DebiChem Project
Summary
3d visualization
DebiChem - 3D prehliadače

Tento metabalík nainštaluje 3D prehloadače, čo sa môže hodiť chemikom.

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

DebiChem 3d visualization packages

Official Debian packages with high relevance

Adun.app
simulátor molekúl pre GNUstep - grafické používateľské rozhranie
Versions of package adun.app
ReleaseVersionArchitectures
jessie0.81-6amd64,armel,armhf,i386
stretch0.81-9amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid0.81-13amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.81-13amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.81-13amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze0.81-4amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy0.81-5amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package adun.app:
fieldbiology, biology:structural
interfacex11
roleprogram
scopeapplication
suitegnustep
uitoolkitgnustep
useanalysing, organizing, viewing
works-with3dmodel, db
x11application
Popcon: 12 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

Adun je simulátor biomolekúl s možnosťou správy dát a analýzy. Vyvinuli ho v Computational Biophysics and Biochemistry Laboratory, čo je časť Research Unit on Biomedical Informatics v rámci UPF.

Tento balík obsahuje UL, grafické používateľské rozhranie pre Adun.

Please cite: Michael A. Johnston, Ignacio Fdez. Galván and Jordi Villà-Freixa: Framework-based design of a new all-purpose molecular simulation application: The Adun simulator. (PubMed) J. Comp. Chem. 26(15):1647-1659 (2005)
Registry entries: OMICtools 
Screenshots of package adun.app
Avogadro
systém molekulárnej grafiky a modelovania
Versions of package avogadro
ReleaseVersionArchitectures
squeeze1.0.1-3amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
sid1.2.0-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye1.2.0-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.2.0-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch1.2.0-1+deb9u1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie1.0.3-10.1amd64,armel,armhf,i386
wheezy1.0.3-5amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package avogadro:
fieldchemistry
roleprogram
uitoolkitqt
useviewing
Popcon: 86 users (91 upd.)*
Versions and Archs
License: DFSG free
Git

Avogadro je systém molekulárnej grafiky a modelovania cielený na molekuly a biomolekuly. Dokáže vizualizovať vlastnosti ako molekulárne orbitály alebo elektrostatické potenciály a obsahuje inovatívny nástroj na tvorbu molekúl.

Medzi jeho vlastnosti patrí:

  • modelovač molekúl s automatickou optimalizáciou geometrie založenou na silovom poli
  • molekulárna mechanika vrátane obmedzení a hľadaní vyhovujúcich
  • vizualizácia molekulárnych orbitálov a všeobecných isopovrchov
  • vizualizácia vibrácií a kreslenie vibračného spektra
  • podpora jednotiek kryštalografických buniek
  • generovanie vstupu pre balíky kvantovej chémie Gaussian, GAMESS a MOLPRO
  • flexibilná architektúra zásuvných modulov a skriptovanie v Pythone

Avogadro dokáže čítať súborové formáty PDB, XYZ, CML, CIF, Molden a tiež zapisovať výstup do Gaussian, GAMESS a MOLPRO.

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  OMICtools 
Other screenshots of package avogadro
VersionURL
0.8.1-5https://screenshots.debian.net/screenshots/000/001/732/large.png
Screenshots of package avogadro
Ballview
slobodný nástroj na modelovanie a zobrazovanie molekúl
Versions of package ballview
ReleaseVersionArchitectures
squeeze1.3.2-2amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
bullseye1.5.0+git20180813.37fc53c-3amd64,arm64,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.5.0+git20180813.37fc53c-3amd64,arm64,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch1.4.3~beta1-3amd64,arm64,armel,armhf,i386,mips,ppc64el,s390x
jessie1.4.2+20140406-1amd64,armel,armhf,i386
sid1.5.0+git20180813.37fc53c-3amd64,arm64,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy1.4.1+20111206-4amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package ballview:
interfacex11
roleprogram
uitoolkitqt
x11application
Popcon: 10 users (27 upd.)*
Versions and Archs
License: DFSG free
Git

BALLView poskytuje rýchlu vizualizáciu molekulárnych štruktúr založenú na OpenGL, metódy molekulárnej mechaniky (minimalizácia, simulácia MD pomocou silových polí AMBER, CHARMM a MMFF94), výpočty a vizualizácia elektrostatických vlastností (FDPB) a možnosti upravovania molekúl.

