Summary
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
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DebiChem Crystallography packages
Official Debian packages with high relevance
drawxtl
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Versions of package drawxtl |
Release | Version | Architectures |
buster | 5.5-3 | amd64,arm64,armhf,i386 |
stretch | 5.5-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 5.5-3 | amd64,armel,armhf,i386 |
sid | 5.5-6.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 5.5-6.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 5.5-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 5.5-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package drawxtl: |
interface | x11 |
role | program |
uitoolkit | glut |
x11 | application |
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License: DFSG free
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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.
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gamgi
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Versions of package gamgi |
Release | Version | Architectures |
bookworm | 0.17.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.17.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.17.1-1 | amd64,armel,armhf,i386 |
stretch | 0.17.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.17.3-2 | amd64,arm64,armhf,i386 |
bullseye | 0.17.3-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package gamgi: |
role | program |
uitoolkit | gtk |
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License: DFSG free
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GAMGI 是一个用于建立、查看和分析原子结构的图形界面工具。
该程序的目的是:为科学界提供一个研究、演示原子结构的图形软件,为学校老师教学物质
的结构提供一个工具。
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gcrystal
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Versions of package gcrystal |
Release | Version | Architectures |
bookworm | 0.14.17-6.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 0.14.17-6.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.14.9-1 | amd64,armel,armhf,i386 |
stretch | 0.14.15-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.14.17-1.1 | amd64,arm64,armhf,i386 |
bullseye | 0.14.17-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package gcrystal: |
field | chemistry |
interface | x11 |
role | program |
uitoolkit | gtk |
x11 | application |
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License: DFSG free
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GNOME Crystal是一个轻量级的晶体结构观察器.它基于GNONE化学实用工具,可以使用
OpenGL显示晶体的各种微观结构。
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gemmi
library for structural biology - executable
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Versions of package gemmi |
Release | Version | Architectures |
sid | 0.6.5+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.6.5+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.5.7+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 0.6.7 |
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License: DFSG free
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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.
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libmmtf-java
Java API for macromolecular transmission format encoder/decoder
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Versions of package libmmtf-java |
Release | Version | Architectures |
trixie | 1.0.11-1 | all |
sid | 1.0.11-1 | all |
bullseye | 1.0.9-4 | all |
bookworm | 1.0.11-1 | all |
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License: DFSG free
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The Macromolecular Transmission Format (MMTF) is a compact binary format to
transmit and store biomolecular structures for fast 3D visualization and
analysis.
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pdb-tools
tools for manipulating and editing PDB files
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Versions of package pdb-tools |
Release | Version | Architectures |
sid | 2.5.1-2 | all |
trixie | 2.5.1-2 | all |
bookworm | 2.5.0-2 | all |
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License: DFSG free
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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.
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python3-fabio
I/O library for images produced by 2D X-ray detector - Python3
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Versions of package python3-fabio |
Release | Version | Architectures |
buster-backports | 0.10.0+dfsg-1~bpo10+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch-backports | 0.7.0+dfsg-2~bpo9+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.8.0+dfsg-1 | amd64,arm64,armhf,i386 |
stretch | 0.4.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.11.0+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.14.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm-backports | 2023.6.0-3~bpo12+1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
trixie | 2024.4.0-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
sid | 2024.4.0-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
upstream | 2024.9.0 |
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License: DFSG free
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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.
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python3-phonopy
phonon calculations at harmonic and quasi-harmonic levels (Python 3)
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Versions of package python3-phonopy |
Release | Version | Architectures |
trixie | 2.23.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.23.1-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.17.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 2.29.1 |
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License: DFSG free
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Phonopy is an open source package for phonon calculations at harmonic and
quasi-harmonic levels.
This package contains Python 3 module.
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shelxle
graphical user interface for SHELXL
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Versions of package shelxle |
Release | Version | Architectures |
sid | 1.0.1552-1 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.0.1552-1 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.1472-1 | amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.952-1 | amd64,arm64,i386 |
bullseye | 1.0.1179-1 | amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.816-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.677-1 | amd64,armel,armhf,i386 |
upstream | 1.0.1695 |
Debtags of package shelxle: |
uitoolkit | qt |
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License: DFSG free
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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
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xcrysden
Crystalline and Molecular Structure Visualizer
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Versions of package xcrysden |
Release | Version | Architectures |
sid | 1.6.2-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.5.60-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.5.60-1 | amd64,armel,armhf,i386 |
bookworm | 1.6.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.6.2-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.6.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 1.6.3~rc2 |
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License: DFSG free
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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.
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