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RapiData 2005

IMPORTANT VISA INFORMATION for our overseas guests.

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
10-15 April 2005

Course Agenda

Organized by: R.M. Sweet, D. Robertson, 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 9 April:

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

Sunday 10 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. We will take a mid-day break sufficiently long 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 11 April:

7:15 AM: NSLS User Office will be open for any final registrations.

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)
11:15 Data reduction with d*TREK -- Jim Pflugrath (Rigaku/MSC)
12:00 Lunch -- In Berkner Hall, rooms A and B
1:00 Special properties of SR: polarization, bandwidth, collimation -- Lonny Berman (BNL)
1:40 Data reduction with The DPS/Mosflm Package -- Frank vonDelft (Structural Genomics Consortium Oxford)
2:25 Coffee
2:40 Automatic control of data collection with the "dna" system -- Graeme Winter (Daresbury Lab.)
3:25 Operation of beam line software: CBass, PXDB -- John Skinner (BNL)
4:00 Head to the NSLS

Training at the NSLS:

4:15 Collect Film Badges at NSLS User Office
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 12 April

8:00 Breakfast in Biology Dept.

Lectures -- Biology Dept.:

8:30 Modern CCD-based x-ray detectors -- Chris Nielsen (Area Detector Systems Corp.
9:05 Are we MAD or are we SAD? -- Howard Robinson (BNL)
9:50 Structure solving with SHELX -- Bram Schierbeek (Bruker AXS)
10:35 Coffee
10:50 Structure solving with SOLVE and Phenix -- Tom Terwilliger (LANL)
11:35 Structure solving with autoSHARP -- Clemens Vonrhein (Global Phasing)
12:20 Lunch -- In Medical Dept. Seminar Room
1:05 A tutorial on FORTRAN Jiffies -- Mark Rould (UVM)
1:10 Structure solving with Shake-and-Bake -- Chuck Weeks (HWMRI)
1:55 Data reduction with the HKL suite -- Wladek Minor (U. Va)

Laboratory work -- NSLS

2:40 Coffee, etc. available at X8 and the lunch room between X17 and X20
2:50 Introduction to the beam lines at the beam line -- Individual instructors

Beam line Operations and Safety Awareness Training
Demonstration of Specimen mounting and test shots

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


Beamline	X4-A	X8-C	X9-A	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.

Beam line configuration (Beam line labels are selectable here -- have a look at beam line documentation):

Beamline X4-A
X8-C X9-A X12-B
X12-C X26-C

Morning Startup Schwanof
MacMillan Babu Schneider
Saxena Héroux

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

Helpers Klei
Enemark
Abramowitz
Szebenyi
Rould
Birktoft
Dauter
Ramu
Soares
Pauluhn
J. Cowan
Nielsen
Pflugrath
Nassar
Schierbeek

Beamline	X4-A	X8-C	X9-A	X12-B	X12-C	X26-C
Morning Startup	Schwanof	MacMillan	Babu	Schneider	Saxena	Héroux
Software	HKL2000	DPS/Mosflm	HKL2000	HKL2000	d*TREK	DPS/Mosflm
Helpers	Klei Enemark Abramowitz	Szebenyi Rould Birktoft	Dauter Ramu	Soares Pauluhn J. Cowan	Nielsen Pflugrath	Nassar Schierbeek

Group assignments and very rough data-collection schedule:

Time X4-A
X8-C X9-A 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	X4-A	X8-C	X9-A	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 13-14 April:

8:00 AM: Breakfast in NSLS Library

Data Collection Sessions and tutorials, including crystal preparation at X12, will run concurrently throughout the day. There will be sign-up sheets for all of the tutorials. There will be a tutorial in the X12 Crystal Room from about noon on Wed to noon on Thurs by Prof. Robert Thorne of Cornell Univ. He will demonstrate and provide practice time on his new MicroMounts. See some of his publications here.

Noon: Lunch in NSLS Library

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

6:00 PM: Supper in NSLS Library

Friday 15 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 7 April 2005