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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Links to other tasks
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DebiChem Molecular Modelling packages
Official Debian packages with high relevance
avogadro
Molecular Graphics and Modelling System
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Versions of package avogadro |
Release | Version | Architectures |
jessie | 1.0.3-10.1 | amd64,armel,armhf,i386 |
stretch | 1.2.0-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.2.0-4 | amd64,arm64,armhf,i386 |
bullseye | 1.93.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.97.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package avogadro: |
field | chemistry |
role | program |
uitoolkit | qt |
use | viewing |
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License: DFSG free
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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.
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ballview
free molecular modeling and molecular graphics tool
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Versions of package ballview |
Release | Version | Architectures |
jessie | 1.4.2+20140406-1 | amd64,armel,armhf,i386 |
stretch | 1.4.3~beta1-3 | amd64,arm64,armel,armhf,i386,mips,ppc64el,s390x |
buster | 1.5.0+git20180813.37fc53c-3 | amd64,arm64,i386 |
bullseye | 1.5.0+git20180813.37fc53c-6 | amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.5.0+git20180813.37fc53c-11 | amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.5.0+git20180813.37fc53c-11 | amd64,arm64,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 1.5.0+git20220524.d85d2dd |
Debtags of package ballview: |
interface | x11 |
role | program |
uitoolkit | qt |
x11 | application |
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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.
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ghemical
GNOME molecular modelling environment
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Versions of package ghemical |
Release | Version | Architectures |
stretch | 3.0.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.0.0-4 | amd64,arm64,armhf,i386 |
bullseye | 3.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
Debtags of package ghemical: |
field | chemistry |
interface | 3d, x11 |
role | program |
suite | gnome |
uitoolkit | gtk |
use | editing, learning, viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
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Ghemical is a computational chemistry software package written in C++.
It has a graphical user interface and it supports both quantum-
mechanics (semi-empirical) models and molecular mechanics models.
Geometry optimization, molecular dynamics and a large set of
visualization tools using OpenGL are currently available.
Ghemical relies on external code to provide the quantum-mechanical
calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come
from the MOPAC7 package (Public Domain), and are included in the
package. The MPQC package is used to provide ab initio methods: the
methods based on Hartree-Fock theory are currently supported with
basis sets ranging from STO-3G to 6-31G**.
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mmb
model the structure and dynamics of macromolecules
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Versions of package mmb |
Release | Version | Architectures |
bullseye | 3.2+dfsg-2+deb11u1 | amd64,arm64,ppc64el |
bookworm | 4.0.0+dfsg-2 | amd64,arm64 |
experimental | 4.0.0+dfsg-3.1~exp1 | amd64,arm64,armhf |
trixie | 4.0.0+dfsg-4 | amd64,arm64 |
sid | 4.0.0+dfsg-4 | amd64,arm64 |
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License: DFSG free
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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.
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openstructure
Open-Source Computational Structural Biology Framework
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Versions of package openstructure |
Release | Version | Architectures |
bullseye | 2.2.0-6 | amd64,mips64el,mipsel |
bookworm | 2.3.1-9 | amd64,mips64el,mipsel |
trixie | 2.5.0-3 | amd64,mips64el |
sid | 2.5.0-3 | amd64,mips64el |
experimental | 2.6.1-1~exp | amd64,mips64el |
upstream | 2.8.0 |
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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.
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promod3
protein homology modelling engine
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Versions of package promod3 |
Release | Version | Architectures |
bookworm | 3.2.1+ds-6 | amd64 |
sid | 3.4.0+ds-1 | all |
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License: DFSG free
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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.
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pymol
Molecular Graphics System
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Versions of package pymol |
Release | Version | Architectures |
jessie | 1.7.2.1-1 | amd64,armel,armhf,i386 |
stretch | 1.8.4.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.2.0+dfsg-4 | all |
bullseye | 2.4.0+dfsg-2 | all |
bookworm | 2.5.0+dfsg-1 | all |
trixie | 3.0.0+dfsg-1 | all |
sid | 3.0.0+dfsg-1 | all |
Debtags of package pymol: |
field | biology:structural, chemistry |
interface | 3d, x11 |
role | program |
scope | utility |
uitoolkit | tk |
use | learning, viewing |
works-with | image |
x11 | application |
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License: DFSG free
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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.
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No known packages available
nmoldyn
interactive analysis program for Molecular Dynamics simulations
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License: unknown
Debian package not available
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nMOLDYN is especially designed for the computation and decomposition of neutron
scattering spectra, but also computes other quantities.
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