SLAC National Accelerator Laboratory

RapiData 2021 at SSRL - Data Collection and Structure Solving: A Practical Course in Macromolecular X-Ray Diffraction Measurement
May 5-15 2021

Schedule for RapiData 2021

The course will begin each day at 8:00am PDT, which is 11:00am EDT, 4:00pm London time, 5:00pm Paris time, 11pm Singapore time.

Zoom will be used as the virtual platform. Attendees will receive every day an email with the agenda and the zoom link/s. Please be sure not to share the link/s since it should be accessed by registered workshop participants only. Note: the workshop will be videorecorded.

Wednesday 5 May

  • 8:00 - 12:15 Crystallography 101: Bob Sweet

    The topics that will be covered in this short course are the following:

    - Waves and diffraction; the relationship with optical imaging

    - Bragg’s Law and reciprocal space

    - Doing the X-ray experiment

    - The actual physics of diffraction, described by Fourier analysis and synthesis

    - Symmetry space groups and crystal systems

    - Solving the phase problem

    This lecture will include several short breaks, made at times that seem appropriate to the lecture, and maybe a longer one about 10 am.

  • 12:15 - 12:30 Break

  • 12:30 - 13:30 NX Client installation and remote desktop workshop: Edgar Estebañez

  • 13:30 - 14:30 Welcome Social

Thursday 6 May

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

  • 8:30 - 9:15   Macromolecular Cryocrystallography: Some opinions about best practices: Jim Pflugrath

  • 9:15 - 10:00   Room and elevated temperature data collection: New tools and automation: Silvia Russi

  • 10:00 - 10:15   Break

  • 10:15 - 11:00   Radiation damage: Elspeth Garman

  • 11:00 - 11:45   Getting the best data from photon counting detectors: Andreas Foerster

  • 11:45 - 12:30   Data processing fundamentals: Harry Powell

  • 12:30 - 13:30   Flash introduction of the participants

Friday 7 May

  • 8:00 - 8:30   A roadmap to structural molecular biology at SSRL: Jeney Wierman

  • 8:30 - 9:15   SAD and MAD: Ana Gonzalez

  • 9:15 - 10:00   Shelx: Andrea Thorn

  • 10:00 - 10:15   Break

  • 10:15 - 11:00   Data processing and analysis for experimental phasing with SHARP/autoSHARP: Clemens Vonrhein

  • 11:00 - 11:45   Solve and Phenix: Dorothee Liebschner

  • 11:45 - 12:30   Molecular Replacement: Raji Edayathumangalam

  • 12:30 - 13:00   Introduction to Small Angle Scattering: Thomas Weiss

Monday 10 May

  • 8:00 - 8:45   A structural biologist's guide to serial crystallography: Artem Lyubimov

  • 8:45 - 9:30   Data collection at Free Electron Lasers: Nick Sauter

  • 9:30 - 10:15   Studying metalloenzymes with complimentary in-situ spectroscopic techniques: Aina Cohen

  • 10:15 - 10:30   Break

  • 10:30 - 11:30   SSRL Virtual Tour

  • 11:30 - 12:30   LCLS Virtual Tour

Tuesday 11 May

  • 8:00 - 8:45 Data processing with XDS: James Holton

  • 8:45 - 9:30 Data processing with HKL3000: Maksymilian Chruszcz

  • 9:30 - 10:15 DIALS: Harry Powell

  • 10:15 - 10:30 Break

  • 10:30 - 11:30 Introduction to COOT: Paul Emsley

  • 11:30 – 12:30 Guest lecture: Wah Chiu

  • 12:30 – 13:00 Introduction to tutorials: Clyde Smith

Wednesday 12 May

Thursday 13 May

  • 8:00 - 12:30 Software and beamline tutorials (SHARP/autoSHARP/autoPROC/STARANISO/BUSTER, CCP4/DIALS, HKL3000, MR, Coot and MAD/SAD)

  • 13:00 - 14:00   Guest lecture: James Fraser

  • 14:00 - 18:30 Software and beamline tutorials (XDS, Phenix, SAXS, Data collection, UV-Vis Microspec introduction, RT data collection/crystal dehydration, Sample preparation)

Friday 14 May

Saturday 15 May

  • 10:00-11:00 Recapitulation and final discussions

NX client installation and remote desktop workshop

On Wednesday May 5, 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 cannot attend and need help with the NX client, please contact the organizers.

Flash Introductions of Participants

On Thursday May 6, 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.

Beamline Tutorials

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 (the beamtime schedule will be published soon).

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 contact 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 BL12-2 Data collection BL9-2 UV-Vis Microspec BL9-2 MAD/SAD data collection BL14-1 RT data collection/Crystal dehydration BL14-1
Thu 8:00 Unavailable Unavailable Unavailable Sign-up Unavailable
Thu 10:30 Unavailable Unavailable Unavailable Sign-up Unavailable
Thu 14:00 Van Loon/DeBouver/Johnson/Juárez Quintero/Martinez Gutierrez/Zhai/Burris/Campbell/Campos/Cerqueira Unavailable Unavailable Unavailable
Thu 16:30 Ahmed/Nunez Aguilar/Miyamoto/Noske/Oliva/Conley Unavailable Sign-up Unavailable Sign-up
Thu after 18:30 Spare Spare Spare Spare Spare
Fri 8:00 Unavailable Unavailable Unavailable Sign-up Unavailable
Fri 10:30 Unavailable Unavailable Unavailable Sign-up Unavailable
Fri 13:00 Vecchioni/Bidart/Kapoor/Shaw/Pandelo Martins/Pinney Czarnota/Dean/Dinh/Shankar/D'Ordine/Geeraerts Unavailable Unavailable Unavailable
Fri 15:30 Corpuz/Malone/Qi/Rebelo/Saha Unavailable Sign-up Unavailable Sign-up
Thu after 17:30 Spare Spare Spare Spare Spare
  • Data collection on BL9-2: Irimpan Mathews
  • UV-Vis Microspectrophotometer introduction: Aina Cohen
  • RT data collection/crystal dehydration: Silvia Russi
  • Data collection on BL12-2: Clyde Smith, Jeney Wierman
  • MAD/SAD data collection on BL14-1: Ana Gonzalez
  • Sample preparation tips and tricks: Jim Pflugrath

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 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: Maksymilian Chruszcz
  • Coot: Paul Emsley
  • 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. Instructions on how to access the sign-up sheets will be given during the course.