Progress report on Crank:Model building

Biophysical Structural ChemistryLeiden University, The Netherlands

Extending the limits of the SHELXCDE->ARP/wARP pipeline

Resol.

(Å)

Anom.

atoms

Exp. Time

(min)

Residues

RICE/SAD/FINAL

MutS 3.0 46 Se SAD 156.2 493/1093/1600

subtilisin 1.77 3 Ca, S SAD 55.65 6/259/275

thioesterase 2.5 8 Se SAD (infl) 86.7 300/542/572

gere 2.75 12 Se MAD(p/i) 28.81 43/110/444

cyanase 2.41 40 Se MAD (p/i) 69.44 71/669/1560

thioesterase I 1.81 20 Br SAD(peak) 65.46 35/431/462

#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:http://www.bfsc.leidenuniv.nl/software/crank/(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” pipelineBP3->SOLOMON->PIRATE

->BUCCANEER75 to 100 % 28 48 %

50 to 74 % 4 7 %

25 to 49 % 11 16 %

0 to 24 % 15 26 %

Total: 58 100 %

Results from “CCP4” pipelineBP3->SOLOMON->ARP/wARP

75 to 100 % 45 66 %

50 to 74 % 7 10 %

25 to 49 % 5 7 %

0 to 24 % 11 16 %

Total: 68 100 %

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.