Programme – CCP4 Crystallographic School in South Africa

Programme

Colour Code

Lecture session

Questions and answers and one-on-one problem-solving

Tutorials

Meals and Coffee breaks

Other

February 15

Workshop preparation session

11:00 – 11:05	Welcome	C. Tolmie
11:05 – 12:00	Navigating the Diamond cluster	F. Bertram
12:00 – 13:30	Breakout sessions to confirm CCP4 installation, outstanding connectivity tests and data uploads	R. Keegan M. Mazzorana F. Bertram E. Nelson C. Tolmie
13:30 – 14:30	CCP4 Cloud	E. Krissinel
14:30 – 15:30	Navigating Diamond SynchWeb (ISPyB)	M. Mazzorana
15:30 – 16:00	Interactive networking session on Wonder platform	All participants
16:00 – 17:00	Solve outstanding participant problems	R. Keegan M. Mazzorana F. Bertram E. Nelson C. Tolmie

February 22

Introductions of students, speakers, diffraction, software, beamlines

11:00 – 11:05	Welcome	T. Sewell
11:05 – 11:15	Introduction to the workshop, logistics	C. Tolmie
11:15 – 11:40	Speaker self-introduction	All speakers
11:35 – 13:00	Student self-introductions, Projects and Problems	All students

13:00 – 13:45	Lunch

13:45 – 14:35	Introduction to CCP4, CCP4 cloud	E. Krissinel
14:35 – 16:00	Crystal, symmetry and basic diffraction theory	A. Leslie
16:00 – 16:15	General Q/A and discussion	All participants

16:15 – 16:30	Break

16:30 – 17:30	A Synchrotron beamline, crystallographer’s view	R. Sanishvili
17:30 – 18:00	MX, MX beamlines at Diamond	E. Nelson
18:00 – 18:45	Concepts and parameters of data collection	R. Sanishvili
18:45 – 19:00	General Q/A and discussion	All participants

February 23

Data Processing

11:00 – 12:00	Data processing theory	A. Leslie
12:00 – 13:00	Data processing with MOSFLM	A. Leslie
13:00 – 13:15	General Q/A and discussion	All participants

13:15 – 14:00	Lunch

14:00 – 14:45	MOSFLM tutorial; Case study	A. Leslie
14:45 – 15:45	Data processing with DIALS	J. Parkhurst
15:45 – 16:30	DIALS tutorial; Case study	J. Parkhurst
16:30 – 16:45	General Q/A and discussion	All participants

16:45 – 17:00	Break

17:00 – 18:00	Data processing with XDS	K. Diederichs
18:00 – 18:45	XDS tutorial; Case study	K Diederichs
18:45 – 19:00	General Q/A and discussion	All participants

February 24

Data quality; Cryocrystallography; Radiation damage; Symmetry; Data from microcrystals; Data pathologies; Practical guide at DLS

11:00 – 11:45	Cryocrystallography	E. Garman
11:45 – 12:30	Radiation damage	E. Garman
12:30 – 12:50	Quantifying specific radiation damage	K. Shelley
12:50 – 13:00	General Q/A and discussion	All participants

13:00 – 13:45	Lunch

13:45 – 14:30	Data quality	K. Diederichs
14:30 – 15:15	Introduction to symmetry	A. Lebedev
15:15 – 16:15	Multi-crystal approaches	D. Axford
16:15 – 16:30	General Q/A and discussion	All participants

16:35 – 16:45	Break

16:45 – 17:45	Data Pathologies	A. Lebedev
17:45 – 19:00	Practical guide for data collection at Diamond	N. Paterson

February 25

Data Collection

11:00 – 19:00

Data collection at DLS

All with crystals

February 26

Experimental Phasing, Molecular graphics, Model Building

11:00 – 12:00	General theory of experimental phasing	R. Read
12:00 – 12:45	Introduction to Coot	B. Lohkamp
12:45 – 13:00	Q/A and Discussion	All participants

13:00 – 13:45	Lunch

13:45 – 14:30	Experimental phasing: SHELX tutorial; case study	I. Uson
14:30 – 15:15	Automated model building	I. Uson
15:15 – 16:00	Model Building at Lower Resolutions: ISOLDE, Tutorial; Case study	T. Croll
16:00 – 16:15	Q/A and Discussion	All participants

16:15 – 16:30	Break

16:30 – 19:00	Work on own data	Student data

March 1

Molecular Replacement; Molecular graphics

11:00 – 12:00	Molecular Replacement	R. Keegan
12:00 – 12:45	Molecular Replacement Tutorial; Case study	R. Keegan
12:45 – 13:00	Q/A and Discussion	All participants

