The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Molecular and MotifSpace Visualization Toolkit :...
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Transcript of The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Molecular and MotifSpace Visualization Toolkit :...
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
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