DebiChem Project
Summary
Crystallography
DebiChem crystallography

This metapackage will install packages for crystallography which might be useful for chemists.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for DebiChem to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the DebiChem mailing list

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DebiChem Crystallography packages

Official Debian packages with high relevance

Drawxtl
crystal structure viewer
Maintainer: Debichem Team
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DRAWxtl reads a basic description of the crystal structure, which includes unit-cell parameters, space group, atomic coordinates, thermal parameters or a Fourier map, and outputs a geometry object that contains polyhedra, planes, lone-pair cones, spheres or ellipsoids, bonds, iso-surface Fourier contours and the unit-cell boundary.

Four forms of graphics are produced:

  • an OpenGL window for immediate viewing
  • the Persistence of Vision Ray Tracer (POV-RAY) scene language for publication-quality drawings
  • the Virtual Reality Modeling Language (VRML) for dissemination across the Internet
  • a Postscript rendering of the OpenGL window for those who want high-quality output but do not have POV-RAY installed.

File formats DRAWxtl can read include CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS and WIEN2k.

Please cite: Larry W. Finger, Martin Kroeker and Brian H. Toby: DRAWxtl, an open-source computer program to produce crystal-structure drawings. (eprint) J. Appl. Cryst. 40:188-192 (2007)
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Gamgi
General Atomistic Modelling Graphic Interface (GAMGI)
Maintainer: Debichem Team
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The General Atomistic Modelling Graphic Interface (GAMGI) provides a graphical interface to build, view and analyze atomic structures. The program is aimed at the scientific community and provides a graphical interface to study atomic structures and to prepare images for presentations, and for teaching the atomic structure of matter.

The package is enhanced by the following packages: gamgi-data gamgi-doc
Registry entries: SciCrunch  OMICtools 
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Gcrystal
lightweight crystal structures visualizer
Maintainer: Debichem Team
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GNOME Crystal is a light model visualizer for crystal-structures. It is based on the GNOME Chemistry Utils and should display models of all sorts of crystal microscopic structures using OpenGL.

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Python3-fabio
I/O library for images produced by 2D X-ray detector - Python3
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FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a Python dictionary) and datasets (as a numpy ndarray of integers or floats)

This is the Python 3 version of the package.

Shelxle
graphical user interface for SHELXL
Maintainer: Debichem Team
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ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps.

https://dx.doi.org/10.1107/S0021889811043202

Please cite: Christian B. Hübschle, George M. Sheldrick and Birger Dittrich: ShelXle: a Qt graphical user interface for SHELXL. (eprint) J. Appl. Cryst. 44(6):1281-1284 (2011)
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Xcrysden
visualizador de estrutura molecular e cristalina
Maintainer: Debichem Team
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XCrySDen é um programa de visualização de estrutura molecular e cristalina que tem o objetivo de exibir isosuperfícies e contornos, que podem ser sobrepostos em estruturas cristalinas e interativamente rotacionadas e manipuladas. Ele pode ser executado na maioria das plataformas UNIX sem quaisquer requisitos especiais de hardware.

XCrySDen permite a captura em tempo real de exibição. Vários codificadores de filme são suportados, em particular são necessários para conversão de GIF animado (imagemagick), gifsicle ou whirlgif. É necessário para AVI/MPEG mencoder ou ppmtompeg (netpbm). Precisa estar presente para a janela de *dumps", imagemagick ou xwd (x11-apps).

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