Structure Tools and Visualization

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Structure Tools and Visualization

• Gary Van Domselaar
• University of Alberta
• gary.vandomselaar_at_ualberta.ca
• Slides Adapted from Michel Dumontier, Blueprint
  Initiative

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Visualization Communication

• Visualization tools allow us to
• see 3D structure data
• communicate features about 3-D structures to
  colleagues
• illustrate biological processes
  (catalytic/binding)
• educate laypersons about structural biology
• Go beyond Rasmol communicate other structural
  features
• surface shape
• show the surface, transparent over a backbone
• hydrophobicity / charge
• show the binding surfaces or charge
  complementarity
• mutations
• making a simple model (e.g. 1 amino acid change)

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In this lecture we introduce

• Rasmol and CHIME
• Good introductory packages for biomolecule
  visualization
• Cn3D for Structure Annotation
• Good all around viewer that uses OpenGL graphics
• Good annotation engine for exchanging information
  about 3D structure
• Swiss PDB Viewer (Deep View)
• Make molecular surfaces
• Align multiple proteins
• Apply scoring functions
• Simple, fast modeling including site-directed
  mutagenesis
• Complex modeling including loop rebuilding
• PyMOL
• Python based, can be used for scripting

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Rasmol CHIME

• Developed by Roger Sayle
• Open source, binaries available
• http//openrasmol.org/
• Widely used, simple to use (menus) for simple
  operations
• Complex operations require command-line interface

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Rasmol

• Developed by Roger Sayle
• Open source, binaries available
• http//openrasmol.org/
• Widely used, simple to use (menus) for simple
  operations
• Complex operations require command-line interface

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Getting Rasmol Structure Files

• Uses PDB files http//www.rcsb.org/

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Working With the PDB File
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Hen egg-white lysozyme and tri-N-acetylchitotrios
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Rasmol Help

• Quick Reference Card
• http//info.bio.cmu.edu/Courses/BiochemMols/RasFra
  mes/REFCARD.PDF
• Rasmol Manual
• http//openrasmol.org/doc/rasmol.html
• Tutorials
• http//www.umass.edu/microbio/rasmol/rastut.htm
• Gallery
• http//www.umass.edu/microbio/rasmol/galmz.htm

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CHIME

• CHIME Chemical mIME
• A free molecular viewer web browser plugin based
  on Rasmol
• Developed by MDL Information Systems Inc
• http//www.mdl/com/
• Improves on Rasmol
• More commands
• Hypertext button-controlled scripting
• Animations

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CHIME

• What you need to run CHIME
• Netscape / Mozilla / Internet Explorer
• Windows or Macintosh
• A web page designed to use CHIME
• A PDB file

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CHIME and Protein Explorer

• Protein Explorer A website that works with CHIME
  to help you visualize your structures
• http//molvis.sdsc.edu/protexpl/frntdoor.htm

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Cn3D

• Developed by the NCBI
• Open source, binaries available
  http//www.ncbi.nlm.nih.gov/Structure/
• Fast OpenGL Graphics
• Annotation Engine
• Lets you mark up a protein at the residue level
• Can fetch a structure over the Internet
• Can display protein movies
• NMR ensembles
• Protein folding trajectories

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Getting Cn3D Structure Files

• Uses MMDB files
• Entrez (http//www.ncbi.nlm.nih.gov) tightly
  coupled with MMDB structure database
• Retrieve using
• MMDB identifier
• PDB identifer
• Conserved Domain Database
• BLAST search
• PubMed query
• Text search

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Hen egg-white lysozyme and tri-N-acetylchitotrios
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ASN.1 Structure File (ascii)

• MMDB-ID
• PDB ID
• History
• Publications
• Chemical Graph
• Molecule Graph
• taxonomy
• residue sequence
• inter residue bonds
• heterogens
• solvent
• Inter-molecule bonds
• Annotation
• Camera Settings

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Global Style Settings
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Create New Annotation Disulfide Cysteines

• Select Residues
• MenugtStylegtAnnotate
• Create New Annotation
• Give Name and Edit Style

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Edit Style Options
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Selective Annotation of Cysteine Disulfide Bridges
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Annotation Menu

• Turn On/Off Show/Hide selected annotation
• Move Up/Down Change priority
• Show Show annotation and affected residues
• Edit Edit an existing annotation
• Move Move the annotation to selected residues
• Delete Delete the Annotation

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Shortcuts

• Rendering SpaceFill
• Coloring Rainbow

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Another Salient Feature
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Imports

• Import sequences
• BLAST alignments
• Import structures
• Structural Superposition

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BLAST

• Create alignments between sequences
• In this case, an alignment between the structure
  sequence and the natural sequence reveals missing
  N and C termini residues and a loop region, not
  resolved in structure.

