All workshops will take place at Sheraton Centre Toronto Hotel, 123 Queen Street West, Toronto, ON, M5H 2M9, Canada, (416) 361-1000 on Friday, July 20, 2018.

 

Preregistration is MANDATORY and should be indicated on your registration form.

The cost for each workshop is separate from the meeting registration fee.

 

The following schedules, instructor lists and topics are tentative and subject to change.

 

 




Workshop No.: 1:        Cryo-­‐EM -A Guide to High‐Resolution Structure Determination 

Room:       Provincial North

SPONSORED BY:

 

        

 

ORGANIZERS

 

 

Wah Chiu

Stanford University

[email protected]

Lori Passmore

MRC LMB, Cambridge UK

[email protected]

John Rubinstein

Sick Kids, Toronto

[email protected]

 

 

 

INSTRUCTORS

 

 

Wah Chiu

Stanford University

[email protected]

Lori Passmore

MRC LMB, Cambridge UK

[email protected]

Chris Russo

MRC LMB, Cambridge UK

[email protected]

John Rubinstein

Sick Kids, Toronto

[email protected]

Marcus Brubaker

York University

[email protected]

Ali Punjani

University of Toronto

[email protected]

Matthew Baker

Baylor College of Medicine

[email protected]

Corey Hryc

Baylor College of Medicine

[email protected]

 

Over the past five years, cryo-EM has become increasingly popular and is now the method of choice for structure determination of proteins larger than ~200 kDa. It has been particularly successful for proteins that are difficult to crystallize, including membrane proteins, large assemblies and multi-protein complexes. The aim of this workshop is to provide a detailed overview of cryo-EM specimen preparation, image processing and building/refinement of atomic models. The workshop will focus on high-resolution single particle cryo-EM. Aspects of image processing and modelling will be hands-on - state-the-art programs will be used by the students to process sample datasets.

 

User facilities are being established in many universities and these will allow a larger community to access cryo-EM. By teaching the main concepts and challenges in each step, this workshop will benefit those who want to use cryo-EM in the future, or who have recently transitioned into it. The organizers are experts in the topics they will be teaching and all have been involved in methods development. We will strive to include up-to-date discussions of cutting-edge methods and technology.

 

 

Time

Instructor/Topic (Tentative)

 

8:30-9:00

 

Wah Chiu - Welcome And Introduction To Cryo-EM

 

9:00-10:00

Lori Passmore - Cryo-EM Sample Preparation

 

10:00-10:45

Chris Russo -Data Collection Strategies And Radiation Damage

 

 

10:45-11:15

Coffee Break

 

11:15-12:30

John Rubinstein - Image Processing Part I

 

12:30-1:30

Lunch

 

1:30-3:15

Marcus Brubaker And Ali Punjani - Image Processing Part II

 

3:15-3:45

Coffee Break

 

3:45-4:45

Matthew Baker - Model Building And Refinement Part I

 

4:45-5:45

Corey Hryc - Model Building And Refinement Part II

 

5:45-6:00

Wrap Up And Discussion (Wah Chiu, Lori Passmore, John Rubinstein)

 

 

The tutorial by Corey Hryc will require Chimera to visualize both map and model and perform slight alterations of the data. In addition, Phenix (command line tools) will be used to optimize the molecular model with respect to the experimental data. Finally, EMAN2 will be needed to perform validation routines such as computing map / model FSC.

 

Chimera:         https://www.cgl.ucsf.edu/chimera/

Phenix             https://www.phenix-online.org/      

EMAN2           http://blake.bcm.edu/emanwiki/EMAN2     

 

Personal computers can be used and these software packages are available on Mac, Linux and Windows.

 

Registration

 

Student/Post-Doc

$110

All Others

$110

 

 

 



Workshop No.: 2:        Molecular Art & Animation in 3D

Room:       Provincial South

 

 

ORGANIZERS

 

 

Chelsy C. Chesterman

Rutgers University

[email protected]

 

 

 

INSTRUCTORS

 

 

Maria Voig

Protein Data Bank

[email protected]

Krystle McLaughlin

Vassar College

[email protected]

Travis Eisemann

 

[email protected]

 

 

 

 

Beautiful figures and animations have become synonymous with the publication of structural data in top research journals. Demonstrating molecular concepts and structural data using these strategies is also highly effective in scientific presentations or outreach activities. Many crystallographers enter the field with a background in biology or chemistry and are unfamiliar with creating such artwork. This workshop will focus on the creation of figures and animations in multiple software programs including PyMOL, Chimera, Blender 3D, and Maya. Topics will include factors to consider when designing your art and animations, basic operation of these programs, and follow-along examples. The main goal of the workshop will be to give participants an overview of the available tools so that they can start to explore creating their own molecular art.

