Support

Lecture Series

01 Dec 2016 | Teaching Materials

BioXFEL Lecture Series videos are kept here.

Journal Club Seminars

01 Dec 2016 | Teaching Materials

Videos of all past Journal Clubs 

An Introduction to X-Ray Diffraction Physics

10 Aug 2016 | Teaching Materials | Contributor(s): Blessing

These notes present basic principles of the physics that underlies X-ray analysis of the atomic structure of matter. In particular, classical electromagnetic wave theory of X-ray scattering by electrons and atoms is described as background for subsequent study of X-ray diffraction methods for …

The Structural History of RNA Polymerase Transcription Machinery

18 Feb 2016 | Teaching Materials | Contributor(s): Roger Kornberg

Dr. Roger Kornberg, 2006 Nobel Laureate in Chemistry, discusses the structural history of the RNA polymerase II transcription machinery and how it played a role in his successful career.

Interview with Dilano Saldin

05 Jan 2016 | Teaching Materials

Combining data from new facilities with mathematical methods, Professor Dilano Saldin is in pursuit of a technique to determine the structure of molecules without the need for purification or crystallization.

Multitemperature data and diffuse scattering in X-ray crystallography

07 Dec 2015 | Teaching Materials | Contributor(s): James Fraser

Dr. James Fraser will discuss recent advances in mapping the structural basis of protein conformational dynamics using multitemperature data and diffuse scattering from both conventional synchrotron sources and XFELs.

BioXFEL Graduate Student Cross-Training Scholarship

11 Nov 2015 | Teaching Materials

BioXFEL is committed to providing our students with opportunities to diversify their skill sets and integrate themselves into our highly multidisciplinary Center. In addition to the workshops, conferences and online courses, we will now be offering our students the opportunity to train in another …

BioXFEL Scholar Application Form

10 Nov 2015 | Teaching Materials

…

Serial femtosecond crystallography of soluble proteins in lipidic cubic phase

10 Nov 2015 | Teaching Materials

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL …

Indexing ambiguity in SFX resolved using expectation maximization algorithm

10 Nov 2015 | Teaching Materials

Crystallographic auto-indexing algorithms provide crystal orientations and unit-cell parameters and assign Miller indices based on the geometric relations between the Bragg peaks observed in diffraction patterns. However, if the Bravais symmetry is higher than the space-group symmetry, there will …

Introduction to XRayView Crystallographic Software

04 Nov 2015 | Teaching Materials

Dr. George Phillips introduces the basic concepts of crystallography focusing on the reciprocal lattice and Ewald sphere construction and using the XRayView software developed in his lab to help visualize these concepts.

Overview of Serial Femtosecond Crystallography

14 Oct 2015 | Teaching Materials | Contributor(s): Petra Fromme

Dr. Petra Fromme discusses an introductory overview to the field of serial crystallography and recent results showing the potential power of the technique.

Virus Crystallography

14 Oct 2015 | Teaching Materials | Contributor(s): Robert M Lawrence

Dr. Rob Lawrence describes the unique problems associated with crystallization of virus particles and different methods to overcome them.

When Your Crystals Bite

14 Oct 2015 | Teaching Materials | Contributor(s): George Phillips

Dr. George Phillips describes properties of crystals such as twinning and other defects and how they can adversely affect crystallographic analysis.

Optimizing crystallization hits - small to large and large to small

14 Oct 2015 | Teaching Materials | Contributor(s): Joseph Luft

Joe Luft describes methods for optimizing initial results from crystallization screening trials for both macro and nanocrystals.

Practical Considerations for Crystallographic Data Analysis

14 Oct 2015 | Teaching Materials | Contributor(s): Tom Grant

Dr. Thomas Grant explains how crystal quality affects diffraction data and how you can detect and ameliorate problems in crystallographic data.

Applications of TEM for Evaluation and Optimization of Crystal Growth

14 Oct 2015 | Teaching Materials | Contributor(s): Guillermo Calero

Dr. Guillero Calero discusses using transmission electron microscopy to characterize, evaluate and subsequently optimize the growth of crystals.

What is the outcome of your crystallization experiment

14 Oct 2015 | Teaching Materials | Contributor(s): Joseph Luft

Joe Luft discusses the detection of hits in crystallization screening experiments for both macro and nanocrystals.

