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

CCP4 Developers Meeting 2007

CCP4 Molecular Graphics

Liz Potterton and Stuart McNicholas


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


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


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


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


Select drawing style when loading PDB file

(A different interface to picture wizard functionality)


Internal web browser

Clicking image loads the linked picture description file into program


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' } )


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



• 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



• 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.



• 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.


Morphing

• CCP4MG can calculate both internal angle and linear morphs.

• Still to do:– GUI– Automatic atom selection and superposition– Movie generation.


QuickTime™ and aYUV420 codec decompressor

are needed to see this picture.


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


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


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


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

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

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