The Diamond Light Source Macromolecular Crystallography group would like to invite both our academic and industrial users to MX beamline training sessions on the 15th -16th July 2015.

The aim is to provide MX users with sufficient training to be able to operate any of the Diamond MX beamlines efficiently and to get the most benefit from their beamtime. The training will involve hands-on sessions on the suite of five operational MX beamlines (http://www.diamond.ac.uk/mx-home/) as well as optional offline software sessions.

Sessions include:

15th July, afternoon session and 16th July, morning session on MX beamlines:

• MX software: automation in data analysis
• Mini-Kappa goniometry / Anomalous data collection
• Sample humidity control (HC1) • I24 new end station/ In-situ diffraction
• Fragment screening â€" I04-1/Lab36
• Experiment database: new ISPyB

16th July afternoon optional session Hands on software:

Two tutorial sessions:

• CCP4: structure solution and model building with CCP4 (CCP4 team)
• Manual processing with iMosflm (Harry Powell)

The Center for Computational Biology & Bioinformatics at The University of Texas at Austin is proud to host the 2nd annual Summer School for Big Data in Biology.

The Summer School offers intensive four-day workshops on diverse topics for analysis of large-scale DNA, RNA, and protein datasets. The summer schools provides a unique hands-on opportunity to acquire valuable skills directly from experts in the field, with courses tailored towards novices or intermediate and advance users.

This year we offer 10 workshops. Each workshop will meet for four half-days (either mornings or afternoons) for a total of twelve hours. Instructors will post lectures, datasets, exercises, and course information on a website accessible to enrolled participants. There will be no examinations, but participants may request certificates of completion. Academic credit will not be issued. Please carefully check the specified prerequisite knowledge before enrolling in a course.

The school content:

Software workshop: the workshop will be taught by authors and other experts, including Garib Murshudov (refmac), Victor Lamzin (arp/warp), Robbie Joosten (pdb_redo) and Phil Evans (aimless). It will be organized in three Sections - lectures, tutorials and hands-on trouble-shooting. We will also be covering the use of DIALS for data processing and the new ccp4 interface.

There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions.

Applicants:

Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 25 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets so the problems can be addressed during data collection workshop and/or hands-on sessions.

Application:

Application deadline is 22 August. Application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/OIST-2015

Fees:

There is no fee for the workshop. The students will be responsible for their transportation costs outside Okinawa. Lodging will be provided at the OIST Guest House "Seaside House". The workshop will also cover the expenses for all meals and refreshments.

The workshop will be held the day prior to the ACA conference

 *Workshop format:*

The workshop will start with an introductory seminar, followed by most of
the day dedicated to detailed, hands-on tutorials with data sets collected
at LCLS using the software suites Cheetah and CrystFEL, two of the most
commonly used packages for SFX analysis.Â

*Target audience:*

This workshop is intended for graduate students, postdocs and young
scientists interested in the details of serial femtosecond crystallography
data analysis. It is not intended as an introduction to crystallography.
Participants will be assumed to have at least a basic knowledge of
conventional crystallographic data analysis, as we will focus on the
specific features of SFX analysis. Participants will also be expected to
have familiarity with Unix commands. Practice data (from cxidb.org <
http://cxidb.org > ) will be available, and participants are welcome to
bring their own SFX data.

Computing resources and temporary data storage space will be provided by
LCLS, SLAC National Accelerator Laboratory. Students will be sent detailed
information prior to the workshop to ensure they have an active Unix
account at SLAC, and should bring laptops with appropriate software
preinstalled.

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The BioXFEL National Science Foundation Science and Technology Center is pleased to announce that it will be hosting its third annual international conference in San Juan, Puerto Rico January 13th - 15th, 2016. Â This segment of the series will focus on biological methods and exciting results from X-ray free electron laser sources as well as half a day on the interplay between synchrotron based studies and XFEL applications. #BioXFEL3
Conference Co-Chairs: Dr Edward Snell (HWI) and Dr George Phillips (Rice)