BALLView je možné považovať za grafické používateľské rozhranie založené na BALL (Biochemical Algorithms Library) so zameraním na najbežnejšie požiadavky, obzvlášť bielkovinových chemikov a biofyzikov. Vyvíjajú ho skupiny, ktoré vedú Hans-Peter Lenhof (Saarland University, Saarbruecken, nemecko) a Oliver Kohlbacher (University of Tuebingen, Nemecko). BALL je aplikačná platforma v C++, ktorá bola konkrétne navrhnutá na rýchly vývoj softvéru v oblasti molekulárneho modelovania a výpočtovej molekulárnej biológie. Poskytuje rozsiahlu sadu údajových štruktúr a tried pre molekulárnu mechaniku, pokročilé procesy rozpúšťania, porovnania a analýzy bielkovinových štruktúr, import/export súborov a vizualizáciu.

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  OMICtools 
Screenshots of package ballview
Cclib
Parsers and algorithms for computational chemistry
Versions of package cclib
ReleaseVersionArchitectures
bullseye1.6-1all
stretch1.3.1-1all
jessie1.1-1all
sid1.6.1-1all
wheezy1.0.1-2all
buster1.6-1all
Popcon: 8 users (13 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Please cite: Noel M. O'Boyle, Adam L. Tenderholt and Karol M. Langner: cclib: A library for package-independent computational chemistry algorithms. (eprint) J. Comp. Chem. 29(5):839-845 (2008)
Drawxtl
crystal structure viewer
Versions of package drawxtl
ReleaseVersionArchitectures
wheezy5.5-3amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze5.4+dfsg-5amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
sid5.5-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye5.5-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster5.5-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch5.5-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie5.5-3amd64,armel,armhf,i386
Debtags of package drawxtl:
interfacex11
roleprogram
uitoolkitglut
x11application
Popcon: 17 users (12 upd.)*
Versions and Archs
License: DFSG free
Svn

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.

Screenshots of package drawxtl
Gabedit
grafické používateľské rozhranie k balíkom Ab Initio
Versions of package gabedit
ReleaseVersionArchitectures
stretch2.4.8-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.4.8-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2.4.8-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid2.5.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie2.4.8-1amd64,armel,armhf,i386
wheezy2.4.2-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze2.2.12-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Debtags of package gabedit:
fieldchemistry
roleprogram
uitoolkitgtk
Popcon: 17 users (29 upd.)*
Versions and Archs
License: DFSG free
Git

Gabedit je grafické používateľské rozhranie k balíkom výpočtovej chémie ako:

  • MPQC
  • GAMESS-US
  • Gaussian
  • Molcas
  • Molpro
  • Q-Chem

Tieto balíky softvéru Ab Inition môžu bežať lokálne alebo na vzdialenom serveri (s podporou FTP, RSH a SSH). Gabedit dokáže zobrazovať rozličné výsledky výpočtov vrátane najčastejších formátov súborov molekúl. Pokročilý „Molecule Builder“ umožňuje tvoriť rýchle náčrty molekúl a prezerať ich v 3D. Grafiku je možné ďalej exportovať do rozličných formátov vrátane animácií.

Please cite: Abdul-Rahman Allouche: Gabedit - A graphical user interface for computational chemistry softwares. (eprint) J. Comp. Chem. 32:174-182 (2011)
Gamgi
General Atomistic Modelling Graphic Interface (GAMGI)
Versions of package gamgi
ReleaseVersionArchitectures
wheezy0.15.8-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie0.17.1-1amd64,armel,armhf,i386
stretch0.17.1-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze0.14.8-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
buster0.17.3-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.17.3-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid0.17.3-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package gamgi:
roleprogram
uitoolkitgtk
Popcon: 18 users (16 upd.)*
Versions and Archs
License: DFSG free
Git

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.

