ccp4 developers meeting 2007 ccp4 molecular graphics liz potterton and stuart mcnicholas
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CCP4 Developers Meeting 2007
CCP4 Molecular Graphics
Liz Potterton and Stuart McNicholas
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
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
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
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
CCP4 Developers Meeting 2007
Select drawing style when loading PDB file
(A different interface to picture wizard functionality)
CCP4 Developers Meeting 2007
Internal web browser
Clicking image loads the linked picture description file into program
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' } )
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
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
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.
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.
CCP4 Developers Meeting 2007
Normal Mode Analysis
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.
CCP4 Developers Meeting 2007
QuickTime™ and aYUV420 codec decompressor
are needed to see this picture.
CCP4 Developers Meeting 2007
Objectives for 07/08Building 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
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
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
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