1. Lecture 3.41 Structure Tools and Visualization † Gary Van Domselaar University of Alberta gary.vandomselaar@ualberta.ca † Slides Adapted from Michel Dumontier, Blueprint Initiative

2. Lecture 3.42 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. Lecture 3.43 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. Lecture 3.44 Rasmol & CHIME Developed by Roger Sayle Open source, binaries available –http://openrasmol.org/http://openrasmol.org/ Widely used, simple to use (menus) for simple operations Complex operations require command-line interface

5. Lecture 3.45 Rasmol Developed by Roger Sayle Open source, binaries available –http://openrasmol.org/http://openrasmol.org/ Widely used, simple to use (menus) for simple operations Complex operations require command-line interface

6. Lecture 3.46 Getting Rasmol Structure Files Uses PDB files: http://www.rcsb.org/ 1 2 3

7. Lecture 3.47 Working With the PDB File “select cys115.cb” “select lys116”

8. Lecture 3.48 Hen egg-white lysozyme and tri-N-acetylchitotriose

9. Lecture 3.49 Rasmol Help Quick Reference Card: –http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/REFCARD.PDFhttp://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/REFCARD.PDF Rasmol Manual –http://openrasmol.org/doc/rasmol.htmlhttp://openrasmol.org/doc/rasmol.html Tutorials: –http://www.umass.edu/microbio/rasmol/rastut.htmhttp://www.umass.edu/microbio/rasmol/rastut.htm Gallery: –http://www.umass.edu/microbio/rasmol/galmz.htmhttp://www.umass.edu/microbio/rasmol/galmz.htm

10. Lecture 3.410 CHIME CHIME: “Chemical mIME” A free molecular viewer web browser plugin based on Rasmol Developed by MDL Information Systems Inc: –http://www.mdl/com/http://www.mdl/com/ Improves on Rasmol: –More commands –Hypertext button-controlled scripting –Animations

11. Lecture 3.411 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. Lecture 3.412 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. Lecture 3.413 Cn3D Developed by the NCBI Open source, binaries available http://www.ncbi.nlm.nih.gov/Structure/ 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. Lecture 3.414 Getting Cn3D Structure Files Uses MMDB files Entrez (http://www.ncbi.nlm.nih.gov) tightly coupled with MMDB structure databasehttp://www.ncbi.nlm.nih.gov Retrieve using –MMDB identifier –PDB identifer –Conserved Domain Database –BLAST search –PubMed query –Text search

15. Lecture 3.415 Hen egg-white lysozyme and tri-N-acetylchitotriose

16. Lecture 3.416 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. Lecture 3.417 Global Style Settings

18. Lecture 3.418 Create New Annotation Disulfide Cysteines 1.Select Residues 2.Menu>Style>Annotate 3.Create New Annotation 4.Give Name and Edit Style

19. Lecture 3.419 Edit Style Options

20. Lecture 3.420 Selective Annotation of Cysteine Disulfide Bridges

21. Lecture 3.421 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. Lecture 3.422 Shortcuts Rendering: SpaceFill Coloring: Rainbow Rendering: Ball and Stick Coloring: Hydrophobicity

23. Lecture 3.423 Another Salient Feature Show/Hide>Select by distance

24. Lecture 3.424 Imports Import sequences –BLAST alignments Import structures –Structural Superposition

25. Lecture 3.425 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. Lecture 3.426 Conserved Domain Alignments

27. Lecture 3.427 Folding Simulations

28. Lecture 3.428 NMR Solution Structures

29. Lecture 3.429 Finishing Your Work Save –Annotations –Camera Settings Export –PNG image

30. Lecture 3.430 Other Cn3D Resources Online Help Application Help

31. Lecture 3.431 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. Lecture 3.432 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. Lecture 3.433 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. Lecture 3.434 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. Lecture 3.435 Molecular Surfaces

36. Lecture 3.436 Electrostatic Potentials Useful for evaluating the effects of a potential mutation Analysis of binding site

37. Lecture 3.437 SPDBV Home Page http://expasy.org/spdbv

38. Lecture 3.438 http://www.usm.maine.edu/~rhodes/SPVTut/index.html

39. Lecture 3.439 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. Lecture 3.440 POV RAY http://www.povray.org/documentation

41. Lecture 3.441 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/ar mandhttp://wwwchem.leidenuniv.nl/metprot/ar mand

42. Lecture 3.442

43. Lecture 3.443 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 http://www.chem.ufl.edu/~der/der_pov2.htm –PPOVIT (PERL) http://huron.cem.msu.edu/~rstc/ppovit/ http://huron.cem.msu.edu/~rstc/ppovit/

44. Lecture 3.444 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/http://pymol.sourceforge.net/

45. Lecture 3.445 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/http://pymol.sourceforge.net/

46. Lecture 3.446 PyMOL External GUI Command line interface Standard menu bar Some Handy Buttons

47. Lecture 3.447 PyMOL External GUI VIEWING WINDOW Mouse Bindings Movie Controls Command Line Named Groups Panel

48. Lecture 3.448 PyMOL Actions Menu (A) VIEWING WINDOW Mouse Bindings Movie Controls Command Line Named Groups Panel

49. Lecture 3.449 PyMOL Show Menu (S) VIEWING WINDOW Mouse Bindings Movie Controls Command Line Named Groups Panel

50. Lecture 3.450 PyMOL Hide Menu (S) VIEWING WINDOW Mouse Bindings Movie Controls Command Line Named Groups Panel

51. Lecture 3.451 PyMOL Labels Menu (L) VIEWING WINDOW Mouse Bindings Movie Controls Command Line Named Groups Panel

52. Lecture 3.452 PyMOL Color Menu (C) VIEWING WINDOW Mouse Bindings Movie Controls Command Line Named Groups Panel

53. Lecture 3.453 Hen egg-white lysozyme and tri-N-acetylchitotriose

54. Lecture 3.454 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