Strategies to sample crystallization space

14 Oct 2015 | Teaching Materials | Contributor(s): Joseph Luft

Joe Luft discusses crystallization screening strategies to maximize the likelihood of success.

Fundamentals of Crystal Growth

14 Oct 2015 | Teaching Materials | Contributor(s): Edward Snell, Eaton E Lattman

Dr. Ed Lattman discusses the foundations of crystallography and theoretical and practical considerations including X-ray radiation and production and crystallization nucleation, growth and optimization.

Using XFELs to measure the solution structures of biomolecules

13 Oct 2015 | Teaching Materials

Dr. Lois Pollack presents an introduction to small and wide angle X-ray solution scattering techniques and describes the advances made possible by XFELs.

Single Particle Reconstruction

13 Oct 2015 | Teaching Materials

Dr. Dilano Saldin discusses recent advances in algorithms for single particle reconstruction from solution scattering data at XFELs.

Extraction of fast changes in the structure of a disordered ensemble of photoexcited biomolecules

13 Oct 2015 | Teaching Materials

Using pump-probe experiments of varying time intervals between pump and probe, the method of time-resolved crystallography has given many insights into the fast time variations of crystallized molecules as a result of photoexcitation. We show here that quantities extractable from multiple …

Ab-initio phasing using nanocrystal shape transforms with incomplete unit cells

13 Oct 2015 | Teaching Materials

X-ray free electron lasers are used in measuring diffraction patterns from nanocrystals in the `diffract-before-destroy' mode by outrunning radiation damage. The finite-sized nanocrystals provide an opportunity to recover intensity between Bragg spots by removing the modulating function that …

Post-refinement method for snapshot serial crystallography

13 Oct 2015 | Teaching Materials

A post-refinement procedure has been devised for ‘snapshot’ diffraction data consisting entirely of partially recorded reflections, each diffraction pattern from a crystal in an orientation unrelated to the others. Initial estimates of the diffraction geometry are used to calculate initial …

Mapping the continuous reciprocal space intensity of X-ray serial crystallography

13 Oct 2015 | Teaching Materials

Serial crystallography using X-ray free-electron lasers enables the collection of tens of thousands of measurements from an equal number of individual crystals, each of which can be smaller than 1 µm in size. This manuscript describes an alternative way of handling diffraction data recorded by …

Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser

13 Oct 2015 | Teaching Materials

We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast …

Double-focusing mixing jet for XFEL study of chemical kinetics

13 Oct 2015 | Teaching Materials

Several liquid sample injection methods have been developed to satisfy the requirements for serial femtosecond X-ray nanocrystallography, which enables radiation-damage-free determination of molecular structure at room temperature. Time-resolved nanocrystallography would combine structure analysis …

High-resolution structure of viruses from random diffraction snapshots

13 Oct 2015 | Teaching Materials

The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. Algorithmic means must then be used to determine the snapshot orientations and thence the …

Deducing fast electron density changes in uncrystallized biomolecules

13 Oct 2015 | Teaching Materials

We propose a method for deducing time-resolved structural changes in uncrystallized biomolecules in solution. The method relies on measuring the angular correlations of the intensities, when averaged over a large number of diffraction patterns from randomly oriented biomolecules in solution in a …

Serial femtosecond crystallography of G-protein coupled receptors

13 Oct 2015 | Teaching Materials

G protein–coupled receptors (GPCRs) are eukaryotic membrane proteins that have a central role in cellular communication and have become key drug targets. To overcome the difficulties of growing GPCRs crystals, Liu et al. (p. 1521) used an x-ray free-electron laser to determine a …

Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel

09 Oct 2015 | Teaching Materials

Traditional macroscale protein crystallization is accomplished nontrivially by exploring a range of protein concentrations and buffers in solution until a suitable combination is attained. This methodology is time-consuming and resource-intensive, hindering protein structure determination. Even …

3D Single Particle Structure Recovery

07 Oct 2015 | Teaching Materials | Contributor(s): Ahmad Hosseinizadeh

Dr. Ahmad Hosseinizadeh discuss different pathways to recovering the structure of single particles from XFEL snapshots.

Energy Landscapes

07 Oct 2015 | Teaching Materials | Contributor(s): Ali Dashti

Energy landscapes and continuous conformational mapping of molecular machines.

Manifold Embedding

07 Oct 2015 | Teaching Materials | Contributor(s): Peter Schwander

From single particle snapshots to movies of molecular machines and energy landscapes.

