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Structure Tools and Visualization

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Title: Structure Tools and Visualization


1
Structure Tools and Visualization
  • Gary Van Domselaar
  • University of Alberta
  • gary.vandomselaar_at_ualberta.ca
  • Slides Adapted from Michel Dumontier, Blueprint
    Initiative

2
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)

3
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

4
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

5
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

6
Getting Rasmol Structure Files
  • Uses PDB files http//www.rcsb.org/

1
2
3
7
Working With the PDB File
8
Hen egg-white lysozyme and tri-N-acetylchitotrios
e
9
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

10
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

11
CHIME
  • What you need to run CHIME
  • Netscape / Mozilla / Internet Explorer
  • Windows or Macintosh
  • A web page designed to use CHIME
  • A PDB file

12
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

13
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

14
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

15
Hen egg-white lysozyme and tri-N-acetylchitotrios
e
16
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

17
Global Style Settings
18
Create New Annotation Disulfide Cysteines
  • Select Residues
  • MenugtStylegtAnnotate
  • Create New Annotation
  • Give Name and Edit Style

19
Edit Style Options
20
Selective Annotation of Cysteine Disulfide Bridges
21
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

22
Shortcuts
  • Rendering SpaceFill
  • Coloring Rainbow

23
Another Salient Feature
24
Imports
  • Import sequences
  • BLAST alignments
  • Import structures
  • Structural Superposition

25
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.

26
Conserved Domain Alignments

27
Folding Simulations
28
NMR Solution Structures
29
Finishing Your Work
  • Save
  • Annotations
  • Camera Settings
  • Export
  • PNG image

30
Other Cn3D Resources
  • Online Help

31
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

32
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

33
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)

34
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.

35
Molecular Surfaces
36
Electrostatic Potentials
  • Useful for evaluating the effects of a potential
    mutation
  • Analysis of binding site

37
SPDBV Home Page
  • http//expasy.org/spdbv

38
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39
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)

40
POV RAY
  • http//www.povray.org/documentation

41
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

42
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43
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/

44
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/

45
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/

46
PyMOL External GUI
  • Command line interface
  • Standard menu bar
  • Some Handy Buttons

47
PyMOL External GUI
Named Groups Panel
48
PyMOL Actions Menu (A)
Named Groups Panel
49
PyMOL Show Menu (S)
Named Groups Panel
50
PyMOL Hide Menu (S)
Named Groups Panel
51
PyMOL Labels Menu (L)
Named Groups Panel
52
PyMOL Color Menu (C)
Named Groups Panel
53
Hen egg-white lysozyme and tri-N-acetylchitotrios
e
54
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
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