SLAC National Accelerator Laboratory

RapiData 2017 at SSRL - Data Collection and Structure Solving: A Practical Course in Macromolecular X-Ray Diffraction Measurement
April 16-21 2017

Schedule for RapiData 2017

Note: The schedule is subject to changes.

All lectures on Sunday, Monday and Tuesday will take place in the Redwood Rooms C & D (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.

Sunday 16 April

  • Crystallographic Fundamentals Course

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

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

  • 12:00 Lunch

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

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

Monday 17 April

  • Lectures on data collection and data reduction

  • 8:00 - 8:30 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 Autoindexing, integration and data reduction: Harry Powell

  • 12:00 Lunch

  • 13:00 Data reduction with the HKL Suite: Ivan Shabalin

  • 13:45 Introduction to XDS: Michel Fodje

    14:30 Coffee break

  • 14:45 X-Ray sources: James Holton

  • 15:30 Data collection at Free Electron Lasers: Nick Sauter

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

  • 18:15-19:30 Banquet dinner

Tuesday 18 April

  • Lectures on detector, structure solution and complementary methods

  • 8:45 Getting the best data from photon counting detectors: Andreas Foerster

  • 9:30 SAD and MAD: Ana Gonzalez

    10:15 Coffee break

  • 10:30 Molecular Replacement: Raji Edayathumangalam

  • 11:15 SHELX: Matt Benning

  • 12:00 Lunch

  • 12:45-13:00: Group picture

  • 13:00 Solve and Phenix: Tom Terwilliger

  • 13:45 Introduction to Small Angle Scattering: Thomas Weiss

    14:30 Coffee break

  • 14:45

  • 15:00 In situ optical spectroscopy: Aina Cohen

  • 16:00-18:00 Tour of LCLS (if allowed by ongoing construction)

  • 18:15 Dinner

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

Wednesday 19 April

  • All day (8:00-22:00): 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
  • 22:00- Data collection

Thursday 20 April

  • All day (8:00-22:00): 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 21 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 17th, after the afternoon lectures, there will a compulsory orientation to experiments at SSRL, covering safety, at building 120.

Data collection practicals

During the beamline 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; setting up data collection on PAD detectors; and UV-Vis Spectrophotometry. 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.

Participants collecting data on their own samples will be scheduled 2-3 hours of additional beamtime on the microfocus beamline BL12-2.

Time Data collection from participants' samplesMicrospecphotometer MAD/SAD data collection Data collection with PADs Sample preparation
Tues 19:30- - - - BL7-1
Wed 8:00 - - - - BL7-1
Wed 10:30 BL12-2 BL11-1 BL14-1 BL9-2 BL7-1
Wed 14:00 BL12-2 BL11-1 BL14-1 BL9-2 BL7-1
Wed 19:00 BL12-2 - BL14-1 BL9-2 BL7-1
Wed 22:00 - - - - -
Thu 8:00 BL12-2 - BL14-1 BL9-2 BL7-1
Thu 10:30 BL12-2 BL11-1 BL14-1 BL9-2 BL7-1
Thu 14:00 BL12-2 BL11-1 BL14-1 BL9-2BL7-1
Thu 19:00 BL12-2 - BL14-1 BL9-2 BL7-1
Thu 22:00 - - - - -

See A map of the SSRL beamlines.

Tutors

  • BL7-1: Sample preparation: Jim Pflugrath, Irimpan Mathews, Tzanko Doukov, T.J. Lane, Marc Deller
  • BL9-2: Data collection using PAD detectors: Irimpan Mathews, Silvia Russi, Enrique Rudiño
  • BL12-2: Data collection from participants' samples: Clyde Smith, Enrique Rudiño
  • BL14-1: MAD/SAD data collection: Tzanko Doukov, Ana Gonzalez
  • BL11-1: Microspectrophotometer applications: Aina Cohen

Software tutorials

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

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.

Time Phenix CCP4/DIALSShelxMolecular ReplacementXDSHKLSAXS software
Tuesday 19:30-21:30Phenix GUI introduction

SAD structure determination with phenix.autosol

Ligand fitting with phenix.ligandfit

-
B. 452, room 101B. 278 room 104B. 274, conf. roomB. 452, room 103B. 270 room 19AB. 130 room 214
Wed 8:00-10:30Phenix GUI introduction

Molecular replacement with phenix.phaser

Refinement with phenix.refine

B. 120, room 300
B. 452, room 101B. 278 room 104B. 274, conf. roomB. 452, room 103B. 270 room 19A-
Wed 10:30-13:00Phenix GUI introduction

Refinement with phenix.refine

SAD structure determination with phenix.autosol

B. 120, room 300
B. 452, room 101B. 278 room 104B. 274, conf. roomB. 452, room 103B. 270 room 19AB. 130 room 214
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 101B. 278 room 104B. 274, conf. roomB. 452, room 103B. 270 room 19AB. 130 room 214
Wed 19:00-22:00Phenix GUI introduction

Refinement with phenix.refine

Molecular replacement with phenix.phaser

B. 120, room 300
B. 452, room 101B. 278 room 104B. 274, conf. roomB. 452, room 103B. 270 room 19A-
Thu 8:00-10:30Ligand preparation with phenix.elbow

Ligand fitting with phenix.ligandfit

Molecular replacement with phenix.phaser

B. 120, room 300
B. 452, room 101B. 278 room 104B. 274, conf. roomB. 452, room 103B. 270 room 19A-
Thu 10:30-13:00Ligand preparation with phenix.elbow

Ligand fitting with phenix.ligandfit

SAD structure determination with phenix.autosol

B. 120, room 300
B. 452, room 101B. 278 room 104B. 274, conf. roomB. 452, room 103B. 270 room 19AB. 130 room 214
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 101B. 278 room 104B. 274, conf. roomB. 452, room 103B. 270 room 19AB. 130 room 214
Thu 19:00-22:00Ligand preparation with phenix.elbow

Ligand fitting with phenix.ligandfit

Molecular replacement with phenix.phaser

B. 120, room 300
B. 452, room 101B. 278 room 104B. 274, conf. roomB. 452, room 103B. 270 room 19A-