Angular Momentum Decomposition

07 Oct 2015 | Teaching Materials | Contributor(s): Dilano Saldin

Dr. Dilano Saldin discusses using angular momentum decomposition in the analysis of single and multi-particle imaging with XFELs.

SFX Indexing and Integration with CrystFEL

25 Jul 2015 | Teaching Materials

Dr. Thomas White discusses how to index and integrate serial crystallography images using the CrystFEL software package.

SFX Data Reduction and Preprocessing with Cheetah

25 Jul 2015 | Teaching Materials | Contributor(s): Nadia Zatsepin

Dr. Nadia Zatsepin discusses how to use the software program Cheetah to reduce raw SFX data from LCLS to a set of crystal "hits".

Recent Advances in SFX at BioXFEL

25 Jul 2015 | Teaching Materials | Contributor(s): John Spence

Dr. John Spence, Scientific Director for BioXFEL, discusses recent advances in the field of serial crystallography.

2D Crystallography

06 May 2015 | Teaching Materials

Dr. Mattias Frank discusses new possibilities in the field of 2D crystallography made possible by XFEL sources.

Mentoring Manual

14 Apr 2015 | Teaching Materials

This manual was written by the members of the Institute for Broadening Participation and their affiliates. "Each section of this manual is devoted to the perspective and experience of each of the distinct roles in program-based mentoring environments, and organized according to the major …

Structure Validation in Phenix

08 Apr 2015 | Teaching Materials

Paul Adams describes how to use the Phenix crystallographic software package to assess the accuracy of crystallographic models.

Structure Refinement in Phenix

08 Apr 2015 | Teaching Materials

Pavel Afonine describes an introduction to crystallographic structure refinement, structure refinement with Phenix.refine, and real space refinement tools for CryoEM and low resolution X-ray data

Molecular Replacement in Phenix

08 Apr 2015 | Teaching Materials

Paul Adams describes molecular replacement methods to solve the phase problem of crystallography and how to evaluate success in Phenix.  He also describes the latest advances in Phenix molecular replacement methods.

Experimental Phasing

08 Apr 2015 | Teaching Materials

Tom Terwilliger introduces experimental phasing techniques for X-ray crystallography and describes recent developments in SAD phasing using the Phenix software package.

Nanocrystallography

04 Feb 2015 | Teaching Materials

Joe Luft describes the theory and practice behind crystallography and nanocrystallography and discuss recent advances in the production, characterization, and optimization of nanocrystals.

Production and Properties of XFEL Radiation

13 Nov 2014 | Teaching Materials

Dr. Pietro Musumeci (UCLA) discusses an introduction to the physics and characteristics of X-ray free electron lasers.

Crystallographic Methods - Crystallographic Symmetry - Part III

22 Oct 2014 | Teaching Materials | Contributor(s): Edward Snell

Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

Crystallographic Methods - Crystallographic Symmetry - Part II

20 Oct 2014 | Teaching Materials

Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

Crystallographic Methods - Crystallographic Symmetry - Part I

20 Oct 2014 | Teaching Materials | Contributor(s): Edward Snell

Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

Crystallographic Methods - X-ray Diffraction Physics - Part IX

03 Oct 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part VIII

01 Oct 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part VII

28 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part VI

25 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part V

22 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - Geometrical Crystallography - Part I

19 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing Geometrical crystallography     Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5

Crystallographic Methods - X-ray Diffraction Physics - Part IV

18 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part III

15 Sep 2014 | Teaching Materials

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part II

11 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - X-ray Diffraction Physics - Part I

08 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

Crystallographic Methods - Geometrical Crystallography - Part II

04 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing Geometrical crystallography     Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5

Psana Tutorial

03 Sep 2014 | Teaching Materials

Chris O'Grady (SLAC) Psana is the main analysis tool developed by LCLS, upon which some other tools are based. It uses a combination of C++ and python. I will discuss recent psana developments and future plans. Recent developments include the ability to express complex analysis ideas with simple …

Cheetah Tutorial

03 Sep 2014 | Teaching Materials

Anton Barty (CFEL)

CASS and SFX SAD Tutorial

03 Sep 2014 | Teaching Materials

Karol Nass (MPI) Extraction of diffraction images of the lysozyme Gadolinium derivative (Barends et al. Science 2013) from the raw LCLS format to HDF5 format. Integration of CrystFEL analysis with CASS start-up scripts. Ab initio SAD phasing of SFX data.

