Summary
3D Visualization
This metapackage will install 3D Viewers 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 3D Visualization packages
Official Debian packages with high relevance
adun.app
Molecular Simulator for GNUstep (GUI)
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Versions of package adun.app |
Release | Version | Architectures |
jessie | 0.81-6 | amd64,armel,armhf,i386 |
stretch | 0.81-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.81-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.81-13 | amd64,arm64,armhf,i386 |
Debtags of package adun.app: |
field | biology, biology:structural |
interface | x11 |
role | program |
scope | application |
suite | gnustep |
uitoolkit | gnustep |
use | analysing, organizing, viewing |
works-with | 3dmodel, db |
x11 | application |
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License: DFSG free
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Adun is a biomolecular simulator that also includes data management and
analysis capabilities. It was developed at the Computational Biophysics
and Biochemistry Laboratory, a part of the Research Unit on Biomedical
Informatics of the UPF.
This package contains UL, the Adun GUI frontend.
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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 |
trixie | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.97.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.93.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.2.0-4 | amd64,arm64,armhf,i386 |
sid | 1.99.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.2.0-1+deb9u1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,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 |
sid | 1.5.0+git20180813.37fc53c-11 | amd64,arm64,i386,mips64el,ppc64el,riscv64,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 |
jessie | 1.4.2+20140406-1 | amd64,armel,armhf,i386 |
stretch | 1.4.3~beta1-3 | amd64,arm64,armel,armhf,i386,mips,ppc64el,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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cclib
Parsers and algorithms for computational chemistry
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Versions of package cclib |
Release | Version | Architectures |
sid | 1.8-1 | all |
trixie | 1.8-1 | all |
bookworm | 1.6.2-2 | all |
bullseye | 1.6.2-2 | all |
buster | 1.6-1 | all |
jessie | 1.1-1 | all |
stretch | 1.3.1-1 | all |
upstream | 1.8.1 |
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License: DFSG free
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A Python library that provides parsers for computational
chemistry log files. It also provides a platform to implement
algorithms in a package-independent manner.
This package contains helper scripts for end users.
If you are looking for the unit tests and data files managed by cclib,
they are distributed separately as in non-free package cclib-data.
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drawxtl
Kiderakenteen katseluohjelma
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Versions of package drawxtl |
Release | Version | Architectures |
jessie | 5.5-3 | amd64,armel,armhf,i386 |
trixie | 5.5-6.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 5.5-6.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 5.5-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 5.5-3 | amd64,arm64,armhf,i386 |
bullseye | 5.5-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 5.5-6 | 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 lukee kiderakenteen peruskuvailun, joka sisältää alkeiskopin
parametrit, avaruusryhmät, atomikoordinaatit, termiset parametrit tai
Fourier-kartan. Ulostulo on geometrinen objekti, joka sisältää
monitahokkaan, tasot, vapaat elektroniparit, pallopinnat tai ellipsoidit,
sidokset, Fourier-isoviivat ja alkeiskopin rajat.
Ohjelma tuottaa neljä erityyppistä grafiikkaa:
- OpenGL-ikkunan välitöntä katselua varten
- POV-Ray julkaisukelpoisille piirroksille
- VRML (virtuaalitodellisuuden kuvauskieli) levittämiselle internetissä
- Postscript renderöinti OpenGL:stä, kun halutaan laadukas ulostulo, mutta
POV-Ray ei ole asennettuna.
Tiedostomuodot, joita DRAWxtl lukee ovat CIF, FDAT, FullProf (pcr), GSAS,
SCHAKAL,SHELX, DISCUS ja WIEN2k.
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gabedit
graphical user interface to Ab Initio packages
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Versions of package gabedit |
Release | Version | Architectures |
stretch | 2.4.8-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.8-3 | amd64,arm64,armhf,i386 |
bullseye | 2.5.1~20200828-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.4.8-1 | amd64,armel,armhf,i386 |
bookworm | 2.5.1+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.5.1+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package gabedit: |
field | chemistry |
role | program |
uitoolkit | gtk |
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License: DFSG free
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Gabedit is a graphical user interface to computational chemistry
packages like:
- MPQC
- GAMESS-US
- Gaussian
- Molcas
- Molpro
- Q-Chem
These Ab Initio software packages might run locally or on a remote
server (supporting FTP, RSH and SSH). Gabedit can display a variety
of calculation results including most major molecular file formats.