 

 

Time

Instructor/Topic

 

8:30 - 9:00

 

Software Installation Assistance

 

9:00 - 9:15

Chelsy Chesterman - Introduction/Program Outline

 

9:15 - 9:45

Maria Voigt - Best Practices In Visual Communication

 

9:45 - 10:30

Krystle Mclaughlin - Showcasing Molecular Models With

Pymol

 

10:30 - 10:45

Coffee Break

 

10:45 - 11:30

Chelsy Chesterman - Bringing Cryo-­‐EM Structures To Life In

Chimera

 

11:30 - 12:30

Lunch On Your Own (Not Provided)

 

12:30 - 12:45

Travis Eisemann - Simplifying Your Story Into A Cartoon

 

12:45 - 2:00

Travis Eisemann - Molecular Cartoons In Blender 3D

 

2:00 - 3:00

Maria Voigt - Introduction To Molecular Maya And Autodesk Maya

 

3:00 - 3:30

Coffee Break

 

3:30 - 5:00

Maria Voigt - Animation With Autodesk Maya

 

 

Software required will be PyMOL, Chimera, Blender 3D, Maya, and Molecular Maya and participants will use their personal computers. These programs are free or have a free educational version. Installation instructions will be distributed to participants by e-mail prior to the workshop and participants will be asked to install as much as they can ahead of time. Many of these programs will benefit from using a 3-button mouse not available on most laptops. Participants are asked to bring their own mouse.

 

 

Registration

Before 5/31

After 5/31

Student/Post-Doc

$65

$85

All Others

$90

$110

 

 

 

 

 

 

 



Workshop No.: 3:        X-Ray Crystallography: Structure Preparation, Electron Density and Solvent Analysis

 

 

 

 






 

Workshop No.: 4:        Applications of Small Angle Scattering to Structural Biology: An Introduction

Room:      Chestnut West

 


SPONSORED BY:

                    

 

 

 

ORGANIZERS

 

 

Kushol Gupta

Perelman School of Medicine | University of Pennsylvania

[email protected]

Richard Gillilan

Macromolecular Diffraction Facility | Cornell High Energy Synchrotron Source

[email protected]

Jesse Hopkins

Macromolecular Diffraction Facility | Cornell High Energy Synchrotron Source

[email protected]

Haydyn Mertens

BIOSAXS Group | EMBL Hamburg

[email protected]

Srinivas Chakravarthy

BioCAT Group |Advanced Photon Source

[email protected]

 

 

 

INSTRUCTORS

 

 

Angela Criswell

Rigaku Corporation

 

Srinivas Chakravarthy

BioCAT Group, Advanced Photon Source

 

Richard Gillilan

Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source

 

Thomas Grant

University of Buffalo/Hauptman-Woodward Medical Research Institute

 

Jesse Hopkins

BioCAT Group, Advanced Photon Source

 

Maxim Petoukhov

BIOSAXS Group, EMBL Hamburg

 

Soren Skou  

XENOCS (SAXSLAB)

 

 

Over the past two decades, SAS has become a mainstay technique for the study of structure and composition in solution for structural biologists around the world. In contrast to the more intensive SAS courses in Europe that extend across several days, this single-day workshop will be comprised of carefully constructed lectures and tutorials to serve as an introduction to investigators new to the technique. The workshop format will include lectures and a selection of hands-on practical exercises. 

 

Throughout the workshop the emphasis will be on practical application: knowing how to judge data quality, how to troubleshoot during data collection, and the expectations for a successful experiment and acceptable publication. Students will also learn about aspects of home laboratory data collection and will be introduced to experiments at national user facilities (synchrotrons and research reactors).  

 

Time

Instructor/Topic

 

8:00 - 8:30

 

Registration And Software Installation Help; Speaker Introduction

 

8:30 - 9:00

Biosas: Overview: Why Is SAS Helpful?

 

9:00 - 9:30

The Scattering Profile Guinier Analysis, Concentration, Monodispersity, Etc.

 

10:00 - 10:15

Coffee Break

 

10:15 - 11:00

Data Analysis: Model-Independent Features

Molecular Weight Determination, Invariant Plots And Flexibility, The P(R) Function

 

11:00 - 12:00

Tutorial 2: Basic Data Analysis II With RAW

Calculate A P(R) Function, Determine Molecular Weight, Dmax, Rg, Volume, Etc.

 

12:00 - 1:00

Working Lunch - Laboratory Source SAXS

Discussion With Scientists, Experimental Advice

 

1:00 - 1:30

SEC-SAXS

Application And Practical Considerations

 

1:30 - 1:45

Sample Preparation

Sample Purification And Preparation, Aggregation, Buffer Selection, Etc.

