“Pirate applications”...

1. Pirate: phase improvement software Brigantine: bias removal software Unnamed application Kevin Cowtan cowtan@ysbl.york.ac.uk “Pirate applications”...

2. Pirate Status: • Statistical phase improvement software. • Included in CCP4 version 6.0. • Updated in 6.0.2 • Includes: • Basic phase improvement: • Effective handling of order/disorder. • NCS averaging: • Automated NCS determination from heavy atoms and density. • Per-pair weighted NCS averaging.

3. Pirate Status (2006): • Phase improvement works well: • Slower than ‘dm’ • Sensitive to the quality of the input HL coefficients • NCS: • When it works, it works well. • Buggy: works in < 10% of cases! • Why? Because at this meeting last year, I was told that Buccaneer was more important.

4. Pirate Status (2007): • Automation further improved: • Log-likelihood weight now calculated automatically by optimisation of the log-likelihood gain. • Next version will also incorporate a better algorithm for estimating the cell composition. • User interface improved: • User no longer has to provide a reference structure (unless they want to). GUI simplified.

5. Pirate Status (2007): • NCS code heavily updated. Now works fully automatically in 30-50% of cases. • Outstanding issue with NCS along special directions. • When it doesn’t work, it does no harm. • Minor tuning still required. (Timeconsuming!)

6. Pirate Future: • Further NCS improvements. • Use of an input model of electron density map to provided an additional source of information • Integration with buccaneer.

7. Brigantine Brigantine is a bias removal program: “Bias Removal In General Allows New Trace In New Density” Mainly aimed at tackling MR bias problem, but uses ideas and code from Pirate, but has applications to validation and maybe density modification as well.

8. Brigantine Status: Currently performs 3 calculations: • Simple composite omit map. • Fast: seconds to a few minutes. • Sigmaa-weighted composite omit map. • Fairly fast: minute to tens of minutes • Pirate composite omit map. • Fairly slow: tens of minutes to a few hours. All of these are model-free, i.e. Can be used before model building.

9. Brigantine Pirate composite omit map. • Related to a similar idea in Resolve • (CCP4 study weekend 2007) • But does not involve any density modification. • i.e. It can be used in combination with arbitrary density modification methods. Maybe even recycled with several different density modification methods. • Code works. • One tunable parameter needs to be estimated. • It is not clear if the results are useful.

10. Brigantine Applications: • After MR • (to reduce model biad) • Between different density modification procedures. • (speculative) • As part of iterated density modification/model building procedure. • (as validation) • In model completion • (validation, ligands, etc.)

11. Unnamed application An unnamed program to provide an improved method for perturbing a model to reduce bias after refinement. An alternative to simulated annealing. Uses: • Unbiasing a free set. • Precursor to Brigantine.

12. Developments in buccaneer and coot for model building, and application to low resolution problems. Kevin Cowtan cowtan@ysbl.york.ac.uk Buccaneer, Coot, and low resolution

13. Buccaneer: Method Statistical model building software based on the use of a reference structure to construct likelihood targets for protein features.

14. Buccaneer Status (2006): • Successful tool for protein chain tracing, even at low resolutions. Tasks (2006): • Implement sequence assignment/docking. • Implement recycling for model completion • Iterate with refmac

15. Buccaneer Status (2007): • Sequence assignment/docking implemented. • Recycling for model completion implemented. • Iteration with refmac implemented. • In an ad-hoc script, without GUI

16. Buccaneer Sequence assignment/docking: Use the same method for classifying side chains by type as for finding C-alphas in the first place, but with a difference target function: Finding: Classifying: ... x20 ALA CYS HIS MET THR

17. Buccaneer Recycling for model completion implemented. • “Lateral growing”: grow sideways from existing chain fragments by looking for new C-alphas at an appropriate distance “sideways” from the existing chain. • Fast recycling within Buccaneer, or slower recycling with other programs, e.g. refmac.

18. Buccaneer Steps: (bold are new since 2006) • Find C-alphas • Grow into chains • Join the chains • Pre-sequence loop building (up to 2 C-alphas) • Assign sequence • Correct insertions/deletions • Filter based on poor density • Remove clashing chains • Build side chains

19. Buccaneer The positive: • Successfully applied to 2 real unknown structures with good phases at ~3.5A. More than half the model built and sequenced. • Successfully applied to 4.0A truncated data. • First citation this month! The negative: • Model completeness still not as good as Resolve. • What about bad phases at higher resolutions?

23. Coot Coot developments in model building: • Improved helix placement • Improved handling of low resolution maps • Handle ‘UNK’ for use with Buccaneer • Developments towards strand placement • Future integration of Buccaneer functionality

24. Coot Improved helix placement: • Helix built both ways and refined without Cb. • Correct orientation determined from Cb density. Low resolution: • Add terminal residue does RSR • Auto-fit sidechain does RSR • Secondary structure restraints

25. Coot Secondary structure: • Helix • Strand

26. Coot Strand placement • New algorithms are being examined for both helix and strand placement. • First attempt: • Use skeleton and find where ridges cross a sphere containing the feature. • Faster than current method for helices.

27. Coot Integration of Buccaneer features: • 'UNK' residue type handling. • Buccaneer sequencing has been exported to a standalone ‘cootaneer’ library. • For speed, this has to work without a reference structure. • Use pre-calculated resolution dependent libraries. • Just needs integrating. • Buccaneer growing may be added in future. • An alternative engine for current ‘Add terminal residue’? • Or an auto-grow algorithm.

28. Wiki as a tool to organise and expand CCP4 documentation and mailing list answers. Kevin Cowtan cowtan@ysbl.york.ac.uk Wiki and CCP4

29. What is a Wiki? • A website which anyone (or anyone authorised) can edit. • Wikipedia is an example:

30. Why Wiki? • Much easier to update than a website... • Edit through the web browser, even remotely. • Automatic markup (most of the time). • Semi-automatic linking and cross referencing. • Collaborative... • Many people doing the bits they know best when it is convenient to them.

31. Wiki Features • Build in version control. • Track and revert changes. • Access control for admin, writing, (reading). • Initially wikis were open, these days must register. • Per-page access control as well as site wide. • Many allow pages with discussion areas. • A page can be read only but allow comments.

32. How could CCP4 use one? • Take good bits out of the program documentation, manual, bulletin board discussions, and gather and organise them. • Turn bulletin board discussions into FAQ pages. • Host frequently changing info: • Contact details • Useful web resources • Problem pages

33. Case studies: ~2002: Tried to use one to document eHTPX collaboration. Failure: • Unfamiliar. • People forced to contribute. ~2003: Implemented at York for local documentation pages. Success: • Widely read. A smaller group contribute. • Enough enthusiastic contributors to make it work. • There must be a ‘critical mass’ of contributors. • Volunteers: EJD, JPT, KDC

34. YSBL Wiki: 135 pages from 7 people

35. Deploying a Wiki Issues: • The server is web-facing • Wikis are regularly attacked • Software updates must be applied very frequently • Better to have a dedicated machine outside the firewall • Choice of wiki software: • MoinMoin, Twiki, Mediawiki, etc... • Language, database or flat file, access control, version control, comments, images, math, plugins, search, email notification of changes, content export, etc...

36. Deploying a Wiki Issues: • Alternative: Wiki hosting sites: • wikia, wikidot, wikispaces. • Some are free, or $5-$50/month. • Some display adverts • Some demand content be licensed, e.g. CC, FDL • Issues: • Convenience: can I be auto-logged in when I arrive? • Can the content be exported if we need to move?