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
Molecular Graphics and Modelling System
Versions of package avogadro
ReleaseVersionArchitectures
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
forky1.100.0-2amd64,arm64,armhf,i386,ppc64el,riscv64,s390x
Debtags of package avogadro:
fieldchemistry
roleprogram
uitoolkitqt
useviewing
Popcon: 67 users (105 upd.)*
Versions and Archs
License: DFSG free
Git

Avogadro is a molecular graphics and modelling system targeted at molecules and biomolecules. It can visualize properties like molecular orbitals or electrostatic potentials and features an intuitive molecular builder.

Features include:

  • Molecular modeller with automatic force-field based geometry optimization
  • Molecular Mechanics including constraints and conformer searches
  • Visualization of molecular orbitals and general isosurfaces
  • Visualization of vibrations and plotting of vibrational spectra
  • Support for crystallographic unit cells
  • Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry packages
  • Flexible plugin architecture and Python scripting

File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as Gaussian, GAMESS and MOLPRO output.

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
ReleaseVersionArchitectures
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
Popcon: 5 users (17 upd.)*
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License: DFSG free
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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 
Screenshots of package ballview
ghemical
??? missing short description for package ghemical :-(
Versions of 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
Popcon: 8 users (2 upd.)*
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License: DFSG free
Git
Registry entries: Bio.tools  SciCrunch 
Screenshots of package ghemical
mmb
model the structure and dynamics of macromolecules
Versions of package mmb
ReleaseVersionArchitectures
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
Popcon: 6 users (48 upd.)*
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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
Versions of package openstructure
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bookworm2.3.1-9amd64,mips64el,mipsel
trixie2.9.3-2amd64,i386
experimental2.10.0-1~expamd64,i386,mips64el
sid2.9.3-2amd64,i386,mips64el
forky2.9.3-2amd64,i386
bullseye2.2.0-6amd64
upstream2.11.1
Popcon: 5 users (0 upd.)*
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License: DFSG free
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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
Versions of package promod3
ReleaseVersionArchitectures
trixie3.4.2+ds-1all
bookworm3.2.1+ds-6amd64
forky3.4.2+ds-1all
sid3.4.2+ds-1all
upstream3.6.0
Popcon: 0 users (0 upd.)*
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License: DFSG free
Git

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
ReleaseVersionArchitectures
bookworm2.5.0+dfsg-1all
bullseye2.4.0+dfsg-2all
sid3.1.0+dfsg-1all
forky3.1.0+dfsg-1all
trixie3.1.0+dfsg-1all
Debtags of package pymol:
fieldbiology:structural, chemistry
interface3d, x11
roleprogram
scopeutility
uitoolkittk
uselearning, viewing
works-withimage
x11application
Popcon: 63 users (234 upd.)*
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License: DFSG free
Git

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 267811