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ARP/wARP developments

ARP/wARP developments. CCP4-STAB meeting York; March 2007. Layered architecture. Modules (base layer) model editing (arp_warp) main chain tracing (cubes/hmain & pept_hmain) secondary structure elements (helreco/albe) sequence and side chains (snow) loop building (loopy)

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ARP/wARP developments

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  1. ARP/wARP developments • CCP4-STAB meeting • York; March 2007

  2. Layered architecture • Modules (base layer) • model editing (arp_warp) • main chain tracing (cubes/hmain & pept_hmain) • secondary structure elements (helreco/albe) • sequence and side chains (snow) • loop building (loopy) • density based validation (elal) • “externals” (refmac5, fft, mapmask…) • Control system layers • no run-time decisions (arp_warp.sh) • run-time adaptive (pyWARP)

  3. Next release (7.0-soon ?) • New implementations • peptide detection (cubes/hmain) • secondary structure building (helreco/albe) • loop building (loopy) • density based validation (elal) • adaptive control system (pyWARP) • ligand detection (mapread) • Evolution and tuning for the rest.

  4. Logistics • Easy to parse results : • sequence docking outputs most of it results in XML format • adaptive C.S. writes its history in XML • Big structure handling : • “Q&D” fix using 4 letters SEGID • sequence docking start using them when chain ID are not enough. • refmac uses SEGID • arp_warp preserve them

  5. Large scale testing & tuning • Data collected (and available) @ • http://xtal.nki.nl/Depot (demo) • Also accessible via SOAP (simple Java CLI client available on the site)

  6. In Cured No restrictions 50 41 EU/FP 10 7 ARP/wARP 186 177 Some stats…

  7. M.R. Phi/FoM + H.L. No restriction 23 18 11 EU/FP 3 4 1 ARP/wARP 150 27 23 Some stats…

  8. Future work (C.S.) • 4th implementation of the C.S. • More flexible • The processing graph should NOT be hard-coded anymore (ie using a simple file describing the graph) • Better declaration of which statistics are imported from each of the process (into the processing history) • Enable recursive design

  9. Next generationC.S. • 4th implementation of the C.S. • More flexible • The processing graph should NOT be hard-coded anymore (ie using a simple file describing the graph) • Better declaration of which statistics are imported from each of the process (into the processing history) • Enable recursive design

  10. Future work (modules) • NCS cross completion basedon sequence docking • Combination of main chain tracing and secondary structure detection • Better support for big structures (mmCIF subset to replace PDB format ?) • Using omit-map when starting from M.R.

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