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Pirate

Pirate phase improvement software Kevin Cowtan cowtan@ysbl.york.ac.uk. Pirate. Pirate. Status: Statistical phase improvement software. Included in CCP4 version 6.0. Automated: no problem-specific input. Includes: Basic phase improvement: Effective handling of order/disorder.

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Pirate

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  1. Pirate phase improvement software Kevin Cowtan cowtan@ysbl.york.ac.uk Pirate

  2. Pirate Status: • Statistical phase improvement software. • Included in CCP4 version 6.0. • Automated: no problem-specific input. • 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: • 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 Results:

  5. Buccaneer chain tracing software Kevin Cowtan cowtan@ysbl.york.ac.uk Buccaneer

  6. Buccaneer: Method Compare simulated map and known model to obtain likelihood target, then search for this target in the unknown map. Reference structure: Work structure: LLK

  7. Buccaneer: Method • Compile statistics for reference map in 4A sphere about Ca => LLK target. • Use mean/variance. 4A sphere about Ca also used by 'CAPRA' Ioeger et al. (but different target function).

  8. Buccaneer: Method 4 steps: • Finding • Find candidate Ca positions. • Growing • Grow chains from starting positions. • Joining • Merge equivalent segments and resolve branches. • Pruning • Remove remaining clashes.

  9. Buccaneer

  10. Buccaneer

  11. Buccaneer

  12. Buccaneer

  13. Buccaneer Results:

  14. Buccaneer Results:

  15. Buccaneer Results:

  16. Buccaneer Results:

  17. Buccaneer Other details: • Builds helices with astonishing accuracy, even at low resolution. (<0.3A error at 3A resolution!) • Less good at building strands/loops. But: • Using two separate likelihood targets, one for helices and one for other features, looks as though it will improve accuracy and completeness.

  18. Buccaneer Things to do: • Speed up, debug. (Currently 5mins->1hour) • Resolve problem cases where the method fails. • Automate: • Sequence assignment. (coot?) • Refinement (refmac/privateer?) • Recycling (with phase improvement?) • Nucleotides!

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