EMBL-EBI. EM map display & Visualization

Transcription

1 EM map display & Visualization

2 Introduction Biological data comes from & is of interest to: Chemists : reaction mechanism, drug design Biologists : sequence, expression, homology, function. Structure biologists : atomic structure, fold, classification, function. Medicine : clinical effect Education : Media : Presentation of diverse information to a diverse audience. Each has there own point of view (context). Expert = scientist working within their own field of expertise Non-expert = scientist using data/information outside their field Novice = Non-scientist

3 YAMGP (yet another molecular graphics program) Many different programs are available VMD LigPlot Quanta Bobscript InsightII WebMol Chime imol Frodo Grasp Pymol Pymol Spock POVRay Rasmol Yasara Mage Raster3D Chimera O Molscript MolMol Whatif Frodo XtalView Swiss-PDBviewer WebLab-viewer

4 Designed as a web based program (applet) to display information within the Protein Data Bank 3D+1 Display of surfaces 3D structure coordinates 2D chemical sketches 1D sequence Is this any use for EM? Volume data Occasionally coordinate data Can display data stored remotely (ie at from MSD deposition) 3D display by Mike Hartshorn, Astex Therapeutics

5 Why java? Independent of Hardware Independent of OS It requires no installation It does require java 1.1 : normal minimal specification of most web browsers even IE Usually problems Graphics written from scratch by Mike Hartshorn (for solid surfaces) fast Memory issue : JVM is profligate with memory

6 grid maps : Formats CCP4 fomat Handles binary/short/float data Large data files MSD-EM download format Slow read/contour 2.7Mbyte compress O map (DNS6 brick byte format) Historical (legacy) format from X- ray crystallography Compact, good for marching cube contouring + L1 data caching Much more efficient Local link URL link ID = 1048 :bacteriophage T4 baseplate

7 Applet lag time Applet startup lag entire map of ID = second startup over LAN connection : read/contour Connection speed specific 8 seconds over fast network 2 minutes over broadband As application A little faster startup Can run with more memory for JVM EM maps are big

8 Map display type 1 Display : Net contour Allows visibility of internal fine structure Messy, non-professional Practical for map fitting doing real science Used X-ray crystallographic map fitting

9 Map display type 2 Display : translucent View of internal structure Significant performance issue More professional view, not so clear for science Not seen this used for X-ray maps.

10 Map display type 3 Solid surface Clean view for presentation Loose all internal/backface features Suitable for molecular surface Suitable for EM maps but not for coordinate fitting.

11 EM data display type General users of volume data Display as solid surface Probably suitable at this effective resolution Coordinate analysis Use net surfaces to view detail Are you seeing too much detail?

12 Controls for EM does too much for maps, coordinates & sequences. Graphs Chemistry For EM maps Bit of an overkill! Run time option to restrict displays Map list Background colour And?

13 Map dialog : 1 for each map Any number of maps Visible toggle Opacity Solid/wire Radius Contour level What else?

14 Coordinate display Molecular surfaces solid/net/translucent Texture maps Schematics Spheres Atomic display

15 Other displays Sequence alignment 2D, 3D, ND Graphs Chemical sketch

16 Summary can display maps & coordinates As solid, translucent and net surfaces High speed graphics comparable to compiled software Independent of architecture, OS and browser (java 1.1) It can be used at the moment to display EM volume data The menu restriction needs refining.

17 Future developments? Future developments possible Depends on funding (resources) Texture maps can be used to identify regions by protein/na identity Ie colour surface by each identified sub-volume Molecule fitting probably better programs for this