Lecture 3.4 1

Structure Tools and Visualization†

Gary Van Domselaar

University of Alberta

gary.vandomselaar@ualberta.ca

†Slides Adapted from Michel Dumontier, Blueprint Initiative

Lecture 3.4 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)

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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

Lecture 3.4 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

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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/

1

2

3

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Working With the PDB File

“select cys115.cb”

“select lys116”

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Hen egg-white lysozyme and tri-N-acetylchitotriose

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Rasmol Help

• Quick Reference Card:– http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/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-acetylchitotriose

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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

1. Select Residues

2. Menu>Style>Annotate

3. Create New Annotation

4. 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: SpaceFillColoring: Rainbow

Rendering: Ball and StickColoring: Hydrophobicity

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Another Salient Feature

Show/Hide>Select by distance

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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• Application 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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•http://www.usm.maine.edu/~rhodes/SPVTut/index.html

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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/

ppovit/

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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

VIEWING WINDOW

Mouse Bindings

Movie ControlsCommand Line

Named Groups Panel

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PyMOL Actions Menu (A)

VIEWING WINDOW

Mouse Bindings

Movie ControlsCommand Line

Named Groups Panel

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PyMOL Show Menu (S)

VIEWING WINDOW

Mouse Bindings

Movie ControlsCommand Line

Named Groups Panel

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PyMOL Hide Menu (S)

VIEWING WINDOW

Mouse Bindings

Movie ControlsCommand Line

Named Groups Panel

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PyMOL Labels Menu (L)

VIEWING WINDOW

Mouse Bindings

Movie ControlsCommand Line

Named Groups Panel

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PyMOL Color Menu (C)

VIEWING WINDOW

Mouse Bindings

Movie ControlsCommand Line

Named Groups Panel

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Hen egg-white lysozyme and tri-N-acetylchitotriose

Lecture 3.4 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