Workshops

WK.01  Symmetry-mode analysis

8:00-8:30            Introduction to symmetry-mode analysis (M. Perez-Mato)

            Oral presentation

                        Distortions and their order parameters (strain, displacive, occupational, magnetic).

                        Symmetry modes are a relative description that depends on the parent structure.

                        Irreps of the parent symmetry and their basis functions.

                        Irrep basis functions  provide a symmetry-motivated basis for distortions.

                        Define distortion symmetry and  isotropy subgroup (single-irrep distortion).

                        Discuss irrep coupling to get more complicated distortions.

8:30-10:00 Exploring structural distortions with ISODISTORT (B. Campbell and H. Stokes)

            Hands-on tutorial with oral presentation

                        Distortion output

                                    Distortion symmetry - specifies space-group type, origin and basis

                                    Visualization tools, CIF, mode details, primary OPs, domains, other

                        Filtered search tools for generating distortion models

                                    Database search - commensurate single-irrep distortions

                                    Search by supercell and space-group type

                                    Search by k-point/irrep/OPD

                        Domains

                        Primary vs secondary order parameters

                        Coupled order-parameters

                        Include an incommensurate example and discuss superspace-symmetry.

10:00-10:30            Coffee break

10:30-12:00            Symmetry mode analysis with AMPLIMODES & FULLPROF (M. Perez-Mato)

            Hands-on tutorial with oral-components

                        Explain how to define mode amplitudes.

                        Work through mode-decomposition examples.

                        Discuss order-parameter evolution near a phase transition and critical exponents.

                        Work through symmetry-mode refinement(s) using Fullprof.

12:00-1:00                        Lunch

1:00-2:30 Symmetry-mode analysis with ISODISTORT & TOPAS (B. Campbell and H. Stokes)

            Hands-on tutorial with oral components

                        Work through mode decomposition examples.

                        Work through symmetry-mode refinement(s) using TOPAS.

                        Discuss how to "solve" a distorted structure on the symmetry-mode basis.

2:30-3:00            Magnetic symmetry (H. Stokes)

            Oral presentation with hands-on component

                        Review magnetic symmetry and nomenclature.

                        Walk users through of the online magnetic-symmetry database.

                        Discuss the relationship between the OG and BNS settings.

                        How to describe a magnetic structure.

                        Discuss the relationship between the OG and BNS settings.

3:00-3:30                        Coffee break

3:30-4:30            Magnetic distortions (M. Perez Mato)

            Hands-on tutorial mixed with oral components

                        Introduce magnetic distortions.

                        Work through several examples using ISODISTORT.

                        Include an incommensurate magnetic distortion.

4:30-5:00            Magnetic symmetry-mode refinement (B. Campbell)

            Hands-on tutorial mixed with oral components

                        Work through a magnetic refinement using TOPAS

                        Many magnetic structures are "solved" now in P1.  Emphasize utility of mag symmetry.

Fees on or after April 1

Students - $185

All others - $215

Organized by Branton J. Campbell,  Brigham Young Univ., Provo, UT

branton_campbell@byu.edu

WK.02 Introduction to PHENIX for beginning to advanced crystallographers

The purpose of the workshop is to train both beginning and advanced crystallographers in the use of the PHENIX software for macromolecular structure determination. The workshop will benefit the crystallographic community by making this software accessible to a broader group of crystallographers, by teaching crystallographers when and how to use the software properly, and by teaching crystallographers how to get the most out of the software and ultimately their data.

The workshop will consist of two overall parts. Through lectures the morning session will introduce PHENIX and the core algorithms that it uses. The afternoon session will be a group hands-on tutorial for beginning and intermediate users concurrent with individual tutorials for advanced users.

The morning session will begin with an overview of PHENIX that introduces what the PHENIX software can do, how it is organized, and how it is used.  Then the core automation in PHENIX will be presented along with the key algorithms used in structure solution by MIR/MAD/SAD, density modification and model-building.   Next the PHENIX refinement system will be described with emphasis on the core algorithms used. Then the extensive validation available during and after structure determination with PHENIX will be described. Finally the attendees will learn how to use the PHENIX GUI to carry out all the methods used in PHENIX.

During the morning break the attendees that do not already have PHENIX will install PHENIX on their computers. This process takes about 5 minutes with Linux or Mac OSX operating systems. For users with Windows machines self-booting DVD's will be provided that contain the Ubuntu operating system and PHENIX pre-installed. These can be used directly to run PHENIX.

In the afternoon there will be three group tutorials. The first will focus on data analysis (twinning, space groups, structure factor statistics) and structure solution (finding an anomalous substructure in a MAD or SAD dataset, or molecular replacement). The second tutorial will focus on automated model-building and ligand fitting. The third will cover refinement and validation. Concurrent with the tutorials, advanced users will have individual tutorials on their own data.

The workshop will be held on Saturday, May 28. Pre-registration is mandatory.  Lunch is included. The fee is separate from the registration fee:

Fees on or before March 31

Students - $120

All others - $150

Fees on or after April 1

Students - $155

All others - $185

Organized by Paul Adams, Lawrence Berkeley Lab, Berkeley, CA

pdadams@lbl.gov)