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

Links to other tasks

DebiChem Crystallography packages

Official Debian packages with high relevance

Drawxtl
crystal structure viewer
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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)
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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 
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Gcrystal
lightweight crystal structures visualizer
Maintainer: Debichem Team (Adrian Bunk)
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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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Gemmi
library for structural biology - executable
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Library for macromolecular crystallography and structural bioinformatics. For working with coordinate files (mmCIF, PDB, mmJSON), refinement restraints (monomer library), electron density maps (CCP4), and crystallographic reflection data (MTZ, SF-mmCIF). It understands crystallographic symmetries, it knows how to switch between the real and reciprocal space and it can do a few other things.

This package contains main gemmi executable.

Please cite: Wojdyr, Marcin: GEMMI: A library for structural biology. Journal of Open Source Software 7(73):4200 (2022)
Libmmtf-java
Java API for macromolecular transmission format encoder/decoder
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The Macromolecular Transmission Format (MMTF) is a compact binary format to transmit and store biomolecular structures for fast 3D visualization and analysis.

Pdb-tools
tools for manipulating and editing PDB files
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Manipulating PDB files is often painful. Extracting a particular chain or set of residues, renumbering residues, splitting or merging models and chains, or just ensuring the file is conforming to the PDB specifications are examples of tasks that can be done using any decent parsing library or graphical interface. These, however, almost always require 1) scripting knowledge, 2) time, and 3) installing one or more programs.

pdb-tools were designed to be a swiss-knife for the PDB format. They have no external dependencies, besides the Python programming language. They are the descendant of a set of old FORTRAN77 programs that had the particular advantage of working with streams, i.e. the output of one script could be piped into another.

The philosophy of the scripts is simple: one script, one task. If you want to do two things, pipe the scripts together.

This package contains the command line tools.

Please cite: JPGLM Rodrigues, JMC Teixeira, M Trellet and AMJJ Bonvin: pdb-tools: a swiss army knife for molecular structures [version 1; peer review: 2 approved]. F1000Research 7(1961) (2018)
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.

Python3-phonopy
phonon calculations at harmonic and quasi-harmonic levels (Python 3)
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Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels.

This package contains Python 3 module.

Shelxle
graphical user interface for SHELXL
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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)
Xcrysden
Crystalline and Molecular Structure Visualizer
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XCrySDen is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It can run on most UNIX platforms, without any special hardware requirements.

XCrySDen allows for real-time capture of display. Several movie encoders are supported, in particular for Animated-GIF convert (imagemagick), gifsicle, or whirlgif are necessary. For AVI/MPEG mencoder or ppmtompeg (netpbm) is required. For window dumps either imagemagick or xwd (x11-apps) needs to be present.

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