CrystFEL Tutorial

03 Sep 2014 | Teaching Materials

Tom White (CFEL)

cctbx.xfel Tutorial

03 Sep 2014 | Teaching Materials

Nick Sauter (LBNL) Aaron Brewster (LBNL) Oliver Zeldin (Stanford)

Data Analysis and Sample Delivery

29 Aug 2014 | Teaching Materials

John Spence (ASU/LBNL) How XFEL MX differs from MX and why we do it.

Free Electron Lasers and Crystallography

29 Aug 2014 | Teaching Materials

Paul Adams (LBNL) BioXFEL in the greater context of crystallography

SFX Data Reduction and Preprocessing

29 Aug 2014 | Teaching Materials

Anton Barty (CFEL) Photons, detectors and data streams: how to get at the data and what it records. Data reduction and pre-processing: how it works and how to optimize it.

Rapid Data Quality Feedback and Online Monitoring using CASS

29 Aug 2014 | Teaching Materials

Karol Nass (MPI) Description of the layout of CASS software suite and its functionality on the LCLS online and offline data streams. Real time monitoring of the SFX experiment: hit rate, resolution, pixel saturation, 2D powder pattern. Rapid offline processing of the raw LCLS data: crystal hit …

Introduction to CrystFEL

29 Aug 2014 | Teaching Materials

Tom White (CFEL) CrystFEL is a suite of programs that deal with viewing, indexing, integrating and merging serial crystallography data, evaluating its quality and simulating patterns. At the core of CrystFEL is an automated, high throughput processing pipeline which indexes and integrates each …

How good are my data?

29 Aug 2014 | Teaching Materials

Nick Sauter (LBNL) A design goal of the data reduction package cctbx.xfel is to discover and apply the numerous systematic corrections necessary to correctly model XFEL diffraction images. Numerous challenges must be addressed to interpret serial femtosecond diffraction, including an inaccurate …

Practical considerations during processing of serial crystallographic XFEL data

29 Aug 2014 | Teaching Materials

Aaron Brewster (LBNL) Fundamental differences exist between processing rotational data collected at a synchrotron source and data collected during a serial crystallographic XFEL experiment. Practical techniques will be described to enable the user to get the most out of their data using the …

From cctbx to cctbx.xfel and beyond

29 Aug 2014 | Teaching Materials

Johan Hattne (HHMI) Algorithms to process X-ray diffraction images into accurate atomic models of macromolecules have undergone steady refinement over the past decades. As methods by which crystallographic diffraction patters are obtained are further developed, these techniques continue to provide …

Handling sample heterogeneity in serial crystallography

29 Aug 2014 | Teaching Materials

Oliver Zeldin (Stanford) Serial crystallography data is made up of images obtained from a population of slightly in-homogenous crystals. We will discuss clustering and filtering approaches to (1) characterizing sample heterogeneity in unmerged data, and (2) identifying optimal sub-sets of images …

Winning the Battle of Signal vs. Noise

29 Aug 2014 | Teaching Materials

James Holton (UCSF/LBNL) I will review the major sources of error that contribute to macromolecular crystallography (MX) data with a particular focus on MX data from X-ray Free Electron Lasers. The absolute limits will be defined, and the potential of new and future technologies for overcoming …

Clustering and main sources of variance of SFX data

29 Aug 2014 | Teaching Materials

Wolfgang Brehm (University of Konstanz) Clustering approaches and variance analysis are explained using the example of the indexing ambiguity in serial crystallography. Recently published algorithms for detwinning and advancements thereof will be shown. Variance analysis can lead to a more …

BioXFEL Expert Panel Discussion

29 Aug 2014 | Teaching Materials

Expert Panel Discussion including: Anton Barty, Michael Rossman, James Holton, Tom White, Wolfgang Brehm, Oliver Zeldin, John Spence, Karol Nass, Nick Sauter, Aaron Brewster, Johan Hattne

Crystallographic Methods - Introduction and Overview

25 Aug 2014 | Teaching Materials | Contributor(s): Robert H Blessing

Dr. Bob Blessing Introduction     Protein structural elements: 1° aa sequence,  2° α-helix, β strand, β sheet, loop, 3° domain fold,  4° domain assembly; Overview of biomacromolecular crystallography