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Applying EMAN2 to Difficult Problems http:/ /blake.bcm.edu Steve - PowerPoint PPT Presentation

May 08, 2023 •147 likes •253 views

Applying EMAN2 to Difficult Problems http:/ /blake.bcm.edu Steve Ludtke Co-director NCMI Assoc. Prof Biochemistry Baylor College of Medicine NCRR Friday, November 6, 2009 EMAN2 NOW STABLE AND PRODUCING STRUCTURES Workflow infrastructure

  1. Applying EMAN2 to Difficult Problems http:/ /blake.bcm.edu Steve Ludtke Co-director NCMI Assoc. Prof Biochemistry Baylor College of Medicine NCRR Friday, November 6, 2009

  2. EMAN2 NOW STABLE AND PRODUCING STRUCTURES Workflow infrastructure Complete logging/data management with embedded DB New openGL based GUI Improved CTF model Automatic fitting, Energy filters, proper c-film handling Single particle cryoET Easily extensible modular core GPGPU support * SPARX Project ! Friday, November 6, 2009

  3. EMAN2 Design Ease of Use Workflow Interface Integrated Project High-Level Programs Database Command-Line Programs BDB Embedded Database Python Core C++ Core Flexibility Friday, November 6, 2009

  4. Difficult ? High resolution With low/no symmetry Nearly symmetric objects Large objects Structural heterogeneity Small Objects Friday, November 6, 2009

  5. Asymmetric Object with Pseudosymmetry at 4.7 & 4.0 Å Unpublished results excluded from handout Friday, November 6, 2009

  6. Structural Heterogeneity 2-D Iterative Reference Free Classification 3-D Multi-model refinement Single particle cryo-ET Friday, November 6, 2009

  7. Small Objects Hardware, not software (phase plates) More careful image processing Friday, November 6, 2009

  8. Examples Friday, November 6, 2009

  9. Acknowledgements Carboxysome TriC/CCT • Mike Schmid • Yao Cong • Angel Paredes • Matthew L. Baker • Htet Khant • Joanita Jakana • Wah Chiu • David Woolford • Ferda Soyer (Izmir) • Wah Chiu • Henry Aldrich (Deceased) • Alyssa M Redding-Johanson (LBNL) • Jessup Shively (Clemson) • Tanveer S Batth (LBNL) • Aindrila Mukhopadhyay (LBNL) • Erik J. Miller (Stanford) • Stefanie Reissmann (Stanford) FAS • Ramya N. Kumar (Stanford) • Wei Zhang • Judith Frydman (Stanford) • Sub Chirala • Ziwei Gu • Wah Chiu • Salih Wakil • Flo Quiocho Supported by NIGMS, NIH Roadmap Initiative, NCRR & NSF Images created with UCSF Chimera Friday, November 6, 2009

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