The advanced "Molecule Builder" allows one to rapidly sketch in
molecules and examine them in 3D. Graphics can further be exported
to various formats, including animations.
slurm-wlm-torque and gridengine-client are workload managers which
provide wrappers for PBS commands. Gabedit also allows one to
configure it for any other workload manager.
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gamgi
General Atomistic Modelling Graphic Interface (GAMGI)
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Versions of package gamgi |
Release | Version | Architectures |
jessie | 0.17.1-1 | amd64,armel,armhf,i386 |
sid | 0.17.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.17.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.17.3-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.17.3-2 | amd64,arm64,armhf,i386 |
stretch | 0.17.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package gamgi: |
role | program |
uitoolkit | gtk |
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License: DFSG free
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The General Atomistic Modelling Graphic Interface (GAMGI) provides
a graphical interface to build, view and analyze atomic structures.
The program is aimed at the scientific community and provides a
graphical interface to study atomic structures and to prepare images
for presentations, and for teaching the atomic structure of matter.
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garlic
visualization program for biomolecules
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Versions of package garlic |
Release | Version | Architectures |
trixie | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.6-1.1 | amd64,armel,armhf,i386 |
stretch | 1.6-1.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.6-3 | amd64,arm64,armhf,i386 |
bullseye | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.6-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package garlic: |
field | biology, chemistry |
interface | x11 |
role | program |
scope | utility |
uitoolkit | xlib |
use | viewing |
x11 | application |
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License: DFSG free
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Garlic is written for the investigation of membrane proteins. It may be
used to visualize other proteins, as well as some geometric objects.
This version of garlic recognizes PDB format version 2.1. Garlic may
also be used to analyze protein sequences.
It only depends on the X libraries, no other libraries are needed.
Features include:
- The slab position and thickness are visible in a small window.
- Atomic bonds as well as atoms are treated as independent drawable
objects.
- The atomic and bond colors depend on position. Five mapping modes
are available (as for slab).
- Capable to display stereo image.
- Capable to display other geometric objects, like membrane.
- Atomic information is available for atom covered by the mouse
pointer. No click required, just move the mouse pointer over the
structure!
- Capable to load more than one structure.
- Capable to draw Ramachandran plot, helical wheel, Venn diagram,
averaged hydrophobicity and hydrophobic moment plot.
- The command prompt is available at the bottom of the main window.
It is able to display one error message and one command string.
Please cite:
Damir Zucic and Davor Juretic:
Precise Annotation of Transmembrane Segments with Garlic - a Free Molecular Visualization Program
(eprint)
Croatica Chemica Acta
77(1-2):397-401
(2004)
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gausssum
parse and display Gaussian, GAMESS, and etc's output
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Versions of package gausssum |
Release | Version | Architectures |
stretch | 3.0.1.1-1 | all |
sid | 3.0.2-2 | all |
trixie | 3.0.2-2 | all |
bookworm | 3.0.2-2 | all |
bullseye | 3.0.2-2 | all |
buster | 3.0.2-1 | all |
jessie | 2.2.6.1-1 | all |
Debtags of package gausssum: |
field | chemistry |
role | program |
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License: DFSG free
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GaussSum parses the output files of ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar
and PC GAMESS calculations to extract useful information.
GaussSum uses GNUPlot to display the progress of geometry optimisations,
density of states spectrum, UV-VIS spectra, IR spectra, Raman spectra,
and electron density difference maps. It can also display all lines containing
an arbitrary phrase and more.
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gdis
molecular and crystal model viewer
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Versions of package gdis |
Release | Version | Architectures |
sid | 0.90-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.90-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.90-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.90-5 | amd64,arm64,armhf,i386 |
stretch | 0.90-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.90-5 | amd64,armel,armhf,i386 |
Debtags of package gdis: |
field | chemistry |
interface | 3d, x11 |
role | program |
uitoolkit | gtk |
use | editing, learning, viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
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A GTK+ based program for the display and manipulation of
isolated molecules, periodic systems and crystalline habits.