Confirmed Speakers

• Andrew Aquila (SLAC)
• Guillermo Calero (U. Pittsburgh)Â
• Marco Cammarata (U. Rennes)Â
• Henry Chapman (DESY)
• Vadim Cherezov (USC)
• Aina Cohen (SSRL)
• Jeffrey Donatelli (LBL)
• Cathy Drennan (MIT)
• Robert Fischetti (Argonne)
• Petra Fromme (ASU)
• Klaus Giewekemeyer (European XFEL)
• Helen  Ginn (Oxford)
• Heinz Graafsma (DESY)Â
• Arjen Jakobi (EMBL)
• Jan Kern (LBL)
• Rick Kirian (ASU)
• Haiguang Liu (Beijing CSRC)
• Osamu Miyashita (RIKEN)
• Henrike Mueller-Werkmeister (U. Toronto)
• Abbas Ourmazd (UWM)
• Ilme Schlichting (MPI)
• Robert Schoenlein (SLAC)
• Joerg Standfuss (PSI)
• Martin Weik (IBS)
• Rahel Woldeyes (UCSF)

ECM29 satellite meeting organised by Diamond Light Source & Croatian Association of Crystallographers

Accurate calibration and reduction of two dimensional powder X-ray diffraction patterns is crucial to obtain high-quality data for subsequent analysis. The DAWN data analysis platform (www.dawnsci.org) has recently added two new tools to address these issues, which allow simple, rapid and accurate processing of large amounts of data. In this workshop, participants will first learn about the theoretical treatment of the raw data and then see how this is applied through tutorials using the new powder calibration tool within DAWN. They will then gain hands-on experience preparing and using data analysis pipelines to streamline data reduction of large and/or complicated data sets. We will demonstrate the use of these tools in the context of different and demanding experiment types, from in situ crystallisation through to extreme-conditions. As this workshop will provide a very hands-on introduction to the DAWN data analysis package, we recommend that participants bring their own laptops. DAWN can be freely downloaded in advance of the workshop from our website, but we will also be distributing the most up-to-date version of the software on the day. We welcome participants bringing their own data so that they can see how the DAWN package can be applied to their own work, but we would ask that they contact the organisers in advance.

Introduction to the theoretical background of the Rietveld method and principles of crystal structure refinement from powder diffraction data.

This six day long school aims to introduce participants to the way the information about crystal structure and sample microstructure is contained in X-ray powder diffraction patterns and how to get use of it.

The school provides a set of lectures, devoted to the main aspects of crystal structure description and fundamentals of powder diffraction. Main concepts, that Rietveld structure refinement is based on, will be covered as well.

Practical sessions are designed to initiate and promote basic skills for working with powder diffraction data and respective data treatment software. Tutors will be on disposal to help participants in the course of training.

This six day long school aims to introduce participants to the way the information about crystal structure and sample microstructure is contained in X-ray powder diffraction patterns and how to get use of it.
The school provides a set of lectures, devoted to the main aspects of crystal structure description and fundamentals of powder diffraction. Main concepts, that Rietveld structure refinement is based on, will be covered as well.
Practical sessions are designed to initiate and promote basic skills for working with powder diffraction data and respective data treatment software. Tutors will be on disposal to help participants in the course of training.

Workshop of the Cambridge Crystallographic Data Centre (CCDC) in connection with the working group 1Molekülverbindungen' of the German Crystallographic Society â€" DGK. Organisation: Dr. Steven Maginn (CCDC, Cambridge) and Prof. Dr. Martin U. Schmidt (Goethe University, Frankfurt).

The Cambridge Structural Database (CSD) and its accompanying software for search and analysis (ConQuest, Mercury, IsoStar and Mogul) - together known as the CSD System (CSDS) - is a fundamental resource in structural chemistry, finding applications in academia and in industry across a broad range of topics such as drug design and discovery, drug development and formulation, and materials science.

The workshop will provide information about the CSD itself, its content and its production. The CSDS software will be described, and a number of hands-on examples of the use of the CSDS to address real problems of both industrial and academic importance will be followed. These will include:

"Discovery Chemistry"

• Finding similar molecules to known actives
• Understanding factors affecting molecular conformation
• Searching for new medicinal chemistry ideas using structural information on known active molecules
• Checking the reported structures of ligands in protein-ligand crystal structures against observed conformations in the CSD

"Materials Chemistry"

• Looking for similar crystal packing motifs
• Calculating the propensity of a molecule to form multiple accessible polymorphs
• Looking for suitable co-crystallisation partner molecules
• Inspecting the interactions present in a crystal structure and comparing them with those formed by the molecule's constituent functional groups in the CSD, as a guide to polymorphic relative stability
• Inspecting the preferred interactions at a crystal surface as a guide to the design of habit modifiers.

The CSDS is constantly developing to ensure the widest possible use and application of crystallographic knowledge. New ways of accessing this information are being made available, such as API access to CSDS functionality, web services and web applications. These new ways of including crystallographic information in solutions will be described, discussed and demonstrated in the workshop.

