24 June 2009 Beamline orientation and data collection strategies

CCP4/APS summer school program for 2012

Tuesday, June 19. Data collection and processing lectures, Beamline orientation and data collection planning

Registration throughout the day, Sheila Trznadel

8:00 Welcome (D. Mills) and introduction (N. Sanishvili). Bld. 402, Room E1100/E1200

8:30 Breakfast. APS Gallery

9:00 All about data (Data collection theory) – Z. Dauter. Bld. 402, room E1100/E1200

10:00 Data Quality Indicators – K. Diederichs. Bld. 402, room E1100/E1200

11:00 Overview of beamline controls and data collection software – M. Hilgart. Bld. 402, room E1100/E1200

12:00 Lunch. APS Gallery

12:45 Data processing with HKL2000/HKL3000 – D. Borek Bld. 402, room E1100/E1200

13:45 Data processing with MOSFLM – A. Leslie Bld. 402, room E1100/E1200

14:45 Data processing with XDS – K. Diederichs Bld. 402, room E1100/E1200

15:45 Coffee. APS Gallery

16:15 Sector orientation (M. Becker)

16:45 Beamline tour (V. Nagarajan). Bld. 436, Sector 23

17:30 Hands-on training on beamline controls and data collection software – V. Nagarajan, C. Ogata, N. Sanishvili. Beamlines 23ID-B and 23ID-D

19:00 Dinner combined with data collection planning for next day. Short discussion of each project. N. Sanishvili, with all students and GMCA staff. Building 436, conference room C010

20:00 – 22:00 Q/A session. Finish hands-on training, prepare samples for next day – GM/CA staff, Building 436 conference room, GM/CA lab

Wednesday, June 20 – Remote data collection and processing tutorials

Remote session.

Bld. 402, room E1100/1200. Beamline 23ID-D

8 – 10 Beamline set up GM/CA staff. Beamline 23ID-D

8:30 Breakfast. APS Gallery

9:00 Student and problem introduction – all students Bld. 402, room E1100/E1200

10:00 Experimental design, remote data collection, real-time processing and tutorials – GM/CA staff, D. Borek, K Diederichs and A. Leslie rotating

12:00 Working lunch with continued data collection and processing (Q/A session). All participants. APS Gallery

12:45 Experimental design, remote data collection, real-time processing and tutorials – GM/CA staff, D. Borek, K Diederichs and A. Leslie rotating

16:00 Coffee. APS Gallery

16:30 Experimental design, remote data collection, real-time processing and tutorials – GM/CA staff, D. Borek, K Diederichs and A. Leslie rotating

19:00 Dinner. APS Gallery

20:00 – 24:00 Experimental design, remote data collection and real-time processing – GM/CA staff, D. Borek, K Diederichs and A. Leslie rotating - GM/CA staff. D. Borek, K Diederichs, A. Leslie rotating

Thursday, June 21 Data collection and Processing

Beamlines 23ID-B and 23ID-D

Note: All meals and refreshments on June 21 will be served in the conference room of building 436, C010

8:00 – 9:00 Beamline set up GM/CA staff. Beamlines 23ID-B, 23ID-D

8:30 Breakfast. APS Gallery

9:00 Data collection and real-time processing and tutorials - GM/CA staff, D. Borek, K. Diederichs, A. Leslie. Beamlines 23ID-B, 23ID-D

12:00 Working lunch with continued data collection and processing (Q/A session). All participants. Building 436, room C010

12:45 Data collection and real-time processing and tutorials - GM/CA staff, D. Borek, K. Diederichs, A. Leslie. Beamlines 23ID-B, 23ID-D

16:00 Coffee. Building 436, room C010

16:30 Data collection and real-time processing and tutorials - GM/CA staff, D. Borek, K. Diederichs, A. Leslie. Beamlines 23ID-B, 23ID-D

19:00 Dinner. Building 436, room C010

20:00 – 24:00 Data collection and real-time processing and tutorials - GM/CA staff, D. Borek, K. Diederichs, A. Leslie. Beamlines 23ID-B, 23ID-D

Friday June 22 - Data Processing. Experimental phasing

APS Building 402, Rooms E1100 and E1200

8:30 Breakfast. APS Gallery

9:00 Twinning – Z. Dauter

9:45 Twinning and other pathologies, practical aspects – A. Lebedev (Any examples from new data?)

