Oviedo 2011 Tutorials

Modeling crystallographic data

David Watkin

Over & under parametrisation, data completeness, data extent etc, Anscombe's Quartet

Optional: CRYSTALS (internals and/or externals)

Working with the Computational Crystallography Toolbox (cctbx)

Ralf Grosse-Kunstleve

cctbx is a large open source library of fundamental crystallographic tools, in particular for the handling of unit cells and space groups, but also many file formats. Two prepared tutorials are available: refinement of unit cell parameters given Miller indices and associated 2-theta values; simple direct methods. However, students are encouraged to suggest tasks that we will try to solve interactively. Basic knowledge of the Python language is very important. (C++ knowledge is helpful but not essential.)

[Tutorial time table] [Talks]

Olex2, user-level and internals

Horst Puschmann

[Tutorial time table] [Talks]

Direct methods applied to small molecules

Gianluca Cascarano

[Tutorial time table] [Talks]

Application of the Patterson-function direct methods program "XLENS_PD6" to powder diffraction data

Jordi Rius

Application of the program to powder data of some inorganic and hybrid compounds (test examples).

Application of the Patterson-function direct methods program "XLENS_PD6" to powder diffraction data (II)

Discussion on the application of direct methods to powder diffraction data sent by students. Each student can provide a powder diffraction pattern (XY format) together with the unit cell parameters and the estimated chemical composition. The patterns must extend to an upper 2-theta value equivalent to a d-spacing of 1.15-1.10 Angstroms. These data sets will be used for a second tutorial on the application of direct methods to powder diffraction.

[Tutorial time table] [Talks]

Data processing for serial crystallography

Thomas White

[Tutorial time table] [Talks]

Real-space structure determination

Vincent Favre-Nicolin

Real-space structure determination: simulated annealing, differential evolution, small-molecule manipulation

[Tutorial time table] [Talks]

Understanding density modification

Tom Terwilliger

The tutorial will be a presentation and discussion about the principles of density modification in macromolecular crystallography with examples of the kinds of information that can be used.

[Tutorial time table] [Talks]

Understanding PSEUDO : How to detect pseudosymmetries

Emre Tasci

PSEUDO of the Bilbao Crystallographic Server, is a program aimed at finding pseudosymmetries for a given structure by exploring the (minimal) supergroups of the structure's space group. The process includes the usage of a database to retrieve supergroups and corresponding transformation matrixes; Wyckoff splitting compatibility check; the application of the coset representatives of the supergroup with respect to the subgroup and the consideration of the difference between the idealized and the actual structures' atomic positions.

[Tutorial time table] [Talks]

R/RPy for crystallographic applications

Rita Giordano

Description: Statistical model applied to crystallography using R/RPy. Basic and advance method to analyse crystallographic data. RPy is an integration of R with the python language.

[Tutorial time table] [Talks]

Bayesian methods in small-molecule crystallography

Anthony Phillips

[Tutorial time table] [Talks]

Recognizing and processing data from twinned crystals

Andrea Thorn

In this tutorial, different types of twinning and their recognition will be explained for both small and macro-molecules, as well as the most common twinning tests. Algorithms for data processing will be covered with an emphasis on non-merohedral twins.

[Tutorial time table] [Talks]

Querying and depositing data to the Crystallography Open Database (COD) -- new Web based and command line interfaces

Saulius Grazulis

Topcis:

use of Web interface to perform simple queries on COD
use of Web interface to deposit new structures into COD
use of various protocols (http GET, svn, rsync, mysql) and command line tools to query and access COD
using command line (curl) to POST new data to COD

[Tutorial time table] [Talks]

MolecoolQt and InvariomTool - aspherical atom modeling of organic molecules from normal resolution data

Birger Dittrich and Christian Bertram Hübschle

Often the highest peak from a Fo-Fc map from good diffraction data appear in between covalently bonded atoms. It is such bonding and lone-pair valence electron density that we try to include in the scattering factor, i.e. our model electron density. For that purpose we have generated a database of scattering factors that we call invarioms (from invariant atoms, atoms that are invariant in a transfer from one molecule to another). The invariom database covers quite a fraction of organic chemistry, including proteins, DNA and many ligands. Using the database is made (more) easy with InvariomTool and MolecoolQt. These programs currently require the commercial program package XD, to which the two tools are interfaced. Usage of the two programs is explained on an example structure.

[Tutorial time table] [Talks]