With special topic: Phenix

The Canadian Macromolecular Crystallography Facility (CMCF) is pleased to announce an intensive 5-day hands-on synchrotron data collection school at the Canadian Light Source. Participants will attend a series of lectures and be actively engaged in macromolecular crystallography (Mx) data collection at CMCF beamlines. Completing the school will enable participants to make effective use of the beamlines remotely and will better equip participants to collect diffraction data on-site. This year's invited speaker is Dr. Paul Adams from the Lawrence Berkeley Laboratory. He will guide participants through an in-depth look at using Phenix during structure solution. Participants should have a basic grounding in crystallography prior to attending the course. Given enough interest, an optional introductory review will be offered on Monday, June 1.

Molecular Simulation for the Interpretation of NMR Data

Mantid Training Courses Feb 2015

Following the success of our previous sessions of these training courses we would like to offer them again in February 2015. These courses are open to both facility staff and any interested people from other institutions.
The following courses will be based at ISIS, RAL and are:
Monday 16th February 1-5pm: Mantid Introduction An introduction to the Mantid interface, how to graph and visualize your data, manipulate it with the built in algorithms, together with an introduction to curve fitting and live data analysis.
Tuesday 17th February 9-12am: Introduction to Python This half day course will introduce you to the Python scripting language, no previous experience required, although some understanding of loops and conditional if statements will be expected.
Tuesday 17th February 1-5pm: Python in Mantid This course concentrates on using Python to build analysis scripts within Mantid as well as controlling the Mantid GUI from python, and accessing the underlying data within Mantid workspaces.
Wednesday 18th February 9-5pm: Extending Mantid using Python For the more adventurous among you this course will introduce you to the many ways you can use Python to extend the capabilities within Mantid adding Python Algorithms and curve fitting functions, as well as diving deeper into the structure of workspaces. After the feedback from the previous run this course has been extended to a full day course, together with adding more material.
Booking a place If you are interested in any other these courses please send an email to [email protected] letting me know which ones you wish to attend. For the courses we will supply PCs, so there is no need to bring a laptop unless you really want to. Spaces are limited to 13 people per course so please book early to avoid disappointment. If a course is over booked we will try to arrange another session in the future, so if you cannot make that specific date let me know and I’ll let you know about any subsequent courses. I’ll send out calendar appointments to you once your place on the course is booked.
For visitors from UK academic institutions: Are sometimes able to offer assistance with travel and lodging costs while attending the courses. Let me know when you are booking the courses and I’ll get back to you with details. If we are able to help, then you travel and hotel must be booked through the ISIS user office.
For visitors from elsewhere: While we can offer this course for free, we cannot unfortunately offer any help with travel or subsistence costs. However please let me know that you will be visiting when you reply so that I can arrange site access.

Workshop Outline
Powder pattern Indexing and Rietveld structural refinement techniques are complementary and are often used to completely describe the structure of a material. Successful indexing of a powder pattern is considered strong evidence for phase purity. Indexing (with derived space group and lattice symmetry determinations) is considered a prelude to determining the crystal structure, and permits phase identification by lattice matching techniques. The Rietveld method is used to refine crystal structures and is perhaps best considered whole- pattern-fitting structure refinement, i.e., we must account not only for the crystal structure but also the instrumental resolution and diffraction physics effects (e.g., crystallite size and strain). The aim is to perform quantitative phase analysis and identification.

This workshop introduces the theory and formalisms of various indexing methods and structural refinement techniques. One unique aspect of this workshop is the extensive use of computer laboratory problem solving and exercises that teach method development in a hands-on environment.

We will use EXPGUI and GSAS for the Rietveld laboratory work; Crysfire (especially Dicvol, Ito and Treor) will be used for indexing exercises.

Lecture Components
Basic Crystallography

• Emphasis on space groups, conventions, etc.

Powder Pattern Indexing

• Data reduction methods for peak finding
• We will use Dicvol 04, Treor and Ito indexing examples
• Crysfire will also be discussed

Rietveld Structural Refinement

• History and motivation for development of this technique
• Qualitative description of various sample and instrument-related functions for profile shape, background, etc.
• The use of least-squares constraints will be explored

LeBail and Pawley Fitting Procedures

• What to do when atomic coordinates are not available
• Discussion on use of these tools for structure determination
• Use in powder pattern indexing
  

Computer Laboratory Components
Exercise problems will include:

• Single phase indexing
• Single phase refinement (all crystalline materials)
• Multiphase refinement (all crystalline materials)
• Nanophase, and small crystallite size content
• Amorphous phase + crystalline phase(s)

Take the three-day basic workshop, the two-day advanced workshop or both together for a full week of hands-on training. Â The ICDD basic Rietveld workshop is a pre-requisite for attending the advanced workshop. Â A basic understanding of crystallography is also required.

