DebiChem Crystallography packages

DRAWxtl lê uma descrição básica da estrutura cristalina, que inclui parâmetros de célula unitária, grupo espacial, coordenadas atômicas, parâmetros térmicos ou mapa de Fourier, e gera um objeto de geometria que contém poliedros, planos, cones de pares solitários, esferas ou elipsóides, ligações, contornos de Fourier de iso-superfície e o limite da célula unitária.

Quatro formas de gráficos são produzidas:

• uma janela OpenGL para visualização imediata
• a linguagem de cena Persistence of Vision Ray Tracer (POV-RAY) para desenhos com qualidade de publicação
• a Virtual Reality Modeling Language (VRML) para divulgação pela Internet
• uma renderização Postscript da janela OpenGL para quem quer saída de alta qualidade, mas não tem POV-RAY instalado.

Os formatos de arquivo que o DRAWxtl pode ler incluem CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS e 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 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.

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 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).