|
GIAN - 1st Course on Cryo Electron Microscopy and 3D Image Processing of Macromolecular Assemblies and Cellular Tomography (CEM3DIP) - July 2 - July 13, 2016 - Timetable.
|
| Venue |
UDS Kovalam (Seaview Hall) |
|
IISER-TVM (Prateeksha Building) |
UDS Kovalam (Seaview Hall) |
|
| 02/07/2016 Saturday |
|
14:00 Coaches Depart from UDS Kovalam to IISER - TVM Vithura Campus.
16:00** Registration of Participants and Speakers @ IISER-TVM Vithura Campus.
|
17:00** Inauguration by Professor V. Ramakrishnan, Director, IISER Thiruvananthapuram @IISER-TVM Vithura Campus.
17:30** Overview of course. Participants Quick Introduction (R. Natesh, E. Orlova and M. Banerjee).
|
18:00 L1: CEM3DIP Keynote Lecture 1: Professor Wah Chiu. "3D EM History, Basic Principles and its recent advances in Electron Microscopy to obtain High Resolution structures". 19:30 Dinner. 20:30 Coaches Depart to UDS Kovalam.
Lecture Note | Lecture Video
|
| 03/07/2016 Sunday |
L2 : EM sample, specimen preparation methods. - Ramanathan Natesh
Lecture Note | Lecture Video
|
L3: Basic Concepts of Fourier Transform in TEM image analysis. - Steven Ludtke
Lecture Note | Lecture Video
|
Lunch |
Practical 1: EMAN v2.12, Session 1. Steven Ludtke |
Posters session 1 (P1 to P10) |
Dinner |
| 04/07/2016 Monday |
L4: Contrast Transfer Function, Point Spread Function and its effect on image acquisition and concepts of convolution etc. - Steven Ludtke
Lecture Note | Lecture Video
|
L5: Principles of TEM Image formation, Particle detection from TEM images and noise handling Manidipa Banerjee
Lecture Note | Lecture Video
|
Lunch |
Practical 2: EMAN v2.12 Session 2. Steven Ludtke |
Selected participant talks (ST1 to ST3) |
Dinner |
05/07/2016
Tuesday
|
L6: MSA and classification of particles Steve Ludtke
Lecture Note | Lecture Video
|
L7: Refinement of Classifications, Dealing with orientation and Heterogeneity of particles Ramanathan Natesh
Lecture Note | Lecture Video
|
Lunch
|
Practical 3: EMAN v2.12 Session 3. Steven Ludtke
|
Poster Session 2 (P11 to P20)
|
Dinner
|
|
06/07/2016 Wednesday
|
L8: Methods in single particle 3D orientation determination - Kutti Raghunath Vinothkumar
Lecture Note | Lecture Video
|
L9: Methods in single particle 3D reconstruction, Resolution and FSC - Elena Orlova
Lecture Note | Lecture Video
|
Lunch
|
Practical 4: Relion, Session 1. Kutti Raghunath Vinothkumar
|
Poster Session 3 (P21 to P30)
|
Dinner
|
|
07/07/2016 Thursday
|
L10: Conical Tilt (CT) and Projection Matching (PM). Getting the first model using CT and PM Kutti Raghunath Vinothkumar
Lecture Note | Lecture Video
|
L11: Point Group Symmetries. Manidipa Banerjee
Lecture Note | Lecture Video
|
Lunch
|
Practical 5: Relion, Session 2. Kutti Raghunath Vinothkumar
|
Poster Session 4 (P31 to P40)
|
Dinner
|
|
08/07/2016 Friday
|
L12: Single Particle Cryo-electron Microscopy and 3D reconstruction of Viruses Manidipa Banerjee
Lecture Note | Lecture Video
|
L13: General principles of image processing in Cryo EM Elena Orlova
Lecture Note | Lecture Video
|
Lunch
|
Practical 6: IMAGIC, Session 1. MSA Classification and angular reconstitution Elena Orlova & R. Natesh
|
Poster Session 5 (P41 to P50)
|
Dinner
|
|
09/07/2016 Saturday
|
L14: Hybrid methods: Protein Crystallography, computational methods and Cryo EM Ramanathan Natesh
Lecture Note | Lecture Video
|
11:15: L15: FEI: Microscopes for cryo-automated data collection - Rishi Matadeen
Lecture Note | Lecture Video
12:00: L16: Leica: EM Cryo preparation workflows. Update on the latest instrumentation. Ian Lamswood
Lecture Note | Lecture Video
|
Lunch
|
Practical 7: IMAGIC, Session 2. 3D reconstruction Elena Orlova & R. Natesh
|
Poster Session 6 (P51 to P58)
|
Dinner
|
|
10-Jul-2016
|
Sunday (Free Day). Proposed Group Excursion(Depending on Weather) – Poovar Backwaters and Kovalam Beach.
|
|
11/07/2016 Monday
|
L17: Reconstruction principles and applications of Cryo Tomography. Cellular Tomography and Subtomogram averaging. Macromolecular structures, cells and tissues by cryo-electron tomography - Lu Gan
Lecture Note | Lecture Video
|
L18: Gatan : Applications of electron-counting direct-detection cameras in high-resolution cryo-electron microscopy Christopher Booth
Lecture Note | Lecture Video
|
Lunch
|
Practical 8: Tomographic reconstruction practical using IMOD Lu Gan
|
Selected participant talks (ST4 to ST6)
|
Dinner
|
|
12/07/2016 Tuesday
|
L19**: The EMBO Global Exchange Lecture Series – CEM3DIP Keynote Lecture 2: Professor Wolfgang Baumeister. “The Challenge of doing Structural Biology in situ”.
Lecture Note | Lecture Video
|
L20**: Interpretation of maps, fitting / docking of atomic structures Garib N Murshodov
Lecture Note | Lecture Video
|
Lunch
|
Practical 9: Fitting, Refinement of atomic models and Model building in EM maps using Molrep/Refmac/Coot Garib N Murshodov
|
L21: Macromolecular dynamics: Flexible fitting into cryo-EM maps Jayati Sengupta
Lecture Note | Lecture Video
|
Dinner
|
|
13/07/2016 Wednesday
|
L22: Refinement of atomic models against cryo-EM maps (refmac, prosmart etc.) Garib N Murshodov
Lecture Note | Lecture Video
|
L23: Validation, Assessment, Data deposition: EMDB and EMPIAR: trends, developments, opportunities and challenges Ardan Patwardhan
Lecture Note | Lecture Video
|
Lunch
|
Practical 10: Chimera for Interpretation of maps, docking and fitting of atomic structures (Manidipa Banerjee) and MDFF Flexible fitting (Jayati Sengupta)
|
Questions, Suggestions, Summary, feedback, Certificate distribution and departure after dinner.
|
Dinner
|
