1. CCP4 Developers Meeting 2007 CCP4 Molecular Graphics Liz Potterton and Stuart McNicholas

2. CCP4 Developers Meeting 2007 Release Schedule 1.0 Released December ‘06 1.1 Planned for June ‘07 (Finished major coding, requires ‘little’ things and serious testing) 1.2 End of ‘07 1.3,1.4..Regular point releases

3. CCP4 Developers Meeting 2007 New Features in CCP4mg 1.1 Picture Wizard – library of picture styles - complex scene setup automatically Improved ‘neighbourhood’ selection for finding binding site (v. useful in Picture Wizard) Less automatic model superposition Presentation application with internal browser Cartoons of lipid and membrane

4. CCP4 Developers Meeting 2007 New features in 1.1 User readable picture definition language Hardware stereo User customisable mouse bindings (+Coot mode) ‘Run Coot’ button (and more hopefully) Better handling of large numbers of models More documentation

5. CCP4 Developers Meeting 2007 Library of display styles to be applied to any loaded model(s) Templates based on picture definition format User can create own library (uses the picture definition language) Picture wizard

6. CCP4 Developers Meeting 2007 Select drawing style when loading PDB file (A different interface to picture wizard functionality)

7. CCP4 Developers Meeting 2007 Internal web browser Clicking image loads the linked picture description file into program

8. CCP4 Developers Meeting 2007 Picture Definition view = View ( centre_xyz = [-0.75363988921218494, -3.4065418005374246, 0.51530538958489269], radius = 60.0, orientation = [-0.76462865569820082,0.40495505468707682, -0.32522201031031295, 0.38155611196555067]) MolData ( filename = ['PROJECT', 'toxd.pdb', '/Users/stuart/PROJECT/toxd.pdb'] ) MolDisp ( selection = 'all', colour = 'atomtype', style = 'SPLINE', selection_parameters = { 'select' : 'all' } ) MolData ( filename = ['PROJECT', 'adna.pdb', '/Users/stuart/PROJECT/adna.pdb'] ) MolDisp ( selection = 'all', colour = 'atomtype', style = 'SPLINE', selection_parameters = { 'select' : 'all' } )

9. CCP4 Developers Meeting 2007 Normal Mode Analysis CCP4MG can currently perform approximate normal mode calculations using two elastic network models. –Only consider one atom per residue (CA) –Assume all force constants to be the same –Gaussian Network and Anisotropic Network methods employed

10. CCP4 Developers Meeting 2007 Normal Mode Analysis Gaussian Network Model –Very quick calculation (N x N eigenproblem). –Can compare atom mobilities in each mode –Can calculate B-values (sort of) –Only gives relative size of atom fluctuations –No info about directions of motions

11. CCP4 Developers Meeting 2007 Normal Mode Analysis Anisotropic Network Model –Gives direction as well as size of motion –Much larger calculation than GNM (3N x 3N eigenproblem) –B-values are less in agreement with experimental values than GNM.

12. CCP4 Developers Meeting 2007 Normal Mode Analysis Still need to define GUI, etc. for NMA: –Colour by atom mobility, etc. –Create animations (can do with script outside CCP4MG currently) –“Mode Browser” –User selectable parameters such as force constants.

13. CCP4 Developers Meeting 2007 Normal Mode Analysis

14. CCP4 Developers Meeting 2007 Morphing CCP4MG can calculate both internal angle and linear morphs. Still to do: –GUI –Automatic atom selection and superposition –Movie generation.

15. CCP4 Developers Meeting 2007

16. Objectives for 07/08 Building on current strengths.. More graphics display features Presenting the dynamic nature of structures Working within CCP4.. Infrastructure for interoperability Functionality to support other packages e.g. MR Extending functionality.. Structure analysis

17. CCP4 Developers Meeting 2007 Planned for 1.2 (end 2007) processHandler and interface to/from CCP4i Tools to prune MR input models and display results Morph generation - write GUI Normal mode analysis - write GUI Pisa interface

18. CCP4 Developers Meeting 2007 Of interest to other developers..? Available now to present results.. Picture description language to define scene Internal browser HTML links to picture description language script Can be run.. ccp4mg [–nogui] [–nographics] –script myscript.py

19. CCP4 Developers Meeting 2007 processHandler (for 1.2) Extension to Peter & Wendy’s dbHandler Clients must inform processHandler when they start up and close down Clients ask which other processes available ‘Introduction agency’ or ‘go-between’? Provides API for clients (Tcl, Python, JavaScript) Will prototype on i mg interface but will be generally useful