13:00 – 13:45	Lunch

13:45 – 14:30	Phasing with Phaser	R. Read
14:30 – 15:15	Phaser tutorial; Case study	R. Read
15:15 – 16:00	ARCIMBOLDO	E. Jiménez Mellado
16:00 – 16:45	ARCIMBOLDO tutorial; Case study	E. Jiménez Mellado
16:45 – 17:00	Q/A and Discussion	All participants

17:00 – 17:15	Break

17:15 – 19:00	Work on own data	Student data

March 2

Refinement

11:00 – 12:00	Refinement Theory	G. Murshudov
12:00 – 13:00	Refinement with CCP4 (REFMAC); Tutorial; Case study	G. Murshudov
13:00 – 13:15	Q/A and Discussion	All participants

13:15 – 14:00	Lunch

14:00 – 14:45	Coot: advanced features	B. Lohkamp
14:45 – 19:00	Work on own data	Student data

March 3

Pipelines

11:00 – 12:00	Auto-Rickshaw	S. Panjikar
12:00 – 12:45	Auto-Rickshaw tutorial; Case study	S. Panjikar
12:45 – 13:00	Q/A, Discussion	All participants

13:00 – 13:45	Lunch

13:45 – 14:45	Crank2	P. Skubak
14:45 – 15:30	Crank2 tutorial	P. Skubak
15:30 – 15:45	Q/A, Discussion	All participants

15:45 – 16:00	Break

16:00 – 19:00	Work on own data	Student data

March 4

Ligands; Models; Validation

11:00 – 12:00	Ligands and ligand dictionary	G. Murshudov
12:00 – 12:45	Ligands in Coot	B. Lohkamp
12:45 – 13:00	Q/A, Discussion	All participants

13:00 – 13:45	Lunch

13:45 – 14:30	Model Completion and quality	R. Joosten
14:30 – 15:15	Validation, Deposition, Publication	R. Joosten
15:15 – 15:30	Q/A, Discussion	All participants

15:30 – 15:45	Break

15:45 – 19:00	Work on own data	Student data

March 5

Beyond X-ray Crystal structures; Feedback

11:00 – 11:45	Analysis of macromolecular complexes (PISA)	E. Krissinel
11:45 – 12:30	Bioinformatics	D. Rigden
12:30 – 12:45	Q/A and Discussions	As needed

12:45 – 13:30	Lunch

13:30 – 14:30	Introduction to CryoEM	C. Palmer
14:30 – 16:00	Electron diffraction	T. Grune
16:00 – 16:15	Summary Q/A and Discussions	As needed
16:15 – 17:00	Start Backups, data transfer	R. Keegan
17:00 – 18:45	Student feedback	All participants
18:45 – 19:00	Concluding remarks	Organizers and Speakers

IUPAP Support for Free Circulation of Scientists / Policy on Harassment

The CCP4 2020 workshop supports the International Union of Pure and Applied Physicists (IUPAP) Policy on Free Circulation of Scientists and the IUPAP policy statement on harassment at conferences.

Free Circulation of Scientists: The principle of the Universality of Science is fundamental to scientific progress. This principle embodies freedom of movement, association, expression and communication for scientists, as well as equitable access to data, information and research materials. In pursuing its objectives with respect to the rights and responsibilities of scientists, the International Union of Pure and Applied Physics (IUPAP) actively upholds this principle, and, in so doing, opposes any discrimination on the basis of such factors as ethnic origin, religion, citizenship, language, political stance, gender, or age. IUPAP should only sponsor conferences and events at institutions and in countries that uphold this principle. If scientists are excluded from attending IUPAP-sponsored international conferences by a host institution or country on the basis of any of these factors, IUPAP should register its concern at the highest level of that institution or country, and should not sponsor any future events in that country until such exclusions have been eliminated. [ Section 1. (http://iupap.org/sponsored-conferences/conference-policies/)]

Harrassment at Conferences: It is the policy of the International Union of Pure and Applied Physics (IUPAP) that all participants in Union, and Union-endorsed activities will enjoy an environment which encourages the free expression and exchange of scientific ideas, and is free from all forms of discrimination, harassment, and retaliation. The conference organisers will name an advisor who will consult with those who have suffered from harassment and who will suggest ways of redressing their problems, and an advisor who will counsel those accused of harassment. The conference organisers may, after due consideration, take such action they deem appropriate, including warning or expulsion from the conference without refund. [Section 4 IUPAP Conference Policies , weblink (http://iupap.org/sponsored-conferences/conference-policies/)]

Gender balance and the IUCr

The International Union of Crystallography strives to achieve gender balance in all its institutions and activities bearing in mind other diversity needs and its existing obligations to geographic and academic discipline representation where appropriate. To achieve this aim the IUCr will adopt procedures to promote gender balance in respect of all of its activities including selection of candidates for positions on its Committees and Commissions. Those seeking support from the Union for Congresses, meetings, workshops and schools will also have to demonstrate their efforts to address gender balance.