10:30 All data processing – D. Borek, K. Diederichs, A. Leslie

12:00 Lunch. APS Gallery

12:45 Finish all data processing – D. Borek, K. Diederichs, A. Leslie

15:20 Coffee. APS Gallery

16:20 Crank/BP3 – G. Murshudov

17:00 ShelxC/D/E – T. Gruene

17:40 Phasing and automation Phenix – T. Terwilliger

18:20 Phaser – EP – G. Bunkoczi

19:00 Dinner. APS Gallery

20:00 Parrot/Buccaneer – B. Lohkamp

20:40 Tutorial Crank/BP3 – G. Murshudov

20:55 Tutorial Pirate Buccaneer – B. Lohkamp

21:10 Tutorial ShelxC/D/E – T. Gruene

21:25 Tutorial Phenix – T. Terwilliger

21:40 Tutorial Phaser EP – G. Bunkoczi

22:00 Finish

Saturday, June 23 - Molecular replacement

APS Building 402, Rooms E1100 and E1200

8:30 Breakfast APS Gallery

9:00 Molecular Replacement - A. Lebedev

9:40 Phaser MR – G. Bunkoczi

10:20 MrBUMP - R. Keegan

11:00 BALBES - G. Murshudov

11:40 Tutorial: Molecular Replacement - A. Lebedev

11:55 Tutorial: Phaser MR - G. Bunkoczi

12:10 Tutorial: MrBUMP - R. Keegan

12:25 Tutorial: BALBES - G. Murshudov

12:40 Lunch. APS Gallery

14:00 Afternoon and evening: Free time

Sunday, June 24 - Refinement and Autobuilding

APS Building 402, Rooms E1100 and E1200

8:30 Breakfast APS Gallery

9:00 Refmac - G. Murshudov

9:45 Phenix refinement and ligand building- P. Adams

10:30 Automated Protein Model Building with ARP/wARP 7.3- T. Wiegels

11:00 Coot: An Introduction – B. Lohkamp

11:30 TLS and all that - E. Merritt

12:00 Lunch. APS Gallery

12:45 Tutorial: Refmac – G. Murshudov

13:00 Tutorial: Phenix – P. Adams

13:15 Tutorial TLS – E. Merritt

13:30 Tutorial: Classic Model Building in ARP/wARP - T. Wiegels

13:45 Tutorial: Coot – B. Lohkamp

14:00 Hands-on problem solving – All participants

16:00 Coffee. APS Gallery

16:30 Hands-on problem solving – All participants

19:00 Dinner. APS Gallery

20:00 – 22:00 Hands-on problem solving – all participants

Monday, June 25 – Refinement, ligands and validation
APS Building 402, Rooms E1100 and E1200

8:30 Breakfast APS Gallery

9:00 Ligands and ligand dictionary - G. Murshudov

9:30 Automatic Building of Ligands and Nucleotides in ARP/wARP - C. Carolan

10:00 Coot ligand building - B. Lohkamp

10:45 PDB-REDO and validation with Whatcheck – R. Joosten

11:30 Validation in phenix - J. Headd

12:00 lunch. APS Gallery

12:45 Tutorials: Ligands and ligand dictionary - G. Murshudov

13:00 Tutorials: Automatic Building of Ligands and Nucleotides in ARP/wARP

13:15 Tutorial: Coot ligand building - B. Lohkamp

13:30 Tutorial: PDB-REDO and validation – R. Joosten

13:45 Hands-on problem solving – All participants

16:00 Coffee. APS Gallery

16:30 Hands-on problem solving – All participants

19:00 Dinner. APS Gallery

20:00 – 22:00 Hands-on problem solving – All participants

Tuesday, June 26 – Structure Analysis, Molecular Graphics and Feedback

APS Building 402, Rooms E1100 and E1200

8:30 Breakfast APS Gallery

9:00 PISA and assemblies - E. Krissinel

9:45 Tutorial: PISA – E. Krissinel

10:00 CCP4mg – Demonstration and Tutorial – S. McNicholas

10:45 Start backups

11:00 Hands-on problem solving – All participants

12:00 Lunch. APS Gallery

12:45 Hands-on problem solving – All participants

16:00 Coffee. APS Gallery

16:30 Overview of problems covered. Backups – All participants

18:30 Dinner. APS Gallery

19:30 Overview of problems covered. Feedback and backups

Wednesday, June 27 (Day 9) – Departure