Discussion summary for the 2012 13 challenge
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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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Past challenges

Past Challenges

Particle Picking

Reconstruction Software

Modeling Challenge


Suggested challenges for cryo em
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


Practical consideration for challenge events
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


Choice of a challenge for 2012 13
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


Establish a data set of 100 micrographs with different experimental conditions
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


Define the fom
Define the FOM experimental conditions

  • 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


Specimen choices
Specimen choices experimental conditions

  • 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


Phases of task in preparing the data
Phases of Task in preparing the Data experimental conditions

  • 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


Road map of challenges in the future
Road Map of Challenges in the Future experimental conditions

  • Suggested meeting in US in the winter of 2013

  • Financed by HHMI, NIH or NSF