SLAC National Accelerator Laboratory
Structural Molecular Biology at SSRL U.S. Department of Energy: Office of Science

RapiData 2024 at SSRL

Data Collection and Structure Solving: A Practical Course in Macromolecular X-Ray Diffraction Measurement

April 29 - May 4, 2024

Schedule for RapiData 2024

All lectures will take place in the Redwood rooms (building 48). Lunch and dinner will also be served in building 48, unless noted otherwise. The practical tutorials will take place at different locations around the SSRL and experimental floor.

See a map of SLAC and a map of SSRL indicating the main course venues.

Monday 29 April

  • 8:30 - 9:30 Registration (Redwood rooms, building 48)

  • 9:30 - 12:00 Crystallography 101: Bob Sweet (Redwood rooms C/D)

      - Waves and diffraction

      - Bragg’s Law and reciprocal space

      - Detection of X-rays

  • 12:00 - 13:00 Lunch

  • 13:00 - 15:30 Crystallography 101: Bob Sweet (Redwood rooms C/D)

      - Fourier synthesis and structure

      - Space groups and crystal systems

      - Solving the phase problem

  • 15:30 - 16:00 Coffee Break

  • 16:00 - 17:00 NX Client installation and remote desktop workshop: Artem Lyubimov (Redwood rooms C/D)

  • 17:30 - 19:30 Welcome Social (Redwood rooms patio)

Tuesday 30 April

    Lectures on crystal handling, data collection, detectors and data reduction (Redwood rooms C/D)

  • 7:30 - 8:00   Registration (Redwood Rooms)

  • 8:00 - 8:30   Introduction to RapiData: Clyde Smith

  • 8:30 - 9:00   A road map to structural molecular biology at SSRL: Silvia Russi

  • 9:00 - 9:45   Macromolecular Cryocrystallography: Some opinions about best practices: Jim Pflugrath

  • 9:45 - 10:30   Room and elevated temperature data collection: New tools and automation: Silvia Russi

  • 10:30 - 10:45   Coffee break

  • 10:45 - 11:30   Radiation damage: Elspeth Garman

  • 11:30 - 12:15   Getting the best data from photon counting detectors: Sofia Trampari

  • 12:15 - 13:30   Lunch

  • 13:30 - 14:15   Data processing fundamentals: Harry Powell

  • 14:15 - 15:00   A structural biology guide to serial crystallography: Artem Lyubimov

  • 15:00 - 15:45   Data collection at Free Electron Lasers: Nick Sauter

  • 15:45 - 16:00   Coffee break and group photo

  • 16:00 - 16:15   Introduction to the tutorials: Clyde Smith

  • 16:30 - 17:30   Orientation to experiments /SSRL Tour (building 120)

  • 18:00 - 19:00   Banquet dinner (Redwood rooms patio)

  • 19:00 - 20:00   Flash introduction of the participants (Redwood room patio or inside)

Wednesday 1 May

    Lectures on structure solution and complementary methods (Redwood rooms C/D)

  • 8:00 - 8:45   Molecular Replacement: Raji Edayathumangalam

  • 8:45 - 9:30   SAD and MAD: Ana Gonzalez

  • 9:30 - 10:15   SHELX: Andrea Thorn

  • 10:15 - 10:30   Coffee Break

  • 10:30 - 11:15   DIALS: Harry Powell

  • 11:15 - 12:00   Data processing and analysis for experimental phasing with SHARP/autoSHARP: Clemens Vonrhein

  • 12:00 - 13:00   Lunch

  • 13:00 - 13:45   Data processing with HKL3000: Dominika Borek

  • 13:45 - 14:30   Solve and Phenix: Dorothee Liebschner

  • 14:30 - 15:15   Coot: Paul Emsley

  • 15:15 - 15:30   Coffee break

  • 15:30 - 16:30   Introduction to Small Angle Scattering: Thomas Weiss

  • 16:45 - 18:45   LCLS Tour

  • 19:00 - 20:00   Dinner (Redwood rooms patio)

  • 20:00 - 20:45   In situ optical spectroscopy: Aina Cohen

Thursday 2 May

    All day concurrent beamline and software tutorials.