It is in development, but is nonetheless fairly functional.
It has the following features:
- Support for several file types (CIF, BIOSYM, XYZ,
XTL, MARVIN, and GULP)
- A simple molecular creation and manipulation tool
- A dialogue for creating starting configurations for
molecular dynamics simulations
- Assorted tools for visualization (geometry information,
region highlighting, etc.)
- Animation of BIOSYM files (also rendered animations,
see below)
GDIS also allows you to perform the following functions
through other packages:
- Model rendering (courtesy of POVRay)
- Energy minimization (courtesy of GULP)
- Morphology calculation (courtesy of cdd)
- Space group processing (courtesy of SgInfo)
- View the Periodic Table (courtesy of GPeriodic)
- Load additional filetypes, such as PDB (courtesy of Babel)
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gdpc
visualiser of molecular dynamic simulations
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Versions of package gdpc |
Release | Version | Architectures |
stretch | 2.2.5-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.2.5-3 | amd64,armel,armhf,i386 |
sid | 2.2.5-16 | amd64,arm64,mips64el,ppc64el,riscv64 |
trixie | 2.2.5-16 | amd64,arm64,mips64el,ppc64el,riscv64 |
bookworm | 2.2.5-15 | amd64,arm64,mips64el,ppc64el |
bullseye | 2.2.5-14 | amd64,arm64,mips64el,ppc64el |
buster | 2.2.5-9 | amd64,arm64,armhf,i386 |
Debtags of package gdpc: |
field | biology, biology:structural, chemistry, physics |
interface | x11 |
role | program |
scope | application |
uitoolkit | gtk |
use | viewing |
works-with | 3dmodel, image, video |
works-with-format | jpg, png |
x11 | application |
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License: DFSG free
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gpdc is a graphical program for visualising output data from
molecular dynamics simulations. It reads input in the standard xyz
format, as well as other custom formats, and can output pictures of
each frame in JPG or PNG format.
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jmol
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Versions of package jmol |
Release | Version | Architectures |
jessie | 12.2.32+dfsg2-1 | all |
stretch | 14.6.4+2016.11.05+dfsg1-3 | all |
buster | 14.6.4+2016.11.05+dfsg1-4 | all |
bullseye | 14.6.4+2016.11.05+dfsg1-4 | all |
bookworm | 14.32.83+dfsg-2 | all |
trixie | 16.2.33+dfsg-1 | all |
sid | 16.2.33+dfsg-1 | all |
upstream | 16.2.37 |
Debtags of package jmol: |
field | chemistry |
role | program |
scope | utility |
use | viewing |
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License: DFSG free
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Jmol is a Java molecular viewer for three-dimensional chemical structures.
Features include reading a variety of file types and output from quantum
chemistry programs, and animation of multi-frame files and computed normal
modes from quantum programs. It includes with features for chemicals,
crystals, materials and biomolecules. Jmol might be useful for students,
educators, and researchers in chemistry and biochemistry.
File formats read by Jmol include PDB, XYZ, CIF, CML, MDL Molfile, Gaussian,
GAMESS, MOPAC, ABINIT, ACES-II, Dalton and VASP.
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kalzium
periodic table and chemistry tools
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Versions of package kalzium |
Release | Version | Architectures |
experimental | 24.08.2-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 4.14.2-1 | amd64,armel,armhf,i386 |
stretch | 16.08.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 17.08.3-1 | amd64,arm64,armhf,i386 |
bullseye | 20.12.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 22.12.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 23.08.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 23.08.5-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 24.08.2 |
Debtags of package kalzium: |
field | chemistry |
interface | 3d, x11 |
role | program |
suite | kde |
uitoolkit | qt |
use | browsing, learning, viewing |
works-with | 3dmodel |
x11 | application |
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License: DFSG free
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Kalzium is a full-featured chemistry application, including a
Periodic Table of Elements, chemical reference, chemical equation solver, and
3D molecule viewer.
This package is part of the KDE education module.
