1. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk Pirate applications... Pirate:phase improvement software Brigantine:bias removal software Unnamed application Kevin Cowtan cowtan@ysbl.york.ac.uk

2. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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 doesnt work, it does no harm. Minor tuning still required. (Timeconsuming!)

6. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk Tools Fast anisotropic scaling (needs tuning) Omit maps Sigma-a maps Refinement?

13. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk Buccaneer, Coot, and low resolution Developments in buccaneer and coot for model building, and application to low resolution problems. Kevin Cowtan cowtan@ysbl.york.ac.uk

14. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk Buccaneer: Method Statistical model building software based on the use of a reference structure to construct likelihood targets for protein features.

15. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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

16. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk Buccaneer Status (2007): Sequence assignment/docking implemented. Recycling for model completion implemented. Iteration with refmac implemented. In an ad-hoc script, without GUI

17. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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: ALA CYSHISMETTHR... x20 Finding: Classifying:

18. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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.

19. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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

20. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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?

21. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk

22. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk

23. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk

24. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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

25. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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

26. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk Coot Secondary structure: Helix Strand

27. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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.

28. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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.

29. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk Wiki and CCP4 Wiki as a tool to organise and expand CCP4 documentation and mailing list answers. Kevin Cowtan cowtan@ysbl.york.ac.uk

30. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk What is a Wiki? A website which anyone (or anyone authorised) can edit. Wikipedia is an example:

31. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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.

32. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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.

33. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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

34. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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

35. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk YSBL Wiki: 135 pages from 7 people

36. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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...

37. Kevin Cowtan, cowtan@ysbl.york.ac.uk CCP4 March 2007cowtan@ysbl.york.ac.uk 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?