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EMBO Course - Programme

Lectures and tutorials will take place in the HASYLAB seminar room, Building 25b


Day 1 : X-ray scattering and instrumentation (Wed, 5 Sep.)
08:45-09:00Introduction - D. Svergun (.pdf file(373 kB))
09:00-09:50Solution scattering: an overview - H.Stuhrmann (.pdf file (393 kB))
09:50-10:10Coffee break
10:10-12:00Scattering of X-rays (basics) - P.Vachette (.pdf file (5.9 MB))
12:30-13:30Lunch, DESY Bistro, Building 9a
14:00-15:00Basic numerical and statistical methods - V.Volkov (.pdf file (928 kB))
15:00-17:00Visit of the EMBL solution scattering beamline at HASYLAB
17:00-17:30Coffee break
17:30-19:30Student presentations (10 min each)
20:00-22:00

Welcome dinner

Day 2 : Data processing (Thu, 6 Sep.)
09:00-09:50X-ray data reduction and processing - D. Svergun (.pdf file (1.7 MB))
09:50-10:40X-ray optics and detectors - W. Bras (.pdf file (1 MB))
10:40-11:00Coffee break
11:00-12:00Indirect transformation method - O.Glatter (.pdf file (792 KB))
12:30-13:30Lunch, DESY Bistro, Building 9a
14:00-15:00ITP program tutorial - O.Glatter
15:00-16:00GNOM program tutorial - D.Svergun
16:00-16:30Comparison of indirect transformation methods - T. Fujisawa (.pdf file (188 KB))
Available tools to download :
  • gnomExtract (144 KB) - Program to extract profiler from GNOM out files
  • Multiplot (144 KB) - Plotting SAS curves
  • XCalc (622 KB) - Implementation of Moore's algorithm.
16:30-17:00Coffee break
17:00-19:00Students presentations (10 min each)
19:00-19:45Supper on the DESY site
19:45-21:30ITP/GNOM practicals
Day 3 : Neutron scattering and instrumentation (Fri, 7 Sep.)
(The session will take place at the GKSS research reactor in Geesthacht)
08:00Meeting point at DESY side entrance (Luruper Chaussee)
08:00-09:30Bus transportation to the GKSS Research Center
09:30-10:00Welcome
10:00-12:00Neutron scattering (basics) - J.Zaccai
12:00-13:30Lunch
13:30-15:00Neutron instrumentation, data reduction - R.Willumeit
15:00-16:30Visit of the experimental hall at the research reactor FRG-1
16:30-17:00Coffee break
17:00-19:00Spin-dependent neutron scattering and the ribosome - H.Stuhrmann, R.Willumeit
19:00-19:30Coffee/snacks and concluding remarks
19:30-21:00Bus transportation from GKSS to DESY
Day : 4 Ab initio methods (Sat, 8 Sep.)
09:00-09:50Ab initio approaches: resolution and uniqueness - D.Svergun (.pdf file (7.9 MB))
09:50-10:40Shape determination using a genetic algorithm - F.Diaz (.pdf file (4.9 MB))
10:40-11:00Coffee break
11:00-12:00Program DALAI_GA tutorial - F.Diaz
12:30-13:30Lunch, DESY Bistro, Building 9a
14:00-14:45Program SASHA tutorial - V.Volkov (.pdf file (633 KB))
14:45-15:45Programs DAMMIN/GASBOR tutorial - D.Svergun, M.Petoukhov)
15:45-16:30Comparison of ab initio methods - T. Fujisawa (.pdf file (1.4 MB))
videos.zip (53 Mb) - Animation videos that can optionally be downloaded to animate the .pdf file. Unpack this zip file in the same directory as the .pdf file and by double clicking on a picture the animation video starts.
16:30-17:00Coffee break
17:00-19:00Shape determination: applications to proteins - S. Koenig, K.Brown, S.Doniach
19:00-19:45Supper on the DESY site
19:45-21:30DALAI_GA/SASHA/DAMMIN/GASBOR practicals (EMBL seminar room/library)
Day 5 : Polydisperse and interacting systems (Sun 9 Sep.)
09:00-10:00Form and structure factors - O.Glatter (.pdf file (1.6 MB))
10:00-10:50GIFT program tutorial - O.Glatter
10:50-11:10Coffee break
11:10-12:00Mixtures: linear and nonlinear modelling - V.Volkov (.pdf file (720 kB))
12:30-13:30Lunch, DESY Bistro, Building 9a
14:00-15:00Programs OLIGOMER/MIXTURE tutorial - V.Volkov, P.Konarev
15:00-16:00Analysis of equilibrium protein solutions - K. Brown
16:00-16:30Coffee break
16:30-18:30Time resolved scattering and protein/RNA folding - S.Doniach
18:30-19:15Supper on the DESY site
19:15-21:30GIFT/OLIGOMER/MIXTURE practical (EMBL seminar room/library)
Day 6 : Studies of different types of systems (Mon, 10 Sep.)
09:00-10:50Lipoproteins and membranes - P.Laggner (.pdf file (4.6 MB))
10:50-11:10Coffee break
11:10-12:00Protein-carbohydrate complexes - P.Vachette
12:00-14:00Lunch, DESY Bistro, Building 9a

