SLAC National Accelerator Laboratory

RapiData 2019 at SSRL - Data Collection and Structure Solving: A Practical Course in Macromolecular X-Ray Diffraction Measurement
May 5-10 2019

Schedule for RapiData 2019

Note: This schedule is subject to changes.

All lectures on Sunday, Monday and Tuesday 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 indicating the main course venues.

Sunday 5 May

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

  • 9:30 - 12:00 Optional concurrent session 1: Crystallography 101: Bob Sweet (Redwood rooms C/D)

      - Waves and diffraction

      - Bragg’s Law and reciprocal space

      - Detection of X-rays

  • 9:30 - 12:00 Optional concurrent session 2: Crystallography 1-on-1: Sample data collection strategy discussions with SSRL beamline and scientific staff (Redwood rooms A/B)

  • 12:00 - 13:00 Lunch

  • 13:00 - 15:30 Optional concurrent session 1:Crystallography 101: Bob Sweet (Redwood rooms C/D)

      - Fourier synthesis and structure

      - Space groups and crystal systems

      - Solving the phase problem

  • 13:00 - 15:30 Optional concurrent session 2: Crystallography 1-on-1: Sample data collection strategy discussions with SSRL beamline and scientific staff (Redwood rooms A/B)

  • 15:30 - 16:00 Coffee Break

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

  • 17:30 - 19:30 Welcome Social (Stanford Guest House patio)

Monday 6 May

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

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

  • 8:30 - 9:00   Introduction to RapiData: Clyde Smith

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

  • 9:45 - 10:30   Room temperature data collection: Silvia Russi

  • 10:30 - 10:45   Coffee break

  • 10:45 - 11:30   Radiation damage: James Holton

  • 11:30 - 12:15   Getting the best data from photon counting detectors: Andreas Foerster

  • 12:15 - 13:30   Lunch

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

  • 14:15 - 15:00   Data collection at Free Electron Lasers: Nick Sauter

  • 15:00 - 15:15   Coffee break

  • 15:15 - 16:00   Cryo-EM: Wah Chiu

  • 16:00   Group photo (Redwood room patio)

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

  • 18:00 - 18:45   Introduction to the tutorials (Redwood room C/D)

  • 18:45 - 19:45   Banquet dinner (Redwood room patio)

  • 19:45   Flash introduction of the participants (Redwood room patio or inside)

Tuesday 7 May

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

  • 8:30 - 9:00   Why solve structures?: Art Lyubimov

  • 9:00 - 9:45   SAD and MAD: Ana Gonzalez

  • 9:45 - 10:30   Molecular Replacement: Raji Edayathumangalam

  • 10:30 - 10:45   Coffee Break

  • 10:45 - 11:30   SHELX: Andrea Thorn

  • 11:30 - 12:15   Data processing and analysis for experimental phasing with SHARP/autoSHARP: Clemens Vonrhein

  • 12:15 - 13:30   Lunch

  • 13:30 - 14:15   Solve and Phenix: Dorothee Liebschner

  • 14:15 - 15:00   In situ optical spectroscopy: Aina Cohen

  • 15:00 - 15:30   Coffee break and tutorial sign-up

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

  • 16:30 - 18:30   LCLS Tour

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

  • 20:00 - 22:00   Tutorials/Sample Transfer tutorial

Wednesday 8 May

    All day (8:00-22:00): Concurrent data collection and tutorials (see schedule below)

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

  • 13:00 - 14:00   Lunch (Redwood rooms patio)

  • 15:30   Coffee served in BL9-2 lounge area

  • 17:00 - 18:00   Guest lecture: Brian Kobilka (Redwood rooms C/D)

  • 18:00 - 19:00   Dinner (Redwood rooms patio)

Thursday 9 May

    All day (8:00-22:00): Concurrent data collection and software tutorials (see schedule below)

  • 10:30 Coffee served in BL9-2 lounge area

  • 13:00 - 14:00   Lunch

  • 15:30   Coffee served in BL9-2 lounge area

  • 17:00 - 18:00   Guest lecture: James Fraser (Redwood rooms C/D)

  • 18:00 - 19:00   Dinner (Redwood rooms patio)

Friday 10 May

NX client installation and remote desktop workshop

On Sunday, 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 Sunday course and need help with the NX client, can contact the organizers to arrange a demo.

