CCP4/APS School in Macromolecular Crystallography: From data collection to structure refinement and beyond

Argonne National Laboratory

 June 19 - 26, 2017

All Lectures will be held in the Conference Center of Advanced Protein Characterization Facility, Building 446. All meals and refreshments will be arranged in the next room from the Conference Center, except for dinner on Monday the 19th, and all meals and refreshments on Tuesday, June 20. These will be served in the conference room C010 of Building 436.

Color code:

Meal or Coffee break

Lecture session

Practical session

Tutorial session

Other


Monday, 19th June

Introduction; Data collection and processing lectures; Beamline training; data collection planning; Registration.

08:00 – 08:30

Welcome and Introduction        

B. Fischetti and N. Sanishvili, Building 446

08:30 - 09:00

Breakfast

Building 446

09:00 – 09:45

All about data

Z. Dauter, Building 446

09:45 – 10:15

Applications of microdiffraction

N. Sanishvili, Building 446

10:15 – 11:00

Optimizing data quality with Hybrid Photon Counting detectors

A. Förster, Building 446

11:00 – 12:00

Data processing with MOSFLM

A. Leslie, Building 446

12:00 – 12:45

Lunch        

Building 446

12:45 – 13:45

Data processing with HKL

D. Borek, Building 446

13:45 – 14:45

DIALS and BLEND        

R. Gildea, Building 446

14:45 – 15:15

Data processing with XDS

T. Gruene, Building 446

15:15 – 15:30

Break. Walk to the sector 23

All students with crystals. The rest are optional

15:30 – 16:00

Sector Orientation

S. Corcoran,

Bld. 436, Sector 23

16:00 – 16:30

Beamline tour

V. Nagarajan

Bld. 436, Sector 23

16:30 – 18:00

Hands on training on Beamline Controls and Data Collection Software

GMCA staff, Beamlines 23ID-B and 23ID-D

18:00 – 19:00

Data collection planning

All participants Building 436, C010

19:00 – 20:00

Dinner

Q&A session.

All participants. Building 436, C010

20:00 – 21:00

Prepare Samples

GM/CA staff GMCA Lab

Tuesday, 20th June

Data collection and processing

Beamlines 23ID-B and 23ID-D

08:00 – 09:00

Beamline setup        

GM/CA staff Beamlines 23ID-D and 23ID-B

08:30 - 09:00

Breakfast

Building 436, conference room C010

09:00 – 12:00

Data collection and real-time processing

GM/CA staff, D. Borek,  R. Gildea, T. Gruene, A. Leslie

12:00 – 12:45

Working Lunch with continued data collection and processing         (Q&A session)

All participants Building 436, conference room C010

12:45 – 16:00

Data collection and real-time processing

GM/CA staff, D. Borek, R. Gildea, T. Gruene, A. Leslie

16:00 – 16:30

Break

16:30 – 19:00

Data collection and real-time processing

GM/CA staff, D. Borek, R. Gildea, T. Gruene, A. Leslie

19:00 – 20:00

Dinner

Building 436, conference room C010

20:00 – 24:00        

Data collection and real-time processing

GM/CA staff, D. Borek, R. Gildea, T. Gruene, A. Leslie


Wednesday, 21st June

Overview of student’s crystallographic problems;