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qutemol
interactive visualization of macromolecules
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Versions of package qutemol |
Release | Version | Architectures |
stretch | 0.4.1~cvs20081111-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.4.1~cvs20081111-12 | amd64,arm64,armhf,i386 |
jessie | 0.4.1~cvs20081111-3.2 | amd64,armel,armhf,i386 |
bullseye | 0.4.1~cvs20081111-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 0.4.1~cvs20081111-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 0.4.1~cvs20081111-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 0.4.1~cvs20081111-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package qutemol: |
interface | x11 |
role | program |
uitoolkit | glut, wxwidgets |
x11 | application |
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License: DFSG free
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QuteMol is an interactive, high quality molecular visualization
system. It exploits the current GPU capabilities through OpenGL shaders
to offer an array of innovative visual effects. QuteMol visualization
techniques are aimed at improving clarity and an easier understanding
of the 3D shape and structure of large molecules or complex proteins.
Qutemol uses advanced OpenGL techniques and might not work correctly
with all video cards and drivers.
Features QuteMol offers include:
- Real time ambient occlusion
- Depth aware silhouette enhancement
- Ball-and-stick, space-filling and liquorice visualization modes
- High resolution antialiased snapshots for creating publication
quality renderings
- Automatic generation of animated gifs of rotating molecules for
web page animations
- Interactive rendering of macromolecules (>100k atoms)
QuteMol reads PDB files as input.
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rasmol
visualization of biological macromolecules
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Versions of package rasmol |
Release | Version | Architectures |
bookworm | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.7.6.0-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.7.5.2-2 | amd64,armel,armhf,i386 |
stretch | 2.7.5.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,s390x |
buster | 2.7.6.0-1 | amd64,arm64,armhf,i386 |
bullseye | 2.7.6.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package rasmol: |
field | chemistry |
interface | x11 |
role | program |
scope | utility |
uitoolkit | gtk |
use | learning, viewing |
x11 | application |
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License: DFSG free
|
RasMol is a molecular graphics program intended for the visualisation of
proteins, nucleic acids and small molecules. The program is aimed at
display, teaching and generation of publication quality images.
The program reads in a molecule coordinate file and interactively displays
the molecule on the screen in a variety of colour schemes and molecule
representations. Currently available representations include depth-cued
wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick,
solid and strand biomolecular ribbons, atom labels and dot surfaces.
Supported input file formats include Protein Data Bank (PDB), Tripos
Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's
(MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol)
format, CHARMm format, CIF format and mmCIF format files.
This package installs two versions of RasMol, rasmol-gtk has a modern
GTK-based user interface and rasmol-classic is the version with the old
Xlib GUI.
The package is enhanced by the following packages:
rasmol-doc
Please register by following this link if you are using rasmol.
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raster3d
tools for generating images of proteins or other molecules
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Versions of package raster3d |
Release | Version | Architectures |
trixie | 3.0-7-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.0-7-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 3.0-3-1 | amd64,armel,armhf,i386 |
stretch | 3.0-3-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.0-3-5 | amd64,arm64,armhf,i386 |
bullseye | 3.0-7-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.0-7-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package raster3d: |
field | biology, biology:structural |
interface | commandline |
role | program |
scope | application |
use | converting, viewing |
works-with | 3dmodel, image, image:raster |
works-with-format | jpg, png |
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License: DFSG free
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Raster3D is a set of tools for generating high quality raster images of
proteins or other molecules. The core program renders spheres, triangles,
cylinders, and quadric surfaces with specular highlighting, Phong shading,
and shadowing. It uses an efficient software Z-buffer algorithm which is
independent of any graphics hardware. Ancillary programs process atomic
coordinates from PDB files into rendering descriptions for pictures composed
of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be
used to render pictures composed in other programs such as Molscript in
glorious 3D with highlights, shadowing, etc. Output is to pixel image files
with 24 bits of color information per pixel.