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Conserved Domain Alignments

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Folding Simulations
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NMR Solution Structures
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Finishing Your Work

• Save
• Annotations
• Camera Settings
• Export
• PNG image

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Other Cn3D Resources

• Online Help

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Swiss PDV Viewer at a Glance

• PDB structure viewer with structure utilities
• Superimposition to compare proteins and their
  components such as active/binding sites
• Measure angles, distances between atoms
• Manual or automated (Swiss-Model) homology
  modeling including loop modeling
• Threading (Fold recognition)
• Mutations and Energy minimization
• Electron density map reading and model building
  (crystallography data)
• Interface to POV-Ray rendering software

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Main Interface

• Tons of menu options reasonably well categorized
• Button bar for image manipulation (center, zoom,
  move, rotate) and some structure measurement and
  mutation tools
• Layers window to select from multiple layers

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Control Panel

• Select
• Individual Residues (one or more)
• All Residues
• Chains
• Secondary Structure
• Show
• Backbone
• Side chains
• Labels
• Molecular surface (VDW)
• Ribbon Cartoons (Helices/Strands)
• Colors (specify backbone /- sidechain, labels,
  etc)

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Alignment and Ramachandran Plot

• Alignment Window shows alignment of sequences to
  one another (structural superposition, threading
  / homology modelling)
• Ramachandran plot showing Phi-Psi angles of
  selected residues. Can move individual residues
  to new Phi-Psi angles.

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Molecular Surfaces
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Electrostatic Potentials

• Useful for evaluating the effects of a potential
  mutation
• Analysis of binding site

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SPDBV Home Page

• http//expasy.org/spdbv

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Persistence of Vision(POV) RAY Visualization

• Ray tracing occurs from the camera to the scene
• Specify
• Camera location
• Light sources
• Objects
• Surface textures
• Atmospheric media (fog, haze, or fire)

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POV RAY

• http//www.povray.org/documentation

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PovRay Molecules...

• Armand Tepper s Energy minimized Yeast
  Cu-metallothionein from an averaged NMR
  structure. 6 copper atoms are in the reddish
  metal texture and the sulfurs of the coordinating
  cysteines appear in yellow. This picture features
  the new smoother ribbon feature (quality 2)
  implemented in SPDBV3.6b2. The surface is at
  detail level 3. 
• http//wwwchem.leidenuniv.nl/metprot/armand

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POV Ray scene generators

• Swiss PDB Viewer can save file as POV scene
• PDB to POV converters available
• MolPov (windows) http//www.chem.ufl.edu/der/der_
  pov2.htm
• PPOVIT (PERL) http//huron.cem.msu.edu/rstc/ppovi
  t/

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PyMOL

• Set of structure tools built on top of Python
• Supports all Standard Features
• Extensible, Scriptable
• Native Ray Tracer
• Freely Available
• http//pymol.sourceforge.net/

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PyMOL

• Set of structure tools built on top of Python
• Supports all Standard Features
• Extensible, Scriptable
• Native Ray Tracer
• Freely Available
• http//pymol.sourceforge.net/

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PyMOL External GUI

• Command line interface
• Standard menu bar
• Some Handy Buttons

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PyMOL External GUI
Named Groups Panel
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PyMOL Actions Menu (A)
Named Groups Panel
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PyMOL Show Menu (S)
Named Groups Panel
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PyMOL Hide Menu (S)
Named Groups Panel
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PyMOL Labels Menu (L)
Named Groups Panel
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PyMOL Color Menu (C)
Named Groups Panel
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Hen egg-white lysozyme and tri-N-acetylchitotrios
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Conclusions

• Several of the more powerful structure tools with
  visualization and structure manipulation features
  are freely available
• Rasmol, Cn3D, Swiss PDB Viewer, PyMOL
• Mark up your structures to convey important and
  useful information
• Ray Trace output scenes for best rendering and
  artistic flash