Crystallographic resources

Crystallographic software list

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Jalview Multiple alignment editor
JaMM The JaMM 2.1 applet gives the user several options for examining the molecular structure. It contains three principal screen elements:a model-rendering area (the heart of JaMM), a control bar (to select drawing modes and options) and a scrollable output area.
Jana2000 Crystallographic computing system for standard, modulated and composite structures.
Jap3D Rendering electron density data into three-dimensional isosurfaces. Electron density data have to be provided in a simple ASCII format or in binary format.
Jas Image contrast enhancement using extended adaptive histogram equalisation. INTEREST AREAS: * General image processing algorithms * Biomedical image processing, image display, radiography * Photography, image manipulation, and recreation
Java Lattice Tool Interactive macromolecular graphics
Java Stereograms Java Stereograms plots stereographic projections of poles onto a Wulff net. The pole distribution is determined by the given unit cell parameters. It is possible to give restraints to the number of generated poles by editing the values for the "maximum order" (maximum value of an index hkl) and the range of interplanar spacings "d" (dmin-dmax). For indexing the poles in the stereographic hemisphere simply click at them. The angles Rho and Phi corespond to rotations of the whole set on the Wulff net (always from zero position).
Jcrystal a computer program for creating, editing, displaying and deploying crystal shapes.
JECP/ED Simulation of selected-area and precession electron diffraction patterns
J-ICE A new interface for Jmol has been developed, called J-ICE, for handling and visualizing crystallographic and electronic properties entirely via a web server, i.e. without the burden of installing complex packages. J-ICE can also be employed as an import/export tool, to transform universal CIF or Protein Data Bank structure files (from experiment or previous calculations) into an input format compatible with programs such as CRYSTAL09, CASTEP, QUANTUM ESPRESSO and VASP.
Jitax77 Conversion of CCD frame data from TIFF format to Photonic Science FLF format.
Jmol Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. The JmolApplet is a web browser applet that can be integrated into web pages. The Jmol application is a standalone Java application that runs on the desktop. The JmolViewer is a development tool kit that can be integrated into other Java applications.
JoinMap Software package for the construction of genetic
JSV Version 1.07. Structure Viewer. Accepts input data for asymmetric unit cell, full unit cell or cartesian coordinates for all spacegroup symmetries. Measuring distances and angles, periodic table for radius and atom color settings. Output PostSript, VRML, GIF JPG. Includes also X-ray intensity calculations and a special reciprocal space viewer for viewing 3D/2D diffraction patterns. Real time rotations are possible for 3D mode, precession mode and Laue mode. Furthermore it includes an improved version of STEREOGRAM software. The Wulff net may be zoomed and dragged. Besides poles (hkl) it can plot zone axes [uvw] and produce PostScript output. Needs the java interpreter JDK1.2 ( to run it.