 

1:45 - 2:00

Complementary Biophysical Methods For Sample Assessment

The Importance Of Supporting Biophysical Methods Including Static And Dynamic Light Scattering And Analytical Ultracentrifugation 

 

2:00 - 2:30

Data Analysis: Model-Dependent Analysis Of SAS Data

Calculated Scattering Profiles From Atomic Models, Shape Reconstruction, Atomistic Modeling

 

2:30 - 3:15

Tutorial 3: Three-Dimensional Modeling From SAS Data

 

3:15 - 3:30

Coffee Break

 

3:30 - 4:30

Guest Research Lecture - Thomas Grant, Research Asst. Professor, University Of Buffalo/Hauptman-Woodward Medical Research Institute

 

4:30 - 5:00

SANS And Contrast Variation

 

5:00 - 5:30

Publishing SAS Data

 

5:30

Conclusion

 

 

Students will be expected to bring laptops with the appropriate pre-installed software. Extra laptops will be provided in case of unexpected hardware or software issues on-site, and network connectivity will be provided as part of the course, as some exercises and tutorials will reply on external computer-server resources.  Preloaded portable disks and memory sticks will be provided to help reduce the need for large downloads over conference bandwidth.

 

Registration

 

Everyone

$185

Corporate

$355

 

 





Workshop No.: 5:        Rietveld Refinement And Pair Distribution Function Analyses Of In Situ X-­‐Ray Scattering 

      Data Within GSAS-­‐II


Room:       City Hall Room

 

ORGANIZERS

 

 

Olaf J. Borkiewicz

Argonne National Laboratory

[email protected]

INSTRUCTORS

 

 

Robert von Dreele

Argonne National Laboratory

[email protected]

 

Brian Toby

 

Argonne National Laboratory

[email protected]

 

Andrey Yakovenko

 

Argonne National Laboratory

[email protected]

 

Kamila Wiaderek

 

Argonne National Laboratory

[email protected]

 

Olaf Borkiewicz

 

Argonne National Laboratory

[email protected]

 

 

This workshop will be a foray into structural analysis of powder X-¬‐ray scattering data - one of the most comprehensive and powerful tools for evaluating crystal structures. The primary goal of this workshop will be to discuss and explain all typical steps involved in structural analysis of X-¬‐ray scattering data with emphasis on data collected at modern users' facilities using large-¬‐area detectors. These will include such aspects of the experiment as measurement calibration, data reduction, peak profile fitting, Rietveld refinement and others.  In addition to "classic" single pattern refinement approach, we will explore strategies for handling large data sets, i.e. sequential refinements and parametric fitting to in situ and operando data. Part of the workshop will be also dedicated to the complementary use of pair distribution function (PDF) analysis, which allow extraction of structural information from amorphous and disordered materials, for which classical crystallographic approaches may not yield satisfactory results.  All tasks pertaining to the workshop will be accomplished within General Structure Analysis System (GSAS-¬‐II). GSAS-¬‐ II is a powerful open-¬‐source Python-based tool that addresses all types of crystallographic studies and handles all standard activities involved in the reduction and analysis of data acquired with both X-ray and neutron probes. This will be an excellent opportunity to learn how to take full advantage of this powerful software directly from the program authors, Robert Von Dreele and Brian Toby, and how to apply this knowledge to real-world applications and experimental data sets presented by beamline scientists, Kamila Wiaderek, Andrey Yakovenko and Olaf Borkiewicz, Advanced Photon Source, Argonne   National Laboratory.

 

Time

Instructor/Topic

 

8:30 - 8:45

 

Introduction Into Powder Diffraction In Situ Experiments

 

8:45 - 9:40

Integration Of 2D PXRD Data And Review Of Counter Plots

 

9:40 - 9:50

Coffee Break

 

9:50 - 10:30

Le Bail Refinement Of Single Powder Patterns

 

10:30 - 11:30

Rietveld Refinement Of Single Powder Pattern

 

11:30 - 1:00

Lunch

 

1:00 - 1:15

Introduction To The Strategy Of Sequential Refinement

 

1:15 - 2:15

Sequential Rietveld Refinement And Analyze Of The Results

 

2:15 - 2:30

Coffee Break

 

2:30 - 3:15

Introduction To PDF Analysis

 

3:15 - 5:00

Extraction And Analysis Of The PDF Data

 

 

GSAS-­‐II is available for free for Windows, Mac and Linux. The quickest and easiest way to install GSAS-­ II on your machine is via the Single Step method using files available for download as follows:

 

 

All materials related to the workshop (lectures, data, instructions, etc.), including a copy of the software will be distributed to the participants at the start of the workshop in digital form on a flash drive.

 

Registration

Before 5/31

After 5/31

Student/Post-Doc

$65

$80

All Others

$95

$115