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Discussion Summary for the 2012-13 Challenge

Discussion Summary for the 2012-13 Challenge. Wah Chiu wah@bcm.edu. Past Challenges. Particle Picking Reconstruction Software Modeling Challenge. Suggested Challenges for Cryo-EM. CTF estimate (determination) 11 Assess quality of micrographs 10

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Discussion Summary for the 2012-13 Challenge

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  1. Discussion Summary for the 2012-13 Challenge Wah Chiu wah@bcm.edu

  2. Past Challenges Particle Picking Reconstruction Software Modeling Challenge

  3. Suggested Challenges for Cryo-EM • CTF estimate (determination) 11 • Assess quality of micrographs 10 • Reconstruction refinement (Quality of the map) 9 • Particle picking 9 • 2-D Image classification 1 • 3-D classification 5 • Meta challenge (e.g. CTF) 0 • Different teams work on different steps 0 • Modeling experimental data 5 • Generate experimental and theoretical phantom 0 • Biochemical homogeneity 0 • Cryo-specimen preparation 3 • Challenge in obtaining the best data set 1 • Establish intersection points among different softwares 0 • Test with published structures (e.g. ATP complex) 0

  4. Practical Consideration for Challenge Events • Resources available in the community • Interesting, challenging and feasible • Eliminate ego (nameless) • Cash for the winners (Euro or $) from the EM companies • Publications in respectable journals • Of interest to the community in general

  5. Choice of a Challenge for 2012-13 • CTF estimate (determination) 11 • Assess quality of micrographs 10 • Reconstruction refinement (Quality of the map) 9 • Particle picking 9

  6. Establish a Data Set of ~100 micrographs with different experimental conditions • Defocus range: 0.5, 1.0, 1.5. 2.0, 3, 5 micron • 200 and 300 kV microscope • “Small” Astigmatism and drift • Variation of defocus within a micrograph due to various reasons • Recording medium: film, CCD, Direct detector • With and without Carbon or graphene film • Size of particles 0.5 -2 MDa • Particle concentration (>50 particles/frame) without C film • Electron dose 20 e/Å2per image different defocus • Magnification is chosen to have Sampling: 1.5-2 Å/pixel • Ice thickness (typical for the experiment) • Cumulative Envelope function

  7. Define the FOM • Determine the defocus U and defocus V and the angle as defined for data interchange • Two photographs with different defocuses in well-calibrated microscopes to validate the true defocus values in all cases

  8. Specimen choices • 60S Ribosome (1.6 MDa), 300 kV, CCD, C film: J Frank • GroEL (800kDa) 200 kV, CCD, DDD, no C film: A Cheng • Lipid nanodisk (1MDa), 300 & 200 kV, CCD and CMOS, C and graphene: Henning • Apoferritin (500 kDa) 200 kV, film, no carbon:Richard Henderson

  9. Phases of Task in preparing the Data • Monthly conference call initiated by J-M Carazo among the experimentalists. (March, April, May) to share progress and hurdles • Focal pair Data generation and analysis by the suppliers of each of the 4 specimens • June 1, 2012 • Use the J-M Carazo infrastructure to share data • Meet at the Gordon conference to assess the collected images and to decide the policy for the competition among the community

  10. Road Map of Challenges in the Future • Suggested meeting in US in the winter of 2013 • Financed by HHMI, NIH or NSF

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