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Lecture 3.4 Molecular Visualization Tools

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Structure Tools and Visualization² Gary Van Domselaar University of Alberta [email protected] ²Slides Adapted from Michel Dumontier, Blueprint Initiative Lecture 3.4 1 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) Lecture 3.4 2 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 3 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 Lecture 3.4 4 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 Lecture 3.4 5 Getting Rasmol Structure Files • Uses PDB files: http://www.rcsb.org/ 1 2 3 Lecture 3.4 6 Working With the PDB File “select cys115.cb” “select lys116” Lecture 3.4 7 Hen egg-white lysozyme and tri-N-acetylchitotriose Lecture 3.4 8 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 Lecture 3.4 9 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 Lecture 3.4 10 CHIME • What you need to run CHIME: – Netscape / Mozilla / Internet Explorer – Windows or Macintosh – A web page designed to use CHIME – A PDB file Lecture 3.4 11 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 Lecture 3.4 12 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 Lecture 3.4 13 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 Lecture 3.4 14 Hen egg-white lysozyme and tri-N-acetylchitotriose Lecture 3.4 15 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 Lecture 3.4 - Annotation 16 - Camera Settings Global Style Settings Lecture 3.4 17 Create New Annotation Disulfide Cysteines 1. Select Residues 2. Menu>Style>Annotate 3. Create New Annotation 4. Give Name and Edit Style Lecture 3.4 18 Edit Style Options Lecture 3.4 19 Selective Annotation of Cysteine Disulfide Bridges Lecture 3.4 20 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 Lecture 3.4 21 Shortcuts Rendering: SpaceFill Rendering: Ball and Stick Coloring: Rainbow Coloring: Hydrophobicity Lecture 3.4 22 Another Salient Feature Show/Hide>Select by distance Lecture 3.4 23 Imports • Import sequences – BLAST alignments • Import structures Structural Superposition Lectur–e 3.4 24 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. Lecture 3.4 25 Conserved Domain Alignments Lecture 3.4 26 Folding Simulations Lecture 3.4 27 NMR Solution Structures Lecture 3.4 28 Finishing Your Work • Save – Annotations – Camera Settings • Export – PNG image Lecture 3.4 29 Other Cn3D Resources • Application Help • Online Help Lecture 3.4 30 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 Lecture 3.4 31 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 Lecture 3.4 32 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) Lecture 3.4 33 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. Lecture 3.4 34 Molecular Surfaces Lecture 3.4 35 Electrostatic Potentials • Useful for evaluating the effects of a potential mutation • Analysis of binding site Lecture 3.4 36 SPDBV Home Page • http://expasy.org/spdbv Lecture 3.4 37 •http://www.usm.maine.edu/~rhodes/SPVTut/index.html Lecture 3.4 38 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) Lecture 3.4 39 POV RAY http://www.povray.org/documentation Lecture 3.4 40 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 Lecture 3.4 41 Lecture 3.4 42 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/ Lecture 3.4 43 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/ Lecture 3.4 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/ Lecture 3.4 45 PyMOL External GUI • Command line interface • Standard menu bar • Some Handy Buttons Lecture 3.4 46 PyMOL External GUI Named Groups Panel VIEWING WINDOW Mouse Bindings Command Line Movie Controls Lecture 3.4 47 PyMOL Actions Menu (A) Named Groups Panel VIEWING WINDOW Mouse Bindings Command Line Movie Controls Lecture 3.4 48 PyMOL Show Menu (S) Named Groups Panel VIEWING WINDOW Mouse Bindings Command Line Movie Controls Lecture 3.4 49 PyMOL Hide Menu (S) Named Groups Panel VIEWING WINDOW Mouse Bindings Command Line Movie Controls Lecture 3.4 50 PyMOL Labels Menu (L) Named Groups Panel VIEWING WINDOW Mouse Bindings Command Line Movie Controls Lecture 3.4 51 PyMOL Color Menu (C) Named Groups Panel VIEWING WINDOW Mouse Bindings Command Line Movie Controls Lecture 3.4 52 Hen egg-white lysozyme and tri-N-acetylchitotriose Lecture 3.4 53 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 Lecture 3.4 54.
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