The package is enhanced by the following packages: gamgi-data gamgi-doc
Registry entries: SciCrunch  OMICtools 
Screenshots of package gamgi
Garlic
program na vizualizáciu biomolekúl
Versions of package garlic
ReleaseVersionArchitectures
squeeze1.6-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
jessie1.6-1.1amd64,armel,armhf,i386
stretch1.6-1.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster1.6-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.6-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye1.6-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy1.6-1.1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package garlic:
fieldbiology, chemistry
interfacex11
roleprogram
scopeutility
uitoolkitxlib
useviewing
x11application
Popcon: 18 users (26 upd.)*
Versions and Archs
License: DFSG free
Git

Garlic je napísaný na vyšetrovanie membránových bielkovín. Je možné ho použiť na vizualizáciu iných bielkovín a tiež niektorých geometrických objektov. Táto verzia Garlic pozná formát PDB verzie 2.1. Garlic je možné použiť na analýzu bielkovinových sekvencií.

Závisí iba od knižníc X, nie sú potrebné žiadne iné knižnice.

Medzi jeho vlastnosti patria:

  • Pozícia a hrúbka platničiek (slab) sú viditeľné v malom okne.
  • Atómové väzby a farby väzieb v závislosti od polohy. Je dostupných päť režimov mapovania (ako pri platničkách).

  • Schopný zobraziť stereoskopický obraz.

  • Schopný zobraziť iné geometrické objekty ako membrány.
  • Atómové informácie sú dostupné pre atóm, na ktorom sa nachádza kurzor myši. Nie je potrebné klikať, len presunúť kurzor nad štruktúru.

  • Schopný načítať viac ako jednu štruktúru.

  • Schopný nakresliť Ramachandranov diagram, závitnicové koleso, Vennov diagram, spriemerovanú hydrofóbnosť a hydrofobický moment.

  • Naspodku hlavného okna je k dispozícii príkazový riadok. Dokáže zobraziť jednu chybovú správu a jeden reťazec príkazov.

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)
Registry entries: Bio.Tools  OMICtools 
Gausssum
parse and display Gaussian, GAMESS, and etc's output
Maintainer: Debichem Team
Versions of package gausssum
ReleaseVersionArchitectures
buster3.0.2-1all
bullseye3.0.2-1all
squeeze2.2.4-1all
wheezy2.2.5-2all
jessie2.2.6.1-1all
sid3.0.2-1all
stretch3.0.1.1-1all
Debtags of package gausssum:
fieldchemistry
roleprogram
Popcon: 39 users (13 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Please cite: Noel M. O'Boyle, Adam L. Tenderholt and Karol M. Langner: cclib: A library for package-independent computational chemistry algorithms. J. Comp. Chem. 29(5):839-845 (2008)
Gdis
prehliadač modelov molekúl a kryštálov
Versions of package gdis
ReleaseVersionArchitectures
buster0.90-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze0.90-3amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy0.90-4amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie0.90-5amd64,armel,armhf,i386
stretch0.90-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.90-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid0.90-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package gdis:
fieldchemistry
interface3d, x11
roleprogram
uitoolkitgtk
useediting, learning, viewing
works-with3dmodel
x11application
Popcon: 24 users (31 upd.)*
Versions and Archs
License: DFSG free
Svn

Program založený na GTK+ na zobrazovanie a manipuláciu s izolovanými molekulami, periodickými systémami a kryštalickými štruktúrami. Program je síce vo vývoji, ale dostatočne použiteľný. Má nasledovné rysy:

  • Podpora viacerých typov súborov (CIF, BIOSYM, XYZ, XTL, MARVIN a GULP)
  • Nástroj na jednoduchú tvorbu a manipuláciu s molekulami
  • Dialóg na tvorbu štartovacích konfigurácií pre molekulárne dynamické simulácie
  • Rôzne nástroje na vizualizáciu (informácia o geometrii, zvýrazňovanie oblastí, atď.)
  • Animácie BIOSYM súborov (tiež vykresľované animácie, pozri ďalej)

GDIS taktiež umožňuje vykonávať nasledujúce funkcie pomocou ďalších balíkov:

