SLAC National Accelerator Laboratory
U.S. Department of Energy: Office of Science

RapiData 2016 at SLAC - Data Collection and Structure Solving: A Practical Course in Macromolecular X-Ray Diffraction Measurement

Schedule for RapiData 2016

All lectures on Sunday, Monday and Tuesday will take place in the Redwood Rooms C & D (building 48). The practical tutorials will take place at different locations around the SSRL and experimental floor.

Sunday 24 April

  • 8:30 - 9:15 Registration (Redwood rooms, building 48)

  • 9:30 - 15:30 Crystallographic Fundamentals Course: Bob Sweet

  • 12:00 Lunch (outside Redwood Rooms)

  • 16:30 - 17:00 NX Client installation workshop: Thomas Eriksson (Redwood rooms, building 48)

  • 17:30 - 19:30 Welcome Reception (Building 53)

Monday 25 April

  • 7:45 - 8:15 Registration (Redwood Rooms)

  • 8:30 Introduction to RapiData: Clyde Smith

  • 8:45 Some issues in data collection: Bob Sweet

  • 9:30 Cryo-crystallography and Radiation Damage: Enrique Rudiño

  • 10:15 Coffee break

  • 10:30: I've got a crystal, now what?: Jim Pflugrath

  • 11:15 X-Ray sources: James Holton

  • 12:00 Lunch

  • 12:30 Autoindexing, integration and data reduction: Harry Powell

  • 13:15 Data reduction with the HKL Suite: Maksymilian Chruszcz

    14:00 Coffee break

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

  • 15:00 In situ optical spectroscopy: Aina Cohen

  • 16:30-18:00 Orientation to experiments/Sample Preparation (Building 120)

  • 18:15-19:30 Banquet dinner (Building 48)

Tuesday 26 April

  • 9:00 Advanced area detectors: Mike Blum

  • 9:45 Getting the best data from photon counting detectors: Andreas Foerster

    10:30 Coffee break

  • 10:45 SAD and MAD: Ana Gonzalez

  • 11:30 Molecular Replacement: Raji Edayathumangalam

  • 12:15 Lunch

  • 12:45-13:00: Group picture

  • 13:00 Sharp/Autosharp: Clemens Vonrhein

  • 14:15 Solve and Phenix: Tom Terwilliger

    15:00 Coffee break

  • 15:15 Introduction to Small Angle Scattering: Thomas Weiss

  • 16:15-18:00 Tour of LCLS

  • 18:15 Dinner (Building 48)

  • 19:30-21:30 Tutorials/Sample Preparation

Wednesday 27 April

  • All day: Concurrent data collection and tutorials (see schedule below)

    10:30 Coffee served in BL9 lounge area

  • 13:00 Lunch

    15:30 Coffee served in BL9 lounge area

  • 17:00 Meeting (Redwood Rooms, building 48)
  • 18:00 Dinner (Building 48)
  • 22:00- Data collection

Thursday 28 April

  • All day: Concurrent data collection and tutorials (see schedule below)

    10:30 Coffee served in BL9 lounge area

  • 13:00 Lunch

    15:30 Coffee served in BL9 lounge area

  • 17:00 Meeting (Redwood Rooms, building 48)
  • 18:00 Dinner (Building 48)
  • 22:00- Data collection

Friday 29 April

  • 8:30-11:00 Recapitulation and final discussions The ending time is approximate (Building 48)

NX client installation workshop

On Sunday, there will be an optional 30 minutes 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 25th, after the afternoon lectures, there will a compulsory orientation to experiments at SSRL, covering safety, at building 120. Participants will be split in two groups.

  • 16:30: Safety talk (groups Yellow, Purple, Magenta, Green)

  • 17:00: Safety talk (groups Coral, Indigo, Red, Cyan)

The group assignments can be found here.

Participants' sample preparation

On Monday 25th, between 17:00 and 18:00, Aina Cohen will do a demo on transferring frozen samples in cryovials to robot cassettes. Participants who have brought frozen samples in cryovials will get the chance to transfer them to SSRL cassettes during the demo or on Tuesday 26th, from 19:30

Participants with unfrozen samples (in crystallization plates or capillaries) can freeze them during the Sample freezing and mounting tutorial on BL7-1 (signup sheets will be available throught the course).

LCLS Tour

Sign up sheets for the optional tour of the free electron laser facility LCLS will be available on Monday. A group will set off from building 48 at ~ 16:00 (there is a ~15 minute walk to the LCLS), with a second group following 15 minutes later. The tour will include visits to the beamlines CXI and XPP (where most macromolecular crystallography experiments take place) and MFX, a new instrument in construction dedicated to serial crystallography. The tour takes about one hour and fifteen minutes.

Data collection practicals

There will be general data collection tutorials at BL9-2 and BL14-1 to learn how to set up data collections for different experimental purposes and using different types of detectors.

Specialized tutorials for Small Angle Scattering and UV-Vis Spectrophotometry will take place in BL4-2 and BL11-1 respectively.

BL12-2 will be dedicated to participants collecting data on their own samples.

