DebiChem Crystallography packages

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.

GAMGI (General Atomistic Modelling Graphic Interface) udostępnia interfejs graficzny do budowania, przeglądania i analizowania struktur atomowych. Program jest skierowany do społeczności naukowej i zawiera interfejs graficzny do badania struktur atomowych i przygotowywania obrazów do prezentacji oraz do nauczania budowy materii atomowej.

GNOME Crystal to lekki wizualizator modeli struktur krystalicznych. Bazuje na GNOME Chemistry Utils (narzędziach chemicznych środowiska GNOME) i powinien wyświetlać modele wszelkiego rodzaju mikroskopijnych struktur kryształów przy użyciu 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 łączy edytor z podświetlaniem składni dla związanych z SHELXL plików wejściowych .ins i plików wyjściowych .res z interaktywnym wyświetlaczem graficznym wyświetlającym trójwymiarowe struktury, w tym mapy gęstości elektronowej (Fo) oraz mapy różnic gęstości (Fo-Fc).

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.