Free afternoon (optional excursion to the Speicherstadt)

Day 7 : Rigid body refinement (Tue 11 Sep.)
09:00-09:50Computation of solution scattering from atomic models - D.Svergun (.pdf file (1.2 MB))
09:50-10:40CRYSOL/CRYSON program tutorial - M.Malfois
10:40-11:00Coffee break
11:00-12:00CRYDAM program tutorial - M. Malfois (.pdf file (117 KB))
12:30-13:30Lunch, DESY Bistro, Building 9a
14:00-15:00Interactive vs automated refinement - D.Svergun (.pdf file (2.9 MB))
16:00-16:00ASSA/MASSHA program tutorial - M.Petoukhov, P.Konarev (.pdf file (265 KB))
16:00-16:30Coffee break
16:30-18:30Rigid body refinement: applications to proteins - K.Brown, S.Koenig
18:30-19:15Supper on the DESY site
19:15-21:30Rigid body refinement practical (EMBL seminar room/library)
Day 8 : Related methods (Wed 12 Sep.)
09:00-09:50Supramolecular complexes and in situ property mapping - P.Laggner (.pdf file (2.1 MB))
09:50-10:40Computation of hydrodynamic parameters - G. de la Torre
10:40-11:00Coffee break
11:00-12:00HYDRO program tutorial - G. de la Torre
12:30-13:30Lunch, DESY Bistro, Building 9a
14:00-15:30Quasielastic light scattering - J.Langowski
15:30-16:00Coffee break
16:00-18:00Detection of aggregates using QELS - J.Langowski (EMBL wetlab)
18:00-18:45Supper on the DESY site
18:45-21:30Free practicals and data analysis (EMBL seminar room/library)
Day 9 : General discussion (Thu 13 Sep.)
09:00-10:30Participating students: presentation of results (30 min each)
10:30-11:00Coffee break
11:00-12:00Participating students: presentation of results (30 min each)
12:30-13:30Lunch, DESY Bistro, Building 9a
14:00-16:30Participating students: presentation of results (30 min each)
16:30-17:00Coffee break
17:00-19:30Participating students: presentation of results (30 min each)
20:00-22:00Course dinner
Day 10 : General discussion (Fri 14 Sep.)
09:00-10:30Participating students: presentation of results (30 min each)
10:30-11:00Coffee break
11:00-12:00Concluding remarks + Departure


Mail address:
EMBL Hamburg
Building 25A, DESY
Notkestrasse 85
22603 Hamburg
Germany

Tel. +49 40 89902110 /
      +49 40 89902111
Fax. +49 40 89902149 /
        +49 40 89902104
 
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