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RapiData 2004

Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement

Biology Department and National Synchrotron Light Source
Brookhaven National Laboratory
25-30 April 2004

Course Agenda

Organized by: R.M. Sweet, D. Kranz, H. Robinson, L. Berman, D. Schneider, A. Héroux, A. Saxena, M. Becker, J. Jiang, and A. Soares

Sponsors:

This course is sponsored by a grant from the National Institute of Health National Center for Research Resources to the Brookhaven Biology Department and National Synchrotron Light Source, and in part by support from the Department of Energy Office of Biological and Environmental Research.

We also thank Brookhaven Science Associates, Area Detector Systems Corp, Hoffmann - La Roche, Bruker AXS, Bristol-Myers Squibb, Molecular Structure Corp., and Hampton Research Corp. for financial assistance for this course.

Saturday 24 April:

6 PM: Meet at Berkner Hall to go out for dinner. Bring a car if you have one.

Sunday 25 April:

Crystallographic Fundamentals.

Get breakfast at Berkner hall with your meal voucher.

8:30 AM: A day-long course will be given from 8:30AM to roughly 3PM to provide additional background to students whose experience might leave them a bit baffled by the lectures in the course. A wide range of fundamentals of diffraction theory, data production, data collection, and structure solving will be presented, with the focus being to provide prerequisite knowledge for the remainder of the course. The course will be in the Seminar room at the far East end of the Biology Department, Building 463, roughly I7 on the BNL site map.

3:00 PM: A few students will be selected to go straight to the NSLS to complete NSLS registration.

3PM and after: Students arrive and register in Berkner Hall, G5 on the BNL site map. Any who haven't done so, please take both the Safety and the Radiological modules of the NSLS safety training now.

3:30 PM: Teachers who need to check electronic lecture materials may do that at the Biology lecture room.

5 - 7 PM: Supper at Berkner.

Monday 26 April:

8:00 AM: Continental Breakfast at Biology Dept. seminar room (Far East End of the building, Bldg. No 463).

Lectures -- Biology Department:

8:30 Welcome and Introduction
8:45 Diffraction Geometry for the Rotation Method -- Bob Sweet (BNL)
9:30 Strategy vs tactics in data collection -- Zbyszek Dauter (NIH)
10:15 Coffee
10:30 Cryocooled specimen preparation for the synchrotron -- Sean Parkin (U. Ky)
11:30 Data reduction with d*TREK -- Jim Pflugrath (Rigaku/MSC)
12:15 Lunch -- In Medical Dept. Seminar Room
1:00 Data reduction with the HKL suite -- Wladek Minor (U. Va)
1:45 Data reduction with The DPS/Mosflm Package -- Frank vonDelft (Structural Genomics Consortium Oxford)
2:30 Coffee
2:45 Structure Solving with ASDP-- Jiansheng Jiang (BNL)
3:10 Operation of beamline software: GrEpx, CBass -- John Skinner (BNL)
3:50 Head to the NSLS

Training at the NSLS:

4:05 Collect Film Badges in NSLS Seminar Room
4:30 Quick Tour of the NSLS in six groups of two sections each.

5:15 Drinks and conversation at Berkner. Music for your listening pleasure by Swinging Moose!

6:15 Dinner

7:30 - 9:30 Back to NSLS for tutorials and conversation. Groups A-F check your crystals!!

Tuesday 27 April

8:00 Breakfast in Biology Dept.

Lectures -- Biology Dept.:

8:30 Ad hoc discussion on special topics and emerging methods -- Jim Pflugrath (Rigaku/MSC)
9:00 Special properties of SR: polarization, bandwidth, collimation -- Lonny Berman (BNL)
9:40 Modern CCD-based x-ray detectors -- Walter Phillips (Brandeis)
10:15 Coffee
10:30 Are we MAD or are we SAD? -- Howard Robinson (BNL)
11:15 Structure solving with SOLVE and Phenix -- Tom Terwilliger (LANL)
12:00 Lunch
1:00 Structure solving with autoSHARP -- Clemens Vonrhein or Gerard Bricogne (Global Phasing)
1:45 Structure solving with Shake-and-Bake -- Chuck Weeks (HWMRI)

Laboratory work -- NSLS

2:30 Coffee, etc. available at X8 and the lunch room between X17 and X20
2:45 Introduction to the beamlines at the beamline -- Individual instructors

Beamline Operations and Safety Awareness Training
Demonstration of Specimen mounting and test shots

3:45 - 4:00 Beamline Meetings: Groups meet with beamline staff to discuss projects and to prepare a schedule for data-collection.


Beamline	X8-C	X9-A	X9-B	X12-B	X12-C	X26-C
Mtg. Room Safety Form	Seminar Room SAF ....	X8 Conf. Room SAF ...	X8 Conf. Room SAF ...	Seminar Room SAF ...	Blue cubicle near X20 SAF ...	Library SAF ...

Check on group assignments here.

Check on computer information for the course.

5:45 Drinks and conversation at Berkner

6:15 Dinner

7:30 - 9:30 Back to NSLS for tutorials, start of data collection, and conversation. The x-tal prep room will be open; X6-A (Vivian Stojanoff and Marc Allaire) will be available for crystal tests and other adventures.

Beamline configuration:

Beamline X8-C
X9-A
X9-B
X12-B
X12-C X26-C

Morning Startup MacMillan Thiru
Dauter
Schneider
Saxena Robinson

Software DPS/Mosflm
HKL2000
HKL2000
HKL2000
d*TREK DPS/Mosflm

Helpers Szebenyi
Flaks
Hung
Rould
Klei
Ramu
Nielsen
Soares
Greensmith
Pflugrath
Schierbeek
vonDelft
Enemark

Beamline	X8-C	X9-A	X9-B	X12-B	X12-C	X26-C
Morning Startup	MacMillan	Thiru	Dauter	Schneider	Saxena	Robinson
Software	DPS/Mosflm	HKL2000	HKL2000	HKL2000	d*TREK	DPS/Mosflm
Helpers	Szebenyi Flaks Hung	Rould Klei	Ramu Nielsen	Soares Greensmith	Pflugrath Schierbeek	vonDelft Enemark

Group assignments and very rough data-collection schedule:

Time X8-C
X9-A
X9-B
X12-B
X12-C X26-C X-tal prep. and tutorials

Tues 8 PM A B C D E F G-L

Wed 2:00 PM G H I J K L A-F

Thurs 8AM A B C D E F G-L

Thurs 8PM G H I J K L --

Time	X8-C	X9-A	X9-B	X12-B	X12-C	X26-C	X-tal prep. and tutorials
Tues 8 PM	A	B	C	D	E	F	*G-L*
Wed 2:00 PM	G	H	I	J	K	L	*A-F*
Thurs 8AM	A	B	C	D	E	F	*G-L*
Thurs 8PM	G	H	I	J	K	L	--

Wednesday - Thursday 28-29 April:

8:00 AM: Breakfast in NSLS Seminar Room

Data Collection Sessions and tutorials, including crystal tests at X6-A, will run concurrently throughout the day.

Noon: Lunch in Seminar Room

3:30 PM: There will be a required meeting in the coffee room both afternoons at 3:30 to compare notes and make announcements.

6:00 PM: Supper in Seminar Room

Friday 30 April:

Recapitulation -- Biology Dept.

8:00 Breakfast in Biology

8:30 The course staff, with the help of students, will recount triumphs, troubles, and interesting observations. Course staff will be available until noon to assist students in tidying up calculations, backing up data, etc.

Version of 20 April 2004