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shelxle
graphical user interface for SHELXL
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Versions of package shelxle |
Release | Version | Architectures |
jessie | 1.0.677-1 | amd64,armel,armhf,i386 |
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 |
bullseye | 1.0.1179-1 | amd64,arm64,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.952-1 | amd64,arm64,i386 |
stretch | 1.0.816-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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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v-sim
Visualize atomic structures
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Versions of package v-sim |
Release | Version | Architectures |
stretch | 3.7.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.7.2-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 3.7.2-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.7.2-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package v-sim: |
field | chemistry, physics |
interface | x11 |
role | program |
science | visualisation |
scope | application |
uitoolkit | gtk |
use | viewing |
x11 | application |
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License: DFSG free
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V_Sim visualizes atomic structures such as crystals, grain boundaries,
molecules and so on (either in binary format, or in plain text format).
The rendering is done in pseudo-3D with spheres (atoms) or arrows (spins).
The user can interact through many functions to choose the view, set the
bindings, draw cutting planes, compute surfaces from scalar fields,
duplicate nodes, measure geometry... Moreover V_Sim allows one to export the
view as images in PNG, JPG, PDF (bitmap), SVG (scheme) and other formats.
Some tools are also available to colorize atoms from data values or to
animate on screen many position files.
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viewmol
graphical front end for computational chemistry programs
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Versions of package viewmol |
Release | Version | Architectures |
jessie | 2.4.1-22 | amd64,armel,armhf,i386 |
stretch | 2.4.1-24 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.1-25 | amd64,arm64,armhf,i386 |
Debtags of package viewmol: |
field | chemistry |
interface | 3d, x11 |
role | program |
uitoolkit | motif |
use | learning, viewing |
x11 | application |
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License: DFSG free
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Viewmol is able to graphically aid in the generation of molecular
structures for computations and to visualize their results.
At present Viewmol includes input filters for Discover, DMol3, Gamess,
Gaussian 9x/03, Gulp, Mopac, PQS, Turbomole, and Vamp outputs as well as
for PDB files. Structures can be saved as Accelrys' car-files, MDL files,
and Turbomole coordinate files. Viewmol can generate input files for
Gaussian 9x/03. Viewmol's file format has been added to OpenBabel so that
OpenBabel can serve as an input as well as an output filter for
coordinates.
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xbs
3-d models and movies of molecules
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Versions of package xbs |
Release | Version | Architectures |
sid | 0-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 0-10 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0-10 | amd64,arm64,armhf,i386 |
bullseye | 0-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 0-8 | amd64,armel,armhf,i386 |
trixie | 0-12 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package xbs: |
field | chemistry |
interface | 3d |
role | program |
scope | application |
uitoolkit | xlib |
use | printing, viewing |
works-with | text |
works-with-format | postscript |
x11 | application |
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License: DFSG free
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xbs ball-and-sticks plotting program can create still
and moving three dimensional models of molecules. X11 and
PostScript output are available. Models can be rotated,
scaled, etc. Various labeling, shading, lighting,
coloring options are available.
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xcrysden
Crystalline and Molecular Structure Visualizer
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Versions of package xcrysden |
Release | Version | Architectures |
bullseye | 1.6.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 1.5.60-1 | amd64,armel,armhf,i386 |
sid | 1.6.2-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.6.2-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.6.2-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.5.60-1 | amd64,arm64,armel,armhf,i386,mips,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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xmakemol
program for visualizing atomic and molecular systems
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Versions of package xmakemol |
Release | Version | Architectures |
stretch | 5.16-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 5.16-7 | amd64,armel,armhf,i386 |
sid | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 5.16-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 5.16-9 | amd64,arm64,armhf,i386 |
Debtags of package xmakemol: |
field | chemistry |
hardware | input, input:mouse |
interface | x11 |
role | program |
scope | application |
uitoolkit | motif |
use | editing, viewing |
x11 | application |
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License: DFSG free
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XMakemol is a mouse-based program, written using the LessTif widget set, for
viewing and manipulating atomic and other chemical systems. It reads XYZ
input and renders atoms, bonds and hydrogen bonds.
Features include:
- Animating multiple frame files
- Interactive measurement of bond lengths, bond angles and torsion angles
- Control over atom/bond sizes
- Exporting to Xpm, Encapsulated PostScript and XYZ formats
- Toggling the visibility of groups of atoms
- Editing the positions of subsets of atoms
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