All lectures on Sunday, Monday and Tuesday will take place in the Redwood Rooms C & D (building 48). Lunch and dinner will also be served in building 48, unless noted otherwise. The practical tutorials will take place at different locations around the SSRL and experimental floor.
See a map of SLAC indicating the main course venues.Sunday 22 April
Crystallographic Fundamentals Course
8:30 - 9:30 Registration (Redwood rooms, building 48)
9:30 - 15:30 Crystallographic Fundamentals Course: Bob Sweet
12:00 Lunch
16:30 - 17:00 NX Client installation workshop: Edgar Estebañez (Redwood rooms, building 48)
17:30 - 19:30 Welcome Reception (Stanford Guest House)
Monday 23 April
Lectures on data collection, data reduction and X-Ray sources
7:30 - 8:30 Registration (Redwood Rooms)
8:30 Introduction to RapiData: Clyde Smith
8:45 Some issues in data collection: Bob Sweet
9:30 Cryo-crystallography: Elspeth Garman
10:15 Coffee break
10:30: I've got a crystal, now what?: Jim Pflugrath
11:15 Autoindexing, integration and data reduction: Harry Powell
12:00 Lunch
12:45-13:00: Group picture
13:00 Data reduction with the HKL Suite: Ivan Shabalin
13:45 X-Ray sources: Clyde Smith
14:30 Coffee break
14:45 Radiation Damage: Elspeth Garman
15:30 Data collection at Free Electron Lasers: Nick Sauter
16:30-18:00 Orientation to experiments /Sample Preparation (Building 120)
18:15-19:30 Banquet dinner
19:30 Flash introduction of the participants (Redwood room, building 48)
Tuesday 24 April
Lectures on detectors, structure solution and complementary methods
8:45 Getting the best data from photon counting detectors: Andreas Foerster
9:30 SAD and MAD: Ana Gonzalez
10:15 Coffee break
10:30 Molecular Replacement: Raji Edayathumangalam
11:15 Data processing and analysis for experimental phasing with SHARP/autoSHARP: Clemens Vonrhein
12:00 Lunch
12:45-13:00: Celebrating RapiData 20th edition - Bob Sweet
13:00 Solve and Phenix: Tom Terwilliger
13:45 Introduction to Small Angle Scattering: Thomas Weiss
14:30 Coffee break
14:45 In situ optical spectroscopy: Aina Cohen
16:00-18:00 Tour of LCLS
18:15 Dinner
19:30-22:00 Tutorials/Sample Preparation
Wednesday 25 April
All day (8:00-22:00): Concurrent data collection and tutorials (see schedule below)
10:30 Coffee served in BL9 lounge area
13:00 Lunch
15:30 Coffee served in BL9 lounge area
17:00 Meeting (Redwood Rooms, building 48)
Thursday 26 April
All day (8:00-22:00): Concurrent data collection and software tutorials (see schedule below)
10:30 Coffee served in BL9 lounge area
13:00 Lunch
15:30 Coffee served in BL9 lounge area
17:00 Meeting (Redwood Rooms, building 48)
Friday 27 April
10:00-11:00 Recapitulation and final discussions The ending time is approximate (Building 48)
On Sunday, there will be an optional 30 minutes workshop to install and configure the NX client in the participants' laptops, and to learn how to access the data and demos in the practical tutorials.
Participants who do not attend the Sunday course and need help with the NX client, can contact the organizers to arrange a demo.
On Monday 23rd, after the afternoon lectures, there will a compulsory orientation to experiments at SSRL, covering safety, at building 120. There will be two talks:
On Monday 23rd, between 16:00 and 18:00, we will do a demo on transferring frozen samples in cryovials to robot cassettes. Participants who have brought frozen samples in cryovials will get the chance to transfer them to SSRL cassettes during the demo or on Tuesday 24th, from 19:30
Participants with unfrozen samples (in crystallization plates or capillaries) can freeze them during the Sample freezing and mounting tutorial on BL7-1 (signup sheets will be available throught the course).
