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Draft Course Agenda 2014

Saturday 26 April

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

Sunday 27 April

Crystallographic Fundamentals Course -- Breakfast: Berkner; Lecture: Biology Department, Bldg. 463, East End

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 2:30 PM, with a mid-day break, to provide a review of fundamental crystallography. The course will be in the Seminar room at the far East end of the Biology Department, Building 463. [ Directions ] 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.

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 Drinks and Dinner for All at Berkner Hall

Monday 28 April

The Lectures -- Biology Department Seminar Room, Bldg. 463

[Directions]
8:00 AM Continental Breakfast Biology Department

Lectures: Biology Seminar Room

8:30 am Welcome & Introduction            
8:45 am Some Issues in Data Collection   - B. Sweet (BNL)
9:30 am Cryogenic Data Collection and Radiation Damage: the Basics
  -- S. Mc Sweeney(BNL)
10:15 am Coffee
10:30 am I've got a crystal, now what?
  -- J. Pflugrath (Rigaku)
11:15 am Special Properties of SR: Polarization, Bandwidth, Collimation
  - L. Berman (BNL)
12:00 pm Lunch (In Medical-Department Seminar Room)
1:00 pm Data Processing: iMosflm/DPS/scala
  - C. Roessler (BNL)
1:45 pm Data Reduction with the HKL Suite
  - M. Chruszcz (U. S. Carolina)
2:30 pm Coffee
2:45 pm Data reduction with XDS
- G. Jogl (Brown U.)
3:30 pm Single crystal optical spectroscopy
  - A. Orville (BNL)
4:00 pm Head to the NSLS

Visit to the NSLS

4:15 pm Quick walking tour of the NSLS.
5:00 pm Hors d'oeuvres, Soft-Drinks, and Conversation at Berkner Hall.
6:15 pm Banquet in Berkner
7:30 pm - 9:30 pm Back to NSLS for tutorials and conversation. The x-tal prep. room will be open with Elspeth Garman and Jim Pflugrath in attendance.
All groups check your dewars, crystals, etc!!

Tuesday 29 April

8:00 pm Breakfast in Biology Department.

Lectures: Biology Dept. Seminar Room

8:30 am Advanced Detectors for Synchrotron Beam Lines
  - C. Nielsen (Area Detectors Systems Corp.)
9:15 am Getting the Best Data Using Photon-Counting Pixel Detectors
 --  M. Mueller (Dectris)
10:00 am Coffee
10:15 am Are we MAD or are we SAD? -- A prelude to structure solving.
 - H. Robinson (BNL)
11:00 am Structure Solving with Molecular Replacement Methods
  - Raji Edayathumangalam (Brandeis)
11:30 pm Structure Solving with SOLVE and Phenix
  - T. Terwilliger (LANL)
12:15 pm Lunch In Medical Department
1:00 pm Data processing and experimental phasing: autoPROC and SHARP/autoSHARP
  - C. Vonrhein (Global Phasing) 
1:45 pm Structure Solving with SHELX and HKL-to-Map
 - A. Héroux (BNL))
2:30 pm Introduction to remote data collection at SSRL
 - C. Smith (SSRL)
3:00 pm Introduction to small-angle x-ray scattering
 - L. Yang (BNL)
3:30 pm Head to the NSLS

Laboratory Work (NSLS)

3:30 pm Coffee, etc. available in the library
3:45 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
~ 4:15 pm Begin Beamline Meetings in rooms listed below:
Groups meet with Beamline staff to discuss projects and to prepare a schedule for data-collection.

Beamline SSRL Remote X4-A X4-C X12-B X12-C X26-C
Mtg. Room
Safety Form
Library X8 Conf. Room X8 Conf. Room X12 Cyber Café X12 Cyber Café X25 Cyber Café

Check on group assignments here
See the NSLS Map for RapiData
Check on computer information for the course here
6:00 pm Supper at Berkner
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 Jim Pflugrath in attendance.

Beamline configuration (beamline names are linked to their NSLS description pages -- have a look at the documentation for your beamline)
Main Course Beamlines
Beamline SSRL Remote X4-A and X4-C
X12-B and X12-C X26-C
Morning Startup Smith
Schwanof Soares, Agarwal Orville
Helpers Doukov
Roessler
Jayaraman
Liu
Guo
Clarke
Raji
Szebenyi
Fuchs
Schneider
Mardones
Andi
Li

Supporting ultra-fast beamlines (X25/X29)
Beamline X25
X29
Morning Startup Héroux
Robinson
Helpers Garcia-Diaz
Guja
Shi
Page
McGrath

Group assignments and very rough data-collection schedule (24-hr clock) on the major course beamlines:
Time X4-A X4-C X12-B X12-C SSRL X26-C Xtal prep & tutorials
Tues 20:00 A B CD E F G-L
Wed 7:30 GH IJ KL A-F
Wed 11:30 A B CD E F G-L
Wed 16:00 GH IJ KL A-F
Wed 19:30 A B CD E F G-L
Thu 7:30 GH IJ KL A-F
Thu 11:30 A B CD E F G-L
Thu 16:00 GH IJ KL A-F
Thu 20:30  

Data-collection schedule for ultra-fast Undulator beamlines:
Time X25 X29
Wed 7:30 CA
Wed 11:00 I G
Wed 16:00 D B
Wed 19:30 J H
Wed 22:30 CLOSED CLOSED
Thu 7:30 E F
Thu 11:30 K L
Thu 16:00 A,B,F,G,H,L C,D,E,I,J,K
Thu 19:00 CLOSED CLOSED
Fri 7:30 OPEN CLOSED

Wednesday 30 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)
3:00 pm There will be a required meeting in the NSLS Seminar Room both afternoons at 3:00 PM to compare notes and make announcements.
The Group Photo will be at the end of this meeting.
6:00 pm Start of informal supper (in the NSLS Library )

Thursday 1 May

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.
11:30 am - 12:20 pm There will be a short program and mass tour of NSLS-II for those who are interested.
12:00 pm Lunch will begin (in the NSLS Library)
3:00 pm There will be a required meeting in the NSLS Seminar Room both afternoons at 3:00 PM to compare notes and make announcements.
6:00 pm Start of informal supper (in the NSLS Library )

Friday 2 May

Recapitulation: Back in Berkner Hall

8:00 am Breakfast in Berkner
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.


This course is sponsored by a grant from the Biomedical Technology Research Centers of NIGMS/NIH 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 the International Union of Crystallography, Brookhaven Science Associates, Area Detector Systems Corp, Dectris Ltd., Rigaku Americas, Hampton Research Corp., and MiTeGen for financial assistance for this course.

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Last Modified: January 30, 2014