Twinning; Data processing and tutorials

Building 446 Auditorium

08:30 - 09:00

Breakfast

Building 446

09:00 – 10:00

Overview of crystallographic problems

All participants

10:00 – 11:00

Twinning

Z. Dauter

11:00 – 12:00

Twinning and other pathologies, practical aspects

A. Lebedev

12:00 – 12:45

Lunch

12:45 - 13:15

Overview of crystallographic problems, continued

All participants

13:15 – 14:45

Processing with MOSFLM. Student data

A. Leslie

14:45 – 16:15

Processing with HKL. Student data

D. Borek

16:15 – 16:30

Break

16:30 – 18:00

Processing with DIALS. Student data

R. Gildea

18:30 – 19:30

Processing with XDS. Student data

T. Guene

19:30 – 20:30

Dinner

20:30 – 22:00

Data processing

All participants 


Thursday, 22nd June

Overview of CCP4; Experimental phasing; Finish data processing

Building 446 Auditorium

08:30 - 09:00

Breakfast

Building 446

9:00 – 09:30

Overview of CCP4

E. Krissinel

9:30 – 10:10

Crank/Crank2

R. Pannu

10:10 – 10:50

SHELXC/D/E

T. Gruene

10:50 – 11:30

Phasing and automation in Phenix

T. Terwilliger

11:30 – 12:10

Phaser – EP

A. Lebedev

12:10 – 13:00

Lunch

13:00 – 13:40

Parrot/Buccaneer

B. Lohkamp

13:40 – 13:55

Tutorial Crank/Crank 2

R. Pannu

13:55 – 14:10

Tutorial Pirate Buccaneer

B. Lohkamp

14:10 – 14:25

Tutorial SHELXC/D/E

T. Gruene

14:25 – 14:40

Tutorial Phenix

T. Terwilliger

14:40 – 15:05

Tutorial Phaser EP

A. Lebedev

15:05 – 15:20

Break

15:20 – 19:00

Hands-on problem solving

All participants

19:00 – 20:00

Dinner

20:00 – 22:00

Hands-on problem solving

All participants


Friday, 23rd June

Molecular replacement

Building 446 Auditorium

08:30 - 09:00

Breakfast

Building 446

09:00 – 09:50

Molecular Replacement in CCP4        

A. Lebedev

09:50 – 10:30

Model Preparation for MR and assessing the solution  

R. Keegan

10:30 – 11:10

AMPLE, a pipeline for unconventional MR

R. Keegan

11:10 – 11:35

SHELXE for Molecular Replacement

T. Gruene

11:35 – 12:00

Structural Biology with Electron Diffraction

T. Gruene

12:00 – 12:45

Lunch

12:45 – 13:00

Tutorial: Molecular Replacement

A. Lebedev

13:00 – 13:15

Tutorial: Phaser MR

A. Lebedev

13:15 – 13:30

Tutorial: MR in CCP4

R. Keegan

13:30 – 13:45

Tutorial: AMPLE

R. Keegan

13:45 – 14:00

Tutorial: SHELX

T. Gruene

14:00        –

Afternoon and evening: free time


Saturday, 24th June

Refinement and Autobuilding

Building 446 Auditorium

08:30 - 09:00

Breakfast

Building 446

09:00 – 09:45

Refmac        

G. Murshudov

09:45 – 10:30

Phenix refinement and ligand building

P. Afonine

10:30 – 11:15

TLS and all that

E. Merritt

11:15 – 12:00

Automated Protein Model Building with ARP/wARP 7.4

G. Chojnowski

12:00 – 12:45

Lunch

12:45 – 13:15

Coot: An Introduction

B. Lohkamp

13:15 – 13:45

CCP4MG: Introduction

S. McNicholas

13:45 – 14:00

Tutorial: Refmac

G. Murshudov

14:00 – 14:15

Tutorial: Phenix        

P. Afonine

14:15 – 14:45

Tutorial: TLS        

E. Merritt

14:45 – 15:00

Tutorial: Classic Model Building in ARP/wARP

G. Chojnowski

15:00 – 15:15

Tutorial: Coot

B. Lohkamp

15:15 – 16:15

Hands on problem solving

All participants

16:15 – 16:30

Break

16:30 – 19:00

Hands on problem solving

All participants

19:00 – 20:00

Dinner

20:00 – 22:00

Hands on problem solving

All participants

                


Sunday, 25th June

Ligands and validation

Building 446 Auditorium

08:30 - 09:00

Breakfast

Building 446

9:00 – 9:30

Ligands and ligand dictionary

G. Murshudov

9:30 – 10:00

Automatic Building of Ligands and Nucleotides in ARP/wARP 7.4

G. Chojnowski

10:00 – 10:40

Coot ligand building

B. Lohkamp

10:40 – 11:20

Validation in Phenix

P. Afonine

11:20 – 12:00

How good is my model and can it be improved?

R. Joosten

12:00 – 12:45

Lunch

12:45 – 13:30

wwPDB OneDep tools for deposition and validation

B. Hudson

13:30 – 13:45

Tutorials: Ligands and ligand dictionary

G. Murshudov

13:45 – 14:00

Tutorials: Automatic Building of Ligands and Nucleotides in ARP/wARP

G. Chojnowski

14:00 – 14:15

Tutorial: Coot ligand building

B. Lohkamp

14:15 – 14:30

Tutorial: PDB-REDO and validation

R. Joosten

14:30 – 16:00

Hands on problem solving

All participants

16:00 – 16:30

Break

16:30 – 19:00

Hands on problem solving

All participants

19:00 – 20:00

Dinner

20:00 – 22:00

Hands on problem solving

All participants


Monday, 26th June

Structure Analysis, Molecular Graphics and Feedback

Building 446 Auditorium

08:30 - 09:00

Breakfast

Building 446

09:00 – 09:20

CCP4 beyond structure solution

E. Krissinel

09:20 – 10:00

Analysis of macromolecular Complexes (PISA)

E. Krissinel

10:00 – 10:45

CCP4mg – Advanced options Demo and tutorial

S. McNicholas

10:45 – 11:30

An introduction to single particle cryo-EM

G. Murshudov

11:30 – 12:00

Start backups

All participants

12:00 – 12:45

Lunch

12:45 – 16:00

Hands on problem solving

All participants

16:00 – 16:15

Break

16:15 – 17:30

Hands on problem solving

All participants

17:30         – 19:30

Overview of crystallographic problems  and backups

All participants

19:30 – 19:40

Concluding remarks

Organizers

19:40 – 20:40

Dinner

Aurevoire