Sign up sheets for the optional tour of the free electron laser facility
LCLS will be available on Monday. A group will set off from building
48 at ~ 16:00 (there is a ~15 minute walk to the LCLS), with a
second group following 30 minutes later. The tour will include
a visit to the beamlines CXI and MFX, used for macromolecular femtosecond crystallography. The tour takes about 45 minutes.
During the data collection tutorials, the participants will learn how to optimize the data collection parameters for different experimental purposes.
We will offer tutorials for sample preparation, freezing, mounting and characterization; SAD/MAD data collection; and UV-Vis spectrophotometry. All the participants will get beamtime to learn how to collect data from their own samples or standard samples. (See beamtime schedule below). For the participants interested in the MAD/SAD, UV-Vis spectrophotometry and sample preparation tutorials, there will be sign-up sheets at the Redwood room during the lectures on Monday and Tuesday and in the BL9 lounge area after that.
The slots marked as 'Spare' in the beamtime schedule can be used for participants to collect data by themselves, once they have been trained on data collection during a previous tutorial. Please see the organizers during the course if you need spare time for data collection or to ask about the possibility to collect data remotely after the course.
Time | Data collection at BL12-2 | UV-Vis Microspectrophotometer (BL9-2) | MAD/SAD data collection (BL14-1) | Data collection at BL9-2 | Sample preparation (BL7-1) |
---|---|---|---|---|---|
Tues 19:30 | Unavailable | Unavailable | Unavailable | Unavailable | Sign-up |
Wed 8:00 | Dubianok / Mena-Aguilar | Unavailable | Sign-up | Yu / Brixius-Anderko / Fadini / Arce / Chang | Sign-up |
Wed 10:30 | Zou / Waldron | Unavailable | Sign-up | Jensen / Ramos / Reis / Wellons / Christenson | Sign-up |
Wed 14:00 | Bahena / Posso | Unavailable | Sign-up | Coban / McFarlane / Ferri / Celia / Riemer / Dharmaiah | Sign-up |
Wed 19:00 | Marin-Trovar / Miranda | Sign-up | Sign-up | Unavailable | Sign-up |
Wed 22:00 | Spare | Unavailable | Unavailable | Spare | Unavailable |
Thu 8:00 | Taylor / Yates-Hansen | Unavailable | Sign-up | D'Arcy | Sign-up |
Thu 10:30 | Daruwalla / Hill | Unavailable | Sign-up | Yadav / Vieira / Maciel / Suraweera / Nakamura | Sign-up |
Thu 14:00 | Czub / Lipowska | Unavailable | Sign-up | Henry / Saxena / Wahome / Jabbarpour | Sign-up |
Thu 19:00 | Salmazo | Sign-up | Sign-up | Unavailable | Sign-up |
Thu 22:00 | Spare | Unavailable | Spare | Spare | Unavailable |
See A map of the SSRL beamlines.
Tutors
Software tutorials will be offered on several different packages for data processing and structure solution, including:
The participants must sign-up in advance for the software tutorials they wish to attend. There will be sign-up sheets at the Redwood room during the lectures on Monday and Tuesday and in the BL9 lounge area after that.
