Skip to main content
U.S. flag

An official website of the United States government

Here’s how you know

Official government website icon

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

icon-https

Secure .gov websites use HTTPS
A lock ( Lock Locked padlock icon )or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

NIH: National Institute of Diabetes and Digestive and Kidney Diseases NIH: National Institute of Diabetes and Digestive and Kidney Diseases

  next up previous contents index  Xplor-NIH home Documentation

Next: Positional Refinement Up: XPLOR Interface Manual Previous: Wilson Plot


Crystallographic Refinement

The following examples show how to carry out various types of crystallographic refinement. They include positional refinement as well as several types of B-factor and occupancy refinements.

For general review of refinement techniques, the reader is referred to Stout and Jensen (1989) and Hendrickson (1985). For more information about simulated annealing refinement, the following articles are suggested: Brünger (1988), Brünger (1991a), Brünger (1991b), Brünger, Karplus, and Petsko (1989), Brünger, Krukowski, and Erickson (1990), Brünger, Kuriyan, and Karplus (1987), and Weis et al. (1990).

Figure 14.1 provides an overview of the crystallographic refinement features in X-PLOR. The boxes enclosed in black lines indicate external input (diffraction data, initial atomic model) or manipulations using “FRODO," “O," or other crystallographic modeling packages.

Figure 14.1: Overview of crystallographic refinement.
\begin{figure}{\epsfxsize =300pt
\noindent\epsffile{xref.eps}
}\end{figure}

To generate the molecular structure, see Section 3.7. The following parameter and topology files are particularly useful for crystallographic refinement of proteins: “tophcsdx.pro" and “parhcsdx.pro" (Section 3.6). If after inspection of the model and electron density maps new atoms have to be added to the model, the molecular structure has to be appended or recreated.



Subsections
  • Positional Refinement
    • Check of Data and Initial Structure and Determination of Weights
    • Conventional Positional Refinement
    • Crystallographic Refinement by Simulated Annealing
    • Rigid-Body Refinement

  • Overall B-Factor Refinement
    • Syntax
    • Requirements
    • Example: Refinement of Overall Anisotropic B-Factors

  • Grouped B-Factor and Occupancy Refinement
    • Syntax
    • Requirements
    • Example

  • Individual B-Factor Refinement
    • Syntax
    • Requirements
    • Example

  • Analysis of Refined Structures

next up previous contents index
Next: Positional Refinement Up: XPLOR Interface Manual Previous: Wilson Plot   Contents   Index
Xplor-NIH 2025-03-21
  • Privacy Policy
  • Freedom of Information Act
  • Accessibility
  • Disclaimers
  • Copyright
  • Vulnerability Disclosure Policy
  • U.S. Department of Health and Human Services
  • National Institutes of Health