The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Molecular and MotifSpace Visualization Toolkit : RasCtrl Jingdan Zhang.

The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL

Molecular and MotifSpace Visualization Toolkit : RasCtrl

Jingdan Zhang

The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL

Molecular Visualization

• Molecular visualization♦ Display a 3D model of a molecule to illustrate its

physical form and structure.

• Rich representation models♦ Lines and sticks♦ Spheres♦ Ribbons and cartoons♦ …

The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL

Molecular Visualization• Molecular Visualization is a hot

research area♦ More than 50 years of history♦ Experienced rapid development in recent

years • Progress in the bio-informatics research• Progress in graphics techniques

• Wide applications♦ Drug design♦ Protein structure analysis♦ Education

The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL

Molecular Visualization Packages

• Many visualization packages♦ Commercial♦ Open source

• Rasmol– Originally developed by Roger Sayle at 1993,

continually evolved over the last ten years– The code is well written and compact– Several widely used programs are derived from Rasmol:

Rastop, Chime, Programs for education purpose• VMD

– Developed by UIUC since 1995– Visualize Molecular Dynamics– A large set of functions to support wide applications

• Pymol– Python-enhanced molecular graphics program

The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL

Our Goal

• Develop a toolkit to visualize queried motifs♦ Show spatial configurations♦ Show position/structure correlations

The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL

Design Issues• Support common molecular

representations♦ Lines and sticks♦ Spheres♦ Ribbons and cartoons

• Support Microsoft Smart Client architecture♦ Currently, no major open source visualization

tools support smart Client architecture

• Flexible and easy to use♦ Can plug into applications easily♦ Support drag & drop interface design

The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL

Design Strategy

• Use Microsoft ActiveX technique to build the toolkit♦ To create a re-usable molecular visualization

component♦ Can be converted to the windows Forms control

by .Net framework tool Aximp.exe

• Develop the toolkit based on the open source program Rasmol♦ Rasmol supports a variety of standard

molecular representations♦ The original code is well written and compact,

only 20k lines of code

The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL

Functionality of RasCtrl

• Parse PDB files to build protein data structures

• Render proteins using a variety of representation

• Support MotifSpace visualization

• Respond to user interaction

The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL

Solution Architecture

Architecture

Demo

The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL

Two Stages of Development I• Stage One:

modify original Rasmol code to create an ActiveX component

• From C code to C++: get rid of static and global variable to enable multiple instances of RasCtrl running at same time.

• Use interface functions to wrap original functions

RasCtrl Interface

CRasAdapter

CRasmol

The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL

Two Stages of Development II

• Stage Two: add functions to support motif visualization♦ Motif structure alignment between

proteins

Demo

The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL

Demo

• Build a molecular visualization application in one minute.