Time | Phenix | CCP4/DIALS | SHARP/autoSHARP autoPROC STARANISO BUSTER | Molecular Replacement | XDS | HKL | SAXS software |
---|---|---|---|---|---|---|---|
Tuesday 19:30 | B. 120, room 300 Phenix GUI introduction SAD structure determination with phenix.autosol Ligand fitting with phenix.ligandfit |
B. 452, room 101 | B. 278 room 104 Data collection strategies and planing Processing diffraction data with autoPROC Analysing and describing anisotropy with STARANISO Solving structures via SAD, MAD, SIRAS, MIRAS in autoSHARP Using partial model information in autoSHARP (MR-SAD, MR-MAD etc) Visualising radiation damage in BUSTER Generation of ligand refinement dictionaries with the Grade webserver Automated ligand fitting with Rhofit Refinement with BUSTER | B. 274, conf. room | B. 452, room 103 | B. 270, room 19A Processing diffraction data with HKL2000/HKL3000 (indexing, integration, scaling SAD structure determination with HKL3000 (SHELX, MLPHARE, DM, Parrot, Resolve, and Profess for getting best phases; ARP/wARP, Buccaneer, Resolve, or HKL Builder for model building) Refinement in HKL3000 (REFMAC for refinement, Coot for visualization) | Unavailable |
Wed 8:00 | B. 120, room 300 Phenix GUI introduction Ligand preparation with phenix.elbow Ligand fitting with phenix.ligandfit Combining MR and SAD in PHENIX: solving weak SAD data with poor MR results |
B. 452, room 101 | B. 278, room 104 Same as first day | B. 274, conf. room | Unavailable | B. 270, room 19A Same as first day | Unavailable |
Wed 10:30 | B. 120, room 300 Phenix GUI introduction SAD structure determination with phenix.autosol Ligand preparation with phenix.elbow Ligand fitting with phenix.ligandfit |
B. 452, room 101 | B. 278, room 104 Same as first day | B. 274, conf. room | B. 452, room 103 | B. 270, room 19A Same as first day | B. 130 room 214 |
Wed 14:00 | B. 120, room 300 Bring your own data and get help solving your structure; phasing refinement and ligands |
B. 452, room 101 | B. 278, room 104 Same as first day | B. 274, conf. room | B. 452, room 103 | B. 270, room 19A Same as first day | B. 130 room 214 |
Wed 19:00 | B. 120, room 300 Phenix GUI introduction Ligand preparation with phenix.elbow SAD structure determination with phenix.autosol Combining MR and SAD in PHENIX: solving weak SAD data with poor MR results |
B. 452, room 101 | B. 278, room 104 Same as first day | B. 274, conf. room | B. 452, room 103 | B. 270, room 19A Bring your own data and get help solving and refining your structure with HKL3000: SAD, MAD, and molecular replacement; model building, ligand and metal identification, validation and refinement | Unavailable |
Thu 8:00 | B. 120, room 300 Phenix GUI introduction Refinement with phenix.refine SAD structure determination with phenix.autosol |
B. 452, room 101 | B. 278, room 104 Same as first day | B. 274, conf. room | Unavailable | B. 270, room 19A Processing diffraction data with HKL2000/HKL3000 (indexing, integration, scaling SAD structure determination with HKL3000 (SHELX, MLPHARE, DM, Parrot, Resolve, and Profess for getting best phases; ARP/wARP, Buccaneer, Resolve, or HKL Builder for model building) Refinement in HKL3000 (REFMAC for refinement, Coot for visualization) | Unavailable |
Thu 10:30 | B. 120, room 300 Phenix GUI introduction Refinement with phenix.refine SAD structure determination with phenix.autosol |
B. 452, room 101 | B. 278, room 104 Same as first day | B. 274, conf. room | B. 452, room 103 | B. 270, room 19A Same as first day | B. 130 room 214 |
Thu 14:00 | B. 120, room 300 Bring your own data and get help solving your structure; phasing refinement and ligands |
B. 452, room 101 | B. 278, room 104 Same as first day | B. 274, conf. room | B. 452, room 103 | B. 270, room 19A Same as first day | B. 130 room 214 |
Thu 19:00 | B. 120, room 300 Phenix GUI introduction Refinement with phenix.refine Combining MR and SAD in PHENIX: solving weak SAD data with poor MR results |
B. 452, room 101 | B. 278, room 104 Same as first day | B. 274, conf. room | B. 452, room 103 | B. 270, room 19A Bring your own data and get help solving and refining your structure with HKL3000: SAD, MAD, and molecular replacement; model building, ligand and metal identification, validation and refinement | Unavailable |
Reservations can be made by phone (650) 926-2800, email guesthouse@stanford.edu
or via their web
site.Please, quote the group code RAPIDATA18.
Course dates: April 22-27 2018
Application deadline: Dec 22nd
2017
Applications received after the deadline will be
placed in a stand-by list.
Ana Gonzalez
Bus: (650) 926-8682
Email: ana@slac.stanford.edu
Clyde Smith
Bus: (650)
926-8544
Email: csmith@slac.stanford.edu
Silvia Russi
Bus: (650) 926-5594
Email: srussi@slac.stanford.edu