Workshop Outline
Powder pattern Indexing and Rietveld structural refinement techniques are complementary and are often used to completely describe the structure of a material. Successful indexing of a powder pattern is considered strong evidence for phase purity. Indexing (with derived space group and lattice symmetry determinations) is considered a prelude to determining the crystal structure, and permits phase identification by lattice matching techniques. The Rietveld method is used to refine crystal structures and is perhaps best considered whole- pattern-fitting structure refinement, i.e., we must account not only for the crystal structure but also the instrumental resolution and diffraction physics effects (e.g., crystallite size and strain). The aim is to perform quantitative phase analysis and identification.

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Lecture Components
Basic Crystallography

• Emphasis on space groups, conventions, etc.

Powder Pattern Indexing

• Data reduction methods for peak finding
• We will use Dicvol 04, Treor and Ito indexing examples
• Crysfire will also be discussed

Rietveld Structural Refinement

• History and motivation for development of this technique
• Qualitative description of various sample and instrument-related functions for profile shape, background, etc.
• The use of least-squares constraints will be explored

LeBail and Pawley Fitting Procedures

• What to do when atomic coordinates are not available
• Discussion on use of these tools for structure determination
• Use in powder pattern indexing
  

Computer Laboratory Components
Exercise problems will include:

• Single phase indexing
• Single phase refinement (all crystalline materials)
• Multiphase refinement (all crystalline materials)
• Nanophase, and small crystallite size content
• Amorphous phase + crystalline phase(s)

Session II - Advanced Methods in X-ray Powder Diffraction

• Brief review of fundamentals
• Factors affecting accuracy of measured 2theta values: intensity aberrations, specimen displacement, specimen transparency, diffractometer alignment, and the use of external and internal standards
• Factors affecting intensities of diffraction peaks: structure-sensitive properties, specimen-sensitive effects, and measurement-sensitive effects
• Use of computer methods for data reduction and qualitative phase identification: peak-hunting methods, alpha2 stripping, search/match techniques and the Powder Diffraction File™, use of elemental data, error windows and probability searching, and scoring algorithms
• Advanced data mining with the PDF
• Exploration of powder pattern indexing methods
• Quantitative analysis: specimen preparation considerations, Reference Intensity Ratios, absorption correction methods, matrix-flushing methods, and whole-pattern analysis using the Rietveld method
• Structure solution and refinement using the Rietveld method

Lectures

• Fundamentals of X-ray Physics
• WDX and EDX X-ray spectrometry instrumentation
• Qualitative and semi-quantitative analysis
• Introduction to quantitative analysis
• Types and sources of error
• Precision and accuracy
• Calibration strategy
• Drift, line and interelement correction application
• Fundamental parameters
• Maintaining instrument integrity
• Specimen preparation
• Submit YOUR SAMPLES for analysis by the experts. Selected results will be the basis for class discussion. Results not presented during class can be discussed in private with the faculty throughout the clinic.

Workshops:

• XRF instrumentation, components, scope, and comparison using live and disabled WDX and EDX instrumentation.
• Selection of parameters for operation
• Demonstration of personal computer exercises in qualitative and semi-quantitative WDX and EDX analysis
• Demonstration of personal computer exercises employing polynomial regression, line overlap, empirical and fundamental parameter corrections during calibration
• Specimen preparation lecture and demonstration of the use of mixers, grinders, presses, fusion apparatus, etcetera
• Discussion of problems encountered by participants

The CSSB Spring School will provide an introduction to advanced biophysical approaches for Structural Systems Biology.Â

• Courses in sample preparation and analysis, advanced microscopy, single particle analysis, structure determination at atomic resolution and modeling of structure and dynamic of complexes.
• It will allow young researchers (experienced students, PhD students and postdocs) to view challenging problems from interdisciplinary scientific topics like Infection Biology from various methodical angles. Â

The material will be presented in form of lectures, demonstrations and practical work.

