DebiChem Project
Summary
Molecular Modelling
DebiChem 3D Molecular Modelling and Visualization

This metapackage will install 3D Molecular Modelling and Visualization which might be useful for chemists.

Description

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DebiChem Molecular Modelling packages

Official Debian packages with high relevance

avogadro
分子可視化およびモデリングシステム
Versions of package avogadro
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sid1.101.0-1amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x
bullseye1.93.0-2amd64,arm64,armhf,i386
bookworm1.97.0-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie1.100.0-2amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky1.101.0-1amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
Debtags of package avogadro:
fieldchemistry
roleprogram
uitoolkitqt
useviewing
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License: DFSG free
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Avogadro は、分子および生体分子をターゲットとする分子グラフィックスおよ び分子モデリングシステムです。分子軌道や静電ポテンシャルなどの分子の物 性を可視化でき、直感的な分子ビルダーを備えています。

次のような機能があります:

  • 力場に基づいた配座の自動最適化機能を備える分子モデリングツール
  • 拘束や配座異性体探索を含む分子力学法ツール
  • 分子軌道その他のな同値面の可視化
  • 振動の可視化、振動スペクトルのプロット
  • 結晶単位格子の編集
  • Gaussian, GAMESS および MOLPRO 量子化学パッケージ用の 入力データの生成

  • 拡張可能なプラグインアーキテクチャ、Python でのスクリプティング

Avogadro は、PDB, XYZ, CML, CIF, Molden ファイルのほか、Gaussian, GAMESS, MOLPRO などの出力ファイルも読み込むことができます。

Please cite: Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison: Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. (eprint) J. Cheminf. 4:17 (2012)
Registry entries: Bio.tools  SciCrunch 
ballview
free molecular modeling and molecular graphics tool
Versions of package ballview
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bookworm1.5.0+git20180813.37fc53c-11amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x
forky1.5.0+git20180813.37fc53c-11.1amd64,arm64,i386,ppc64el,riscv64,s390x
sid1.5.0+git20180813.37fc53c-11.1amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x
bullseye1.5.0+git20180813.37fc53c-6amd64,arm64,i386
upstream1.5.0+git20220524.d85d2dd
Debtags of package ballview:
interfacex11
roleprogram
uitoolkitqt
x11application
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BALLView provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features.

BALLView can be considered a graphical user interface on the basis of BALL (Biochemical Algorithms Library) with a focus on the most common demands of protein chemists and biophysicists in particular. It is developed in the groups of Hans-Peter Lenhof (Saarland University, Saarbruecken, Germany) and Oliver Kohlbacher (University of Tuebingen, Germany). BALL is an application framework in C++ that has been specifically designed for rapid software development in Molecular Modeling and Computational Molecular Biology. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.

Please cite: Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof and Oliver Kohlbacher: BALLView: a tool for research and education in molecular modeling. (PubMed,eprint) Bioinformatics 22(3):365-366 (2006)
Registry entries: SciCrunch 
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ghemical
??? missing short description for package ghemical :-(
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bookworm3.0.0-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye3.0.0-5amd64,arm64,armhf,i386
Debtags of package ghemical:
fieldchemistry
interface3d, x11
roleprogram
suitegnome
uitoolkitgtk
useediting, learning, viewing
works-with3dmodel
x11application
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Registry entries: Bio.tools  SciCrunch 
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mmb
model the structure and dynamics of macromolecules
Versions of package mmb
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sid4.0.0+dfsg-5amd64,arm64,mips64el,ppc64el,riscv64,s390x
bullseye3.2+dfsg-2+deb11u1amd64,arm64
bookworm4.0.0+dfsg-2amd64,arm64
experimental4.0.0+dfsg-3.1~exp1amd64,arm64,armhf
trixie4.0.0+dfsg-5amd64,arm64,ppc64el,riscv64,s390x
forky4.0.0+dfsg-5amd64,arm64,ppc64el,riscv64,s390x
upstream4.2
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MacroMoleculeBuilder, previously known as RNABuilder, can be used for morphing, homology modeling, folding (e.g. using base pairing contacts), redesigning complexes, fitting to low-resolution density maps, predicting local rearrangements upon mutation, and many other applications.

openstructure
Open-Source Computational Structural Biology Framework
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bookworm2.3.1-9amd64,mips64el,mipsel
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experimental2.10.0-1~expamd64,i386,mips64el
sid2.9.3-2amd64,i386,mips64el
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upstream2.11.1
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OpenStructure aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics.

promod3
protein homology modelling engine
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trixie3.4.2+ds-1all
bookworm3.2.1+ds-6amd64
forky3.4.2+ds-1all
sid3.4.2+ds-1all
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ProMod3 is a modelling engine based on the OpenStructure computational structural biology framework that can perform all steps required to generate a protein model by homology. Its modular design aims at implementing flexible modelling pipelines and fast prototyping of novel algorithms.

Please cite: Gabriel Studer, Gerardo Tauriello, Stefan Bienert, Marco Biasini, Niklaus Johner and Torsten Schwede: ProMod3—A versatile homology modelling toolbox. PLOS Computational Biology 17(1):e1008667 (2021)
pymol
Molecular Graphics System
Versions of package pymol
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bookworm2.5.0+dfsg-1all
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sid3.1.0+dfsg-1all
forky3.1.0+dfsg-1all
trixie3.1.0+dfsg-1all
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fieldbiology:structural, chemistry
interface3d, x11
roleprogram
scopeutility
uitoolkittk
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x11application
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PyMOL is a molecular graphics system targeted at medium to large biomolecules like proteins. It can generate high-quality publication-ready molecular graphics images and animations.

Features include:

  • Visualization of molecules, molecular trajectories and surfaces of crystallography data or orbitals
  • Molecular builder and sculptor
  • Internal raytracer and movie generator
  • Fully extensible and scriptable via a Python interface

File formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile, ChemDraw, CCP4 maps, XPLOR maps and Gaussian cube maps.

Registry entries: Bio.tools  SciCrunch 
Topics:

No known packages available

nmoldyn
interactive analysis program for Molecular Dynamics simulations
License: unknown
Debian package not available

nMOLDYN is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 268027