For data collection and tutorials at the beamlines, the participants will be split in 8 groups (named after colors) based on their areas of interest. Participants will also be given the opportunity to collect data remotely overnight or in slots of beamtime marked "unscheduled" (for example, to screen crystals grown during the crystallization workshop). These slots will be assigned based on the number and properties of the samples brought by the participants.

The group assignments can be found here.

TimeBL12-2 (Participants' samples)BL11-1 (Microspec)BL14-1 (MAD/SAD data collection)BL4-2/B. 131 (SAXS)BL9-2 (General data collection, use of PAD)BL7-1 (see "Tutorials")
Tues 19:30Shanbhogue, Rana-----
Wed 8:00Rana, Singh-----
Wed 10:00Gori LusaRedMagentaPurpleCyan-
Wed 14:00Gori Lusa, DomingosCoralPurpleRedYellow-
Wed 19:00Santos, SheltonUnscheduledYellowIndigo, SinghGreen-
Wed 22:00Shelton,O'SullivanUnscheduledSingh, Giannini-RudiñoUnscheduled
Thu 8:00Bueno, de SousaUnscheduledIndigoYellow, GuptaCoral-
Thu 10:30de Sousa, CostaMagenta, Gori LusaRedCoralPurple-
Thu 14:00Costa Indigo, de Sousa, WangCoralMagentaRed-
Thu 19:00Sharma, Gupta, BuzovetskayaWangCyan-Indigo-
Thu 22:00KoenigsbergUnscheduled--UnscheduledUnscheduled

See A map of the SSRL beamlines.

Tutors

  • BL12-2: Data collection from participants' crystals: Clyde Smith, Tzanko Doukov, Irimpan Mathews, Enrique Rudiño
  • BL11-1: Use of microphotospectrometry to monitor metal center reduction: Elena Kovaleva
  • BL14-1: Setting up SAD and MAD experiments: Vivian Stojanoff, Ana Gonzalez
  • BL4-2: SAXS data analysis: Thomas Weiss
  • BL9-2: Setting up data collection, use of photon counting PAD detectors: Silvia Russi, Enrique Rudiño

Tutorials

There will be sign-up sheets for the tutorials at the Redwood room during the lectures on Monday and Tuesday and in the BL9 lounge area after that.

TimePhenixCCP4/DIALSSample freezing and mountingMolecular ReplacementSharp/Autosharp/
Autoproc
HKL
Tuesday 19:30-21:30Phenix GUI introduction

SAD structure determination with phenix.autosol

Ligand fitting with phenix.ligandfit

B. 120, room 300
B. 452, room 101BL7-1B. 274B. 452, room 103B. 270 room 19A
Wed 8:30-10:30Phenix GUI introduction

Molecular replacement with phenix.phaser

Refinement with phenix.refine

B. 120, room 300
B. 452, room 101BL7-1B. 274B. 452, room 103B. 270 room 19A
Wed 11:00-13:00Phenix GUI introduction

Refinement with phenix.refine

SAD structure determination with phenix.autosol

B. 120, room 300
B. 452, room 101BL7-1B. 274B. 452, room 103B. 270 room 19A
Wed 14:00-17:00Phenix GUI introduction

SAD structure determination with phenix.autosol

Refinement and validation with phenix.refine

Ligand fitting with phenix.ligandfit

B. 120, room 300
B. 452, room 101BL7-1B. 274B. 452, room 103B. 270 room 19A
Wed 19:30-21:30Phenix GUI introduction

Refinement with phenix.refine

Molecular replacement with phenix.phaser

B. 120, room 300
B. 452, room 101BL7-1B. 274B. 452, room 103B. 270 room 19A
Thu 8:30-10:30Ligand preparation with phenix.elbow

Ligand fitting with phenix.ligandfit

Molecular replacement with phenix.phaser

B. 120, room 300
B. 452, room 101BL7-1B. 274B. 452, room 103B. 270 room 19A
Thu 11:00-13:00Ligand preparation with phenix.elbow

Ligand fitting with phenix.ligandfit

SAD structure determination with phenix.autosol

B. 120, room 300
B. 452, room 101BL7-1B. 274B. 452, room 103B. 270 room 19A
Thu 14:00-17:00Phenix GUI introduction

SAD structure determination with phenix.autosol

Molecular replacement with phenix.phaser

Ligand preparation with phenix.elbow

Ligand fitting with phenix.ligandfit

B. 120, room 300
B. 452, room 101BL7-1B. 274B. 452, room 103B. 270 room 19A
Thu 19:30-21:30Ligand preparation with phenix.elbow

Ligand fitting with phenix.ligandfit

Molecular replacement with phenix.phaser

B. 120, room 300
B. 452, room 101BL7-1B. 274B. 452, room 103B. 270 room 19A

Tutors

  • Phenix: Tom Terwilliger, Pavel Afonine, Li-Wei Hung, Nigel Moriarty
  • CCP4 and DIALS: Harry Powell
  • Crystal freezing and mounting: Jim Pflugrath, Tzanko Doukov, Irimpan Mathews
  • Molecular Replacement with CCP4: Raji Edayathumangalam
  • Autoproc/Sharp/Autosharp: Clemens Vonrhein, Claus Flensburg
  • HKL2000/HKL3000: Maks Chruszcz