DebiChem Crystallography packages

DRAWxtl читает базовое описание кристаллической структуры, которое включает в себя параметры элементарной ячейки, пространственную группу симметрии, координаты атомов, тепловые характеристики или карту Фурье, и выводит геометрический объект, содержащий многоугольники, плоскости, конусы неподелённых пар электронов, сферы или эллипсоиды, связи, изоповерхностные контуры Фурье и границы элементарной ячейки.

Четыре вида графического представления данных:

• в окне OpenGL для немедленного просмотра;
• на языке описания сцен трассировщика лучей POV-RAY для получения изображений печатного качества;
• на языке моделирования виртуальной реальности (VRML) для распространения информации по сети Интернет;
• визуализация окна OpenGL средствами Postscript для получения высококачественных изображений в отсутствие трассировщика лучей POV-RAY.

DRAWxtl может читать различные форматы файлов, включая CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS и WIEN2k.

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.

GNOME Crystal -- простой визуализатор моделей кристаллических структур. Основан на GNOME Chemistry Utils, показывает модели всех типов микроскопических структур кристаллов используя OpenGL.

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.

The Macromolecular Transmission Format (MMTF) is a compact binary format to transmit and store biomolecular structures for fast 3D visualization and analysis.

Manipulating PDB (Protein Data Bank) 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.

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.

Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels.

This package contains Python 3 module.

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

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.