Structure Determination Schematic

The Structure Determination Process

The flowchart below color codes the three main stages of the structure determination process. A brief description of each part of the process can be obtained by clicking on that particular component on the flow chart. The actions that occur in each stage:

are described in the summaries that follow.



The sequence coded in light orange represents the data reduction/structure solution stage of the structure determination process. At the start, raw diffractometer data is reduced and corrected to produce a data set suitable for crystallographic calculations using data utilities in the diffractometer control or the structure determination software packages. The data are then analyzed by hand or computer (using another data utility) to determine probable space group(s) and set up the initial structure determination parameter file. The initial parameter file, "name.ins", and the reduced data file, "name.hkl", are then input into a structure solution program that calculates possible starting models for the crystal structure that can be further refined in the structure refinement stage.





The sequence coded in red represents the refinement stage of the structure determination process. Here the model developed in the solution stage is developed in full through successive cycles of refinement. In each cycle a model for the structure, given in a "name.ins" file, is input with the X-ray data file, "name.hkl", into a least-squares refinement program. The refinement program tries to adjust the parameters of the model to give the best agreement between X-ray data calculated from the model and the observed X-ray data and then calculates an electron-density difference map that can be used to identify missing atoms or other problems in the structural model. The refined model parameters and difference map peaks are output to a results file, "name.res". This results file is then examined using a graphical display program and or a text editor, improvements to the model are added, a new input "name.ins" file is prepared, and the refinement cycle starts anew.





Once all available improvements to the model have been made and the refinement has converged, i.e. structure parameters now vary only slightly between succesive refinement cycles, the structure determination is complete. At this point three different types of files are output and these are coded in tan on the flowchart.

  1. The structure factor tables (Fo, Fc Tables) contain the X-ray data, are required for review of your manuscript and are frequently included as supplementary material upon publication.
  2. Select information, such as atomic positions, bond lengths and angles, from the data collection/structure determination parameter tables is published in a journal article while the full tables are reproduced in the supplementary material.
  3. Most journals require at least one thermal ellipsoid plot of the structure for the main paper with other plots provided if essential for demonstrating a point. These structure plots can be prepared using the graphical software used in the structure refinement stage.



The components enclosed in the aqua colored box are the heart of the structure determination process and the comuter programs included in the box represent the very miniumum needed to put together an effective crystallography software package.





Go to top of page

Go to clickable structure determination flowchart

Go to Structure Determination Software Page

Go to Main Page

Last modified December 18, 1996