The aim of the School is to bring together experts and young scientists interested in exploiting the anomalous signal from light atoms (e.g. S, P, Ca, K, Mg) native to the protein or crystal for macromolecular structure determination using soft (wavelengths > 1.5Ã...) X-rays in order to help train the next generation of scientists in this maturing field. The 5th Winter School on Soft X-rays in Macromolecular Crystallography is a continuation of similar workshops held in Europe since 2003 as indicated:

1st Winter School:Â Bressanone/Brixen, Italy; Feb. 25-27, 2003

2nd Winter School: Seefeld, Austria; March 22-25, 2006

3rd Winter School:Â Berlin, Germany; February 18-20, 2009

4th Winter School:Â Grenoble, France, February 6-8, 2012

Topics Covered

SAD Theory & Historical Perspectives These lectures will address the theoretical aspects of overcoming the phase problem in using SAD and S-SAD data and highlight the historical perspectives of two initial de novo structures solved by S-SAD.

Source/Beamline Considerations These lectures and Case Studies will cover the optimization of the experiment setup in terms of the hardware, choice of wavelength and other source specific parameters.

Data Collection Strategies This lecture will cover techniques and problems associated with collecting sulfur-SAD data including crystal centering, data collection setup and methods used to increase the anomalous scattering signal to noise ratio in the data. The lecture will highlight common areas where problems can occur and suggest how best to eliminate them.

Data Reduction Theory and Strategies These lectures and Case Studies will focus on the data reduction process (indexing, integration and scaling) using several popular data reduction programs as examples, highlighting critical program input parameters and program output. The lecture will highlight common areas where problems can occur and suggest how best to eliminate them. New methods such as Multi-Crystal and Single Crystal Multi-dataset averaging will be described.

Anomalous Substructure Determination & Phasing This lecture and Case Study will describe the use of SHELXCDE [9] and HKL2MAP to determine the anomalous scattering substructure, the correct handedness of the anomalous scattering substructure, the generation of initial protein phases and interpreting the quality of the resulting electron density map.

The course will be organised by Lari Lehtiö, Kristian Koski, Tiila Kiema, Ari-Pekka Kvist and Rik WierengaÂ

The course is supported by Biostruct-X, Biocenter Oulu, and the University of Oulu

There will be an international X-ray course at the Faculty of Biochemistry and Molecular Medicine of the University of Oulu, Oulu, Finland. The course will focus on data collection and data processing using iMOSFLM and XDS, to be complemented by lectures and tutorials on experimental phasing (SHELX) and molecular replacement phasing (CCP4). In addition there will be lectures on new techniques (XFEL diffraction and neutron crystallography). On the last day of the course there will be a remote data collection demonstration at Diamond Light Source, Oxford. The outline of the course follows the previous format, aiming for approximately 16-20 students, who will be provided with a computer in our linux class room. Data collection from own crystals will be possible using our in-house Bruker microfocus X-ray generator or remotely at Diamond.

Current approximate outline:

Monday, May 18:
Basic concepts of biomolecular crystallography, by Bernhard Rupp (USA)
Emerging techniques: XFEL by Janos Hajdu (Uppsala, Sweden): “The basic principles of the XFEL technology and molecular imaging"

Tuesday, May 19/Wednesday, May 20 (data processing):
XDS, Manfred Weiss, BESSY, Berlin, Germany (also XDSapp as available at Bessy)
iMOSFLM, Harry Powell (LMB, Cambridge, UK) Â (also data processing pipelines at Diamond)
Tuesday afternoon lecture by Bernhard Rupp on ligand binding studies

Wednesday, May 20/Thursday, May 21: (experimental and molecular replacement phasing)
Experimental phasing by SHELX, Thomas Schneider (EMBL, Hamburg)
Molecular replacement phasing by CCP4, Andrey Lebedev (CCP4, STFC)
Wednesday afternoon lecture on neutron crystallography by Dr. Zoe Fisher (ESS, Lund)
Thursday afternoon lecture by Thomas Schneider on the X-ray beamlines at EMBL, Hamburg
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Friday, May 22:
Remote data collection at Diamond (Martin Walsh, Diamond)
Crystal sample management and data tracking from crystal to PDB by xtalPiMS (Ed Daniel, Oulu)
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Throughout the course students will have time to work on their own topics in the linux class room and we will also provide the opportunity to collect data with our own equipment. Crystals that should be used for data collection in house or at Diamond should be available for freezing on the first day of the course or should be sent in advance to Oulu.

There will be a registration fee of 350Euro to cover the costs of accommodation and meals. We will try to make available fellowships to cover these costs. When applying to attend this course follow the instructions attached below.  Please provide information on crystals and/or datasets that you would like to send in advance. Indicate also if such a fellowship is needed when being accepted for this course. In case of oversubscription, students with own crystals and / or own data sets will be prioritised.

Please apply by by 10.01.2015

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