RapiData 2009

Rapid Data Collection & Structure Solving at the NSLS

A Practical Course in Macromolecular X-Ray Diffraction Measurement
19-24 April 2009

See the pictures from this year's course


Saturday 18 April
6 pm Meet at Berkner Hall to go out for dinner. Bring a car if you have one.
 

Sunday 19 April

Crystallographic Fundamentals Course
Morning Get breakfast at Berkner hall with your meal voucher.
9:00 am

A day-long course will be given by R. Sweet from 9:00 AM to roughly 3:30 PM (with a mid-day break) to provide additional background to students who believe they might benefit. 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. [ Directions ]
3 pm
and After		 All students and instructors who do not have a BNL ID should go to the Badging Office in the Research Support Building, Building 400, [ Directions ] before 5:00 PM to complete NSLS registration. Anyone who has not done so, please take both the Safety and the Radiological modules of the NSLS safety training now. Students may complete their registration for RapiData and pick up course materials in Berkner Hall, Building 488. [ Directions ]
5-7 pm Dinner for all at Berkner Hall
 

Monday 20 April

Main Course
7:15 AM NSLS User Office will be open for any final registrations.
8:00 AM Continental Breakfast in the Biology Department Seminar Room (far East end Building 463).
   

Lectures: Biology Department
8:30 am Welcome & Introduction
8:45 am Some Issues in Data Collection (.pdf)
  - Bob Sweet (BNL)
9:30 am Modern CCD-based X-ray Detectors
  - Chris Nielsen (ADSC)
10:15 am Coffee
10:30 am Tactics in Data Collection, Specimen Preparation, and X-ray Damage to Crystals
  - Z. Dauter (NIH/SER-CAT), E. Garman (U. Oxford)
12:00 am Lunch (In the Medical Department Seminar Room)
12:45 pm Special Properties of SR: Polarization, Bandwidth, Collimation (.pdf)
  - Lonny Berman (BNL)
1:30 pm Data Reduction with d*TREK
  - Jim Pflugrath (Rigaku Americas)
2:15 pm Coffee
2:30 pm Data Reduction with the DPS/(i)Mosflm Package
  - Frank von Delft (SGC, U. Oxford)
3:15 pm Data Reduction with the HKL Suite
  - Wladek Minor (U. Va.)
4:00 pm Head to the NSLS
   

Visit to the NSLS
4:15 pm Quick walking tour of the NSLS.
5:15 pm Drinks and Conversation at Berkner Hall.
6:15 pm Dinner
7:30 pm - 9:30 pm Back to NSLS for tutorials and conversation.
All groups check your crystals!!
   

Tuesday 21 April
8:00 pm Breakfast in the Biology Department.
   

Lectures: Biology Department
8:30 am Are we MAD or are we SAD?
  - Howard Robinson (BNL) 
9:15 am Structure Solving with SHELX
  - B. Schierbeek (Bruker/Nonius)
10:00 am Structure Solving with SOLVE and Phenix
  - Tom Terwilliger (LANL)
10:45 am Coffee
11:00 am Structure Solving with AutoSHARP
  - C. Flensburg/C. Vonrhein (Global Phasing) 
11:45 am
Lunch (In the Medical Department Seminar Room)

12:30 am
Structure Solving with Molecular Replacement Methods
  - P. Fitzgerald (Merck Research Laboratories, retired)
1:15 pm Automatic Control of Data Collection with the "edna" System
  - Alexei Soares (BNL)
2:00 pm Operation of beamline Software: CBass, PXDB
  - John Skinner (BNL)
2:30 pm Head to the NSLS
   

Laboratory Work (NSLS)
2:10 pm Coffee, etc. available at X8 and the blue cubicle near X20
2:50 pm Introduction to the beamlines at the beamline - Individual Instructors
  - Beamline Operations and Safety Awareness Training
  - Creation of the SAF for the two groups at each beamline
  - Demonstration of Specimen mounting and test shots
3:45 pm - 4:00 pm Begin Beamline Meetings:
Groups meet with Beamline staff to discuss projects and to prepare a schedule for data-collection.

Beamline X4-A X3-A X12-C X26-C
Mtg. Room
Safety Form		 Seminar Room X8 Conf. Room X12 Cyber Cafe Library

Check on group assignments here: Web Page or Excel Spread Sheet
Check on computer information for the course
 
5:45 pm Drinks and conversation at Berkner Hall.
6:15 pm Dinner
7:30 pm - 9:30 pm Back to NSLS for tutorials, start of data collection, and conversation. The x-tal prep room will be open with Elspeth Garman and Dan Thiel in attendance.

Beamline confuguration (beamline names are linked to their NSLS description pages -- have a look at the documentation for your beamline)

Main course beamlines
Beamline X4-A
 X3-A X12-C X26-C
Morning Startup Schwanof
 Shi
 Soares Orville
Software HKL2000 HKL2000 d*TREK DPS/Mosflm
Helpers Klei
Chen
 Dauter
Ramu
 Pflugrath
Raji E		 Silvaggi
Coincon

Supporting ultra-fast beamlines (X25/X29) and crystal mounting test station (X12B)
Beamline X25
 X29 X12B
Morning Startup Heroux
 Robinson Schneider
Software HKL2000 HKL2000 HKL2000
Helpers Allaire
Garcia
 Page
Jeffrey
 Thiel
Birktoft

Group assignments and very rough data-collection schedule (major course beamlines):
Time X4-A X3-A X12-C X26-C Xtal prep & tutorials
Tues 20:00 A B C D E-H
Wed 7:00 E F G H I-L & A-D
Wed 15:00 I J K L A-D & E-H
Wed 23:00 E F G H I-L
Thu 11:00 A B C D E-H & I-L
Thu 19:00 I J K L A-D

Data-collection schedule for accessory beamlines:
Time X25 X29
Wed 8:00 A B
Wed 12:00 C D
Wed 16:00 E F
Wed 20:00 G H
Thu 0:00 OPEN OPEN
Thu 8:00 I J
Thu 12:00 K L
Thu 16:00 OPEN OPEN

Wednesday - Thursday 22-23 April
8:00 AM Breakfast in the 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.
12:00 pm Lunch (in the NSLS Library)
3:30 pm There will be a required meeting in the NSLS Seminar Room both afternoons at 3:30 PM to compare notes and make announcements.
6:00 pm Dinner (in the NSLS Library )
   

Friday 24 April

Recapitulation: Biology Department
8:00 am Breakfast in the Biology Department
8:30 am 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.