  • 8:00 - 10:00   Tutorials

  • 10:00 - 10:30   Coffee served in BL9-2 longe area

  • 10:30 - 12:30   Tutorials

  • 12:45 - 13:45   Lunch (Redwood rooms patio)

  • 14:00 - 16:00   Tutorials

  • 16:00 - 16:30   Coffee served in BL9-2 longe area

  • 16:30 - 18:30   Tutorials

  • 18:45 - 19:45   Dinner (Redwood rooms patio)

  • 19:45 - 20:45   Guest lecture: Brian Kobilka (Redwood rooms C/D)

Friday 3 May

  • 8:00 - 10:00   Tutorials

  • 10:00 - 10:30   Coffee served in BL9-2 longe area

  • 10:30 - 12:30   Tutorials

  • 12:45 - 13:45   Lunch (Redwood rooms patio)

  • 14:00 - 16:00   Tutorials

  • 16:00 - 16:30   Coffee served in BL9-2 longe area

  • 16:30 - 18:30   Tutorials

  • 18:45 - 19:45   Dinner (Redwood rooms patio)

Saturday 4 May



NX client installation and remote desktop workshop

On Monday, there will be a workshop to install and configure the NX client in the participants' laptops, and to learn how to access the data and demos in the practical tutorials.

Participants who do not attend the Monday course and need help with the NX client, can contact the organizers to arrange a demo.



Orientation to experiments at SSRL

On Tuesday after the afternoon lectures, there will a compulsory orientation to experiments at SSRL, covering safety, at building 120. There will be two talks:

  • 16:30: Safety talk (Last name starting with A-L)

  • 16:45: Safety talk (Last name starting with M-Z)



LCLS Tour

Sign up sheets for the optional tour of the free electron laser facility LCLS will be available on Tuesday. Groups will set off from building 48 (there is a ~15 minute walk to the LCLS). The tour will include a visit to the beamlines CXI and MFX, used for macromolecular femtosecond crystallography. The tour takes about 45 minutes.



Flash Introduction of the Participants

  • On Tuesday after the banquet dinner we will ask all the participants to give a short (1 minute or less) introduction of themselves: their name, where they work and what is the main thing the want to achieve or learn during the course.



    Recapitulation Meeting

  • On Saturday, there will be a recapitulation meeting. We will distribute awards and certificates, and have a joint free format discussion. The students will have the chance to ask questions about the material covered in the course and offer suggestions for future courses.




    • Beamline Tutorials

    We will offer tutorials for sample preparation, cryo-cooling, mounting and characterization; SAD/MAD data collection; RT data collection; crystal dehydration and UV-Vis spectrophotometry. All the participants will get the chance to learn how to collect data from their own samples or standard samples.

    • Data collection on BL12-1: Irimpan Mathews and Darya Marchany
    • Data collection on BL12-2: Clyde Smith and Silvia Russi
    • MAD/SAD data collection on BL14-1: Ana Gonzalez
    • Sample preparation and harvesting tips and tricks on BL9-2: Jim Pflugrath, Tzanko Doukov and Ailiena Maggiolo
    • UV-Vis Microspectrophotometer introduction on 9-2: Aina Cohen
    • RT data collection/crystal dehydration: Silvia Russi and Darya Marchany

    The participants must sign-up in advance for the tutorials they wish to attend. Instructions on how to access the sign-up sheets will be given during the course.



    Software Tutorials

    Software tutorials will be offered on several different packages for data processing and structure solution, including:

    • Structure solution and refinement with Phenix: Li-Wei Hung, Oleg Sobolev, Billy Poon and Dorothee Liebschner
    • Data processing and phasing with DIALS and CCP4: Harry Powell and Andrey Lebedev
    • Molecular Replacement: Raji Edayathumangalam
    • SHARP/autoSHARP, autoPROC, STARANISO, BUSTER: Clemens Vonrhein and Claus Flensburg
    • Data processing with XDS: James Holton
    • Data processing with HKL: Dominika Borek
    • Coot: Paul Emsley and Lucrezia Catapano
    • SAXS data analysis: Tsutomu Matsui and Thomas Weiss

    The participants must sign-up in advance for the tutorials they wish to attend. Instructions on how to access the sign-up sheets will be given during the course.