DebiChem Crystallography packages

DRAWxtl은 단위 셀 파라미터, 공간 그룹, 원자 좌표, 온도 매개 변수 또는 푸리 에 맵을 포함하는 크리스탈 구조의 기본적인 설명을 읽고, 다면체, 평면, 고립 전자쌍 콘, 구 또는 타원체, 결합, iso-surface 푸리에 윤곽, 및 단위 셀 경계를 포함하는 기하학적 객체를 출력합니다.

네개의 그래픽 형식을 만듭니다:

• 바로 볼 수 있는 OpenGL 윈도우
• 출판물 품질의 그림을 위한 비전 레이 추적기의 지속성 (Persistence of Vision Ray Tracer/POV-RAY) 장면 언어
• 인터넷을 통해 제공되는 가상 현실 모델링 언어 (Virtual Reality Modeling Language/VRML)
• 고품질 출력을 원하지만 POV-RAY는 설치되지 않은 사람들을 위한 OpenGL 윈도우의 포스트스크립트 랜더링.

파일 형식 DRAWxtl은 CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS, WIEN2k들을 읽을 수 있습니다.

General Atomistic Modelling Graphic Interface (GAMGI)는 원자 구조를 빌드하 고, 보고, 분석하기 위한 그래픽 인터페이스를 제공합니다. 이 프로그램은 과학 커뮤니티를 목적으로 하며, 원자 구조를 연구하고 프리젠테이션을 위해 이미지를 준비하고 물질의 원자 구조를 가르치는 그래픽 인터페이스를 제공합니다.

GNOME Crystal은 결정 구조에 대한 경량 모델 시각화입니다. 이 프로그램은 그놈 화학 유틸에 기반하며 OpenGL을 사용하여 모든 종류의 결정 미세 구조 모델을 표 시해야 합니다.

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.