaf College, Northfield, MN http://www.stolaf.edu/people/hansonr Center for Biomolecular Modeling Milwaukee School of Engineering Milwaukee, WI 6/2/2014. Rendering in Jmol. - PowerPoint PPT Presentation
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CREST Workshop, 2014:Using Surfaces to DepictContacts and Interactions
Bob HansonSt. Olaf College, Northfield, MN
http://www.stolaf.edu/people/hansonr
Center for Biomolecular ModelingMilwaukee School of Engineering
Milwaukee, WI6/2/2014
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
http://chemapps.stolaf.edu
script "http://chemapps.stolaf.edu/jmol/jsmol/spt/ext/rcsb/gotoLigand.spt"gotoLigand "1eve" "e20"
Jmol Sources on the Web
http://chemapps.stolaf.edu
script "http://chemapps.stolaf.edu/jmol/jsmol/spt/ext/rcsb/gotoLigand.spt"gotoLigand "1eve" "e20"
function gotoLigand(xxxx,ligandAtoms) {// load with hydrogens (13.3.9_2013_11_13c)if (!ligandAtoms) { return }if (xxxx) {
load @{"="+xxxx} filter "addhydrogens" } else {
isosurface delete;contact delete;
}if (ligandAtoms.type == "string" && !ligandAtoms.find("[")) { ligandAtoms = "[" + ligandAtoms + "]"}select @ligandAtomsligandAtoms = {selected}[1]ligandAtoms = {within(group, ligandAtoms)}
// contact surface
//isosurface select {ligandAtoms} only vdw//isosurface slab 60 fullylit
contact ID "surf" {ligandAtoms} surfacecontact 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 =1crnisosurface solvent map property temperatureisosurface colorscheme "bwr"
Surfaces:
Numerical data can be mapped onto surfaces for visualization, or used to change atom properties, such as displayed atom radius
load =1crncolor property temperature “bwr”{*}.radius = {*}.temperature.all.div(20)
Surfaces:
Cavities and Pockets
load =1eveisosurface select {protein} only cavity
Surfaces:
Cavities and Pockets
load =1eveisosurface select {protein} only pocket cavity
Surfaces:
Cavities and Pockets
load =1eveisosurface select {protein} only pocket cavityisosurface slab none slab within 7.5 {e20}select proteinwireframe -0.2center e20zoom {e20} 0background blackset zshadeset 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
Contact Mapping
Contact Mapping
Contact Mapping
Contact Mapping
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.
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