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
크리스탈 구조 뷰어
Versions of package drawxtl
ReleaseVersionArchitectures
buster5.5-3amd64,arm64,armhf,i386
stretch5.5-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie5.5-3amd64,armel,armhf,i386
sid5.5-6.1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
trixie5.5-6.1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm5.5-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye5.5-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package drawxtl:
interfacex11
roleprogram
uitoolkitglut
x11application
Popcon: 12 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

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.

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)
Screenshots of package drawxtl
gamgi
General Atomistic Modelling Graphic Interface (GAMGI)
Versions of package gamgi
ReleaseVersionArchitectures
bookworm0.17.5-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.17.5-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie0.17.1-1amd64,armel,armhf,i386
stretch0.17.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.17.3-2amd64,arm64,armhf,i386
bullseye0.17.3-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package gamgi:
roleprogram
uitoolkitgtk
Popcon: 14 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

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.

The package is enhanced by the following packages: gamgi-data gamgi-doc
Registry entries: SciCrunch 
Screenshots of package gamgi
gcrystal
경량의 결정 구조 시각화
Versions of package gcrystal
ReleaseVersionArchitectures
bookworm0.14.17-6.1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid0.14.17-6.2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
jessie0.14.9-1amd64,armel,armhf,i386
stretch0.14.15-1+deb9u1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.14.17-1.1amd64,arm64,armhf,i386
bullseye0.14.17-6amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package gcrystal:
fieldchemistry
interfacex11
roleprogram
uitoolkitgtk
x11application
Popcon: 13 users (2 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Screenshots of package gcrystal
gemmi
library for structural biology - executable
Versions of package gemmi
ReleaseVersionArchitectures
sid0.6.5+ds-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
trixie0.6.5+ds-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm0.5.7+ds-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream0.6.7
Popcon: 1 users (0 upd.)*
Newer upstream!
License: DFSG free
Git

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
Versions of package libmmtf-java
ReleaseVersionArchitectures
trixie1.0.11-1all
sid1.0.11-1all
bullseye1.0.9-4all
bookworm1.0.11-1all
Popcon: 2 users (5 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package pdb-tools
ReleaseVersionArchitectures
sid2.5.1-2all
trixie2.5.1-2all
bookworm2.5.0-2all
Popcon: 2 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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.

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
Versions of package python3-fabio
ReleaseVersionArchitectures
buster-backports0.10.0+dfsg-1~bpo10+1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch-backports0.7.0+dfsg-2~bpo9+1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.8.0+dfsg-1amd64,arm64,armhf,i386
stretch0.4.0+dfsg-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.11.0+dfsg-3amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm0.14.0+dfsg-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bookworm-backports2023.6.0-3~bpo12+1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el
trixie2024.4.0-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64
sid2024.4.0-2amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64
upstream2024.9.0
Popcon: 27 users (10 upd.)*
Newer upstream!
License: DFSG free
Git

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)
Versions of package python3-phonopy
ReleaseVersionArchitectures
trixie2.23.1-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
sid2.23.1-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bookworm2.17.1-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream2.29.1
Popcon: 3 users (1 upd.)*
Newer upstream!
License: DFSG free
Git

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
Versions of package shelxle
ReleaseVersionArchitectures
sid1.0.1552-1amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x
trixie1.0.1552-1amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x
bookworm1.0.1472-1amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x
buster1.0.952-1amd64,arm64,i386
bullseye1.0.1179-1amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x
stretch1.0.816-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie1.0.677-1amd64,armel,armhf,i386
upstream1.0.1695
Debtags of package shelxle:
uitoolkitqt
Popcon: 5 users (2 upd.)*
Newer upstream!
License: DFSG free
Git

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
Versions of package xcrysden
ReleaseVersionArchitectures
sid1.6.2-4amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
stretch1.5.60-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie1.5.60-1amd64,armel,armhf,i386
bookworm1.6.2-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.6.2-4amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye1.6.2-4amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
upstream1.6.3~rc2
Popcon: 16 users (1 upd.)*
Newer upstream!
License: DFSG free
Git

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.

Screenshots of package xcrysden
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 245494