Progress report on Crank: Model building Biophysical Structural Chemistry Leiden University, The Netherlands.

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Presentation transcript:

Progress report on Crank: Model building Biophysical Structural Chemistry Leiden University, The Netherlands

Extending the limits of the SHELXCDE->ARP/wARP pipeline Resol. (Å) Anom. atoms Exp.Time (min) Residues RICE/SAD/FINAL MutS3.046 SeSAD /1093/1600 subtilisin1.773 Ca, SSAD55.656/259/275 thioesterase2.58 SeSAD (infl) /542/572 gere SeMAD(p/i) /110/444 cyanase SeMAD (p/i) /669/1560 thioesterase I BrSAD(peak) /431/462 # Total Crank time for SAD target in the modied Refmac.

Earlier tests on Crank Pavol’s talk/results: all SAD examples can be automatically built (apart for SAD gere with peak). 33 test cases for SAD/MAD/SIRAS starting from substructure detection to model building: (follow test link)

Preliminary results on JCSG with the CRANK in CCP4 6.1 Started with known heavy atom substructure, but unknown number of monomers/solvent content Using only default values: sequence, mtz, f’, f” only input First sets of jobs run: before substructure detection results (so, more input errors…) DISCLAIMER: analyzed last night after dinner until 3:30 a.m.!

Crank interfaces: UNIX script

Results from “CCP4” pipeline BP3->SOLOMON->PIRATE ->BUCCANEER 75 to 100 %28 48 % 50 to 74 %4 7 % 25 to 49 %11 16 % 0 to 24 %15 26 % Total: %

Results from “CCP4” pipeline BP3->SOLOMON->ARP/wARP 75 to 100 %45 66 % 50 to 74 % 7 10 % 25 to 49 % 5 7 % 0 to 24 %11 16 % Total: %

Issues to be addressed Used default number of building cycles: In some cases more of the model could be built with more cycles (i.e. flex-WARP) Hand determination failed a bit too many times (about 15). In my unsystematic analysis, SHELXE was better than SOLOMON.

Future work Getting windows version of crank Opening up Crank web server Feature freeze on crank and concentrate more on algorithmic developments: –AFRO Fa’s for SAD/MAD/unmerged data –BP3/Refmac phasing – expand multivariate approach (SIRAS/MAD – Pavol’s talk) –Refmac model building: Pavol’s talk

Crank Interfaces: web interface for Crank server (48 nodes)

Acknowledgements Cyttron Program authors: G. Sheldrick, G. Murshudov, V. Lamzin, A. Perrakis, K. Cowtan, P. Emsley and co-workers. R.A.G. de Graaff, I. Sikharulidze, P. Skubak, J.P. Abrahams, JCSG staff, Z. Dauter, and M. Weiss. Debugging/suggestions: CCP4 staff, Auto-Rickshaw guys, users.