Representation, Implementation, and Interaction: Challenges

for Macromolecular Assemblies

Michel F. Sanner

The Scripps Research InstituteLa Jolla, California

The Molecular Graphics Laboratory

Workshop on Visualization of Biological ComplexesOct. 11-12, 2003 Berkeley, CA

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MonolithicMonolithic SoftwareSoftware

InteroperableInteroperableSoftware Components Software Components for programmersfor programmers

InteroperableInteroperableSoftware Software Components Components for usersfor users

Time and complexity

of biological p

roblems

Time and complexity

of biological p

roblems

Software Components Software Components for programmersfor programmers

Conflicting goals?

• Increased usability• Increased flexibility• User-reconfigurable

applications• Transparent

computing

• Increased models complexity

• Increased data sets size and heterogeneity

• Interoperation of interdisciplinary computational methods

• Increased technological complexity

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Python to the rescueHigh level language as a scripting environmentHigh level language as a scripting environment

Molecular

Molecular

Surfaces

Surfaces

Molecular

Molecular

Surfaces

Surfaces

Molecules

Molecules

Molecules

Molecules

DataDataBaseBase

DataDataBaseBase

Electros

tatics

Electros

tatics

Electros

tatics

Electros

tatics

Delaunay

Delaunay

Delaunay

Delaunay

Homology

Homology

Homology

HomologyCSGCSGCSGCSG

3D3DViewerViewer

3D3DViewerViewer

MM-MD

MM-MD

MM-MD

MM-MD

NewNewMethodMethod

NewNewMethodMethod

YourYour

Metho

d

Metho

dYourYour

Metho

d

Metho

d

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PMV: From Building Blocks to Applications

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PMV Architecture

Numeric PyOpenGL Tkinter

DejaVu

ViewerFramework

IdleMolKitMslib

MsmsCommands

Generic Molecule Viewer built from reusable componentsBut meant for programmers

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ViPEr: a Visual Programming Environment

AChE APBS

Does not require the scientist toBecome a programmer

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ViPEr Architecture

NetworkEditor

Numeric

PyOpenGL

Tkinter

DejaVu

Visualization

MolKit

Mslib

MolKitStandard

Web

PIL

Imaging

SymServ

SymServer YourCode

YourLibrary

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ViPEr INNOVATIONS• No constraining data types• Optional data duplication• Scriptable, flexible• On-the-fly node editing• Nodes are lightweight wrappers of

computations• Small (< 13,000 lines of Python code)• Platform independent• A Python package NOT a program !

– Can be added to any program

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NetworkNode

MyNode

Input PortName: inPort1Type: StringN umber: 0Required: TrueSingleConnection: False

Output Portname: outPort1Type: NoneNumber: 0

‘myfile.dat’ ‘file1.dat’

[myfile.dat’, ‘file1.dat’]

def doit(self, inPort1): out =[] for n in names: out.append( read(n)) self.outputData(outPort1=out)

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Interactive Customizationof Molecular Visualizations

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Molecular surface of sliding window of amino acid

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DEMO

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Aknowledgements

• Sophie Coon (PMV)

• Daniel Stoffler PhD (ViPEr)

• National Institute of Health, RR08605

• MGL laboratory