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

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Presentation transcript:

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) density based validation (elal) externals (refmac5, fft, mapmask…) Control system layers no run-time decisions (arp_warp.sh) run-time adaptive (pyWARP)

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.

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

Large scale testing & tuning Data collected (and (demo) Also accessible via SOAP (simple Java CLI client available on the site)

Some stats… InCured No restrictions 5041 EU/FP107 ARP/wAR P

Some stats… M.R.Phi/FoM+ H.L. No restriction EU/FP341 ARP/wAR P

Future work (C.S.) 4 th 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

Next generation C.S. 4 th 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

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.

Miscellaneous Ligand building…