Orientation to experiments at SSRL

On Monday 6th, 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)

Participants' Sample Transfer tutorial

On Tuesday 7th, between 20:00 and 22:00, we will do a demo on transferring frozen samples in cryovials to robot cassettes at the sample loading stations on BL9-2 and BL12-2. Participants who have brought frozen samples in cryovials or with unfrozen samples (in crystallization plates or capillaries) will get the chance to transfer them to SSRL cassettes after the demo.


Sign up sheets for the optional tour of the free electron laser facility LCLS will be available on Monday. Group 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.


  • On Monday 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
  • On Friday, there will be a recapitulation meeting. We will fill a questionnaire about the course, 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.

Data collection practical

During the data collection tutorials, the participants will learn how to optimize the data collection parameters for different experimental purposes.

We will offer tutorials for sample preparation, freezing, mounting and characterization; SAD/MAD data collection; RT data collection; crystal dehydration and UV-Vis spectrophotometry. All the participants will get beamtime to learn how to collect data from their own samples or standard samples. (See beamtime schedule below). For the participants interested in the MAD/SAD, RT, crystal dehydration, UV-Vis spectrophotometry and sample preparation tutorials, there will be sign-up sheets at the Redwood rooms on Tuesday during the afternoon coffee break and in the BL9-2 lounge area after that.

The slots marked as 'Spare' in the beamtime schedule can be used for participants to collect data by themselves, once they have been trained on data collection during a previous tutorial. Please see the organizers during the course if you need spare time for data collection or to ask about the possibility to collect data remotely after the course.

Time Data collection at BL12-2RT data collection/Crystal dehyration/UV-Vis Microspectrophotometer (BL9-2) MAD/SAD data collection (BL14-1) Data collection at BL9-2 Sample preparation (BL7-1)
Tues 20:00 Unavailable Unavailable Unavailable Unavailable Sign-up
Wed 8:00 Haruehanroengran Unavailable Sign-up Bastos/Mazurkewich/Wang/Yang/Edjer Sign-up
Wed 10:30Lei/McQuirter Unavailable Sign-up Meng/Lanz/DeMaria/Hellmich/Kanchugal Sign-up
Wed 14:00 Lee Unavailable Sign-up Nepomuceno/Kluza/Wasserman/Arturo/Kashipathy/Torgeson Sign-up
Wed 19:00 Sigh Sign-up Sign-up Unavailable Sign-up
Wed 21:30 Spare Unavailable Unavailable Spare Unavailable
Thu 8:00 Santiago/Stark Unavailable Sign-up Ortolani/Soh/Carrioza/Escudero/Banjara/D'Agostino Sign-up
Thu 10:30 Nemetcheck/Johnston Unavailable Sign-up Thorsen/Velez/Mueller/Molt/Vanson/Brousseau Sign-up
Thu 14:00 Hansen/Syrenne Unavailable Sign-up Cheng Sign-up
Thu 19:00 Tamura Sign-up Sign-up Unavailable Sign-up
Thu 21:30 Spare Unavailable Spare Spare Unavailable

See A map of the SSRL beamlines.


  • BL7-1: Sample preparation: Jim Pflugrath, Tzanko Doukov, Daniel Fernandez, Mathews Irimpan
  • BL9-2: Data collection on BL9-2: Irimpan Mathews, Jeney Wierman
  • BL12-2: Data collection on BL12-2: Clyde Smith, Silvia Russi
  • BL14-1: MAD/SAD data collection: Ana Gonzalez
  • BL9-2: RT data collection/crystal dehydration/UV-Vis Microspectrophotometer introduction: Silvia Russi, Aina Cohen, Jeney Wierman

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, Billy Poon, Nigel Moriarty, Dorothee Liebschner
  • Data processing and phasing with DIALS and CCP4: Harry Powell and Andrey Labedev
  • Molecular Replacement: Raji Edayathumangalam
  • SHELX: Andrea Thorn
  • SHARP/autoSHARP, autoPROC, STARANISO, BUSTER: Clemens Vonrhein and Claus Flensburg
  • Data processing with XDS: James Holton
  • Data processing with HKL: Ivan Shabalin
  • SAXS data analysis: Tsutomu Matsui, Ivan Rajkovic and Thomas Weiss

The participants must sign-up in advance for the software tutorials they wish to attend. There will be sign-up sheets at the Redwood rooms on Tuesday during the afternoon coffee break and in the BL9-2 lounge area after that.