  • Vykresľovanie modelov (vďaka POVRay)
  • Minimalizácia energie (vďaka GULP)
  • Kalkulácia morfológie (vďaka cdd)
  • Spracovanie priestorových grúp (vďaka SgInfo)
  • Zobrazenie Periodickej tabuľky (vďaka GPeriodic)
  • Načítanie prídavných typov súborov, ako napríklad PDB (vďaka Babel)
Screenshots of package gdis
Gdpc
visualiser of molecular dynamic simulations
Versions of package gdpc
ReleaseVersionArchitectures
bullseye2.2.5-9amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze2.2.5-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
buster2.2.5-9amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy2.2.5-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie2.2.5-3amd64,armel,armhf,i386
stretch2.2.5-6amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid2.2.5-9amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package gdpc:
fieldbiology, biology:structural, chemistry, physics
interfacex11
roleprogram
scopeapplication
uitoolkitgtk
useviewing
works-with3dmodel, image, video
works-with-formatjpg, png
x11application
Popcon: 17 users (30 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Registry entries: OMICtools 
Other screenshots of package gdpc
VersionURL
2.2.5-1https://screenshots.debian.net/screenshots/000/007/396/large.png
Screenshots of package gdpc
Jmol
Molecular Viewer
Versions of package jmol
ReleaseVersionArchitectures
stretch14.6.4+2016.11.05+dfsg1-3all
jessie12.2.32+dfsg2-1all
wheezy12.2.32+dfsg2-1all
buster14.6.4+2016.11.05+dfsg1-4all
bullseye14.6.4+2016.11.05+dfsg1-4all
sid14.6.4+2016.11.05+dfsg1-4all
upstream14.28.4
Debtags of package jmol:
fieldchemistry
roleprogram
scopeutility
useviewing
Popcon: 74 users (90 upd.)*
Newer upstream!
License: DFSG free
Git

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.

Please cite: A. Herráez: Biomolecules in the computer: Jmol to the rescue. (PubMed,eprint) Biochem Mol Biol Educ. 34(4):255-261 (2006)
Registry entries: SciCrunch  OMICtools 
Screenshots of package jmol
Kalzium
periodická tabuľka a chemické nástroje
Versions of package kalzium
ReleaseVersionArchitectures
jessie4.14.2-1amd64,armel,armhf,i386
wheezy4.8.4-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze4.4.5-2amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
stretch16.08.3-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid17.08.3-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye17.08.3-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster17.08.3-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
upstream19.04.3
Debtags of package kalzium:
fieldchemistry
interface3d, x11
roleprogram
suitekde
uitoolkitqt
usebrowsing, learning, viewing
works-with3dmodel
x11application
Popcon: 169 users (495 upd.)*
Newer upstream!
License: DFSG free
Git

Kalzium je plnohodnotná chemická aplikácia vrátane periodickej tabuľky prvkov, chemickej referenčnej tabuľky, riešenia chemických rovníc a 3D prehliadača molekúl.

Tento balík je súčasťou modulu Vzdelávanie KDE.

Other screenshots of package kalzium
VersionURL
4:3.5.9-2https://screenshots.debian.net/screenshots/000/001/228/large.png
Screenshots of package kalzium
P4vasp
visualization suite for the Vienna Ab-initio Simulation Package (VASP)
Versions of package p4vasp
ReleaseVersionArchitectures
sid0.3.30+dfsg-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch0.3.29+dfsg-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el
jessie0.3.29+dfsg-1amd64,armel,armhf,i386
buster0.3.30+dfsg-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.3.30+dfsg-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 7 users (6 upd.)*
Versions and Archs
License: DFSG free
Git

p4VASP is a visualization suite for the Vienna Ab-initio Simulation Package (VASP). It contains an extensible GUI framework, that can be used to view material structure, density of states, band-structure and more.

It provides a Python library, that greatly simplifies the process of manipulation of the VASP input and output data in Python scripts. P4vasp utilizes also many handy routines and objects e.g. for creating 2D graphs, data storage (xml,DOM) or simple matrix library.

Other screenshots of package p4vasp
VersionURL
0.3.29+dfsg-1https://screenshots.debian.net/screenshots/000/013/508/large.png
Screenshots of package p4vasp
Qutemol
interactive visualization of macromolecules
Versions of package qutemol
ReleaseVersionArchitectures
sid0.4.1~cvs20081111-12amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye0.4.1~cvs20081111-12amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.4.1~cvs20081111-12amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch0.4.1~cvs20081111-6amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie0.4.1~cvs20081111-3.2amd64,armel,armhf,i386
wheezy0.4.1~cvs20081111-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
Debtags of package qutemol:
interfacex11
roleprogram
uitoolkitglut, wxwidgets
x11application
Popcon: 12 users (13 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Please cite: Marco Tarini, Paolo Cignoni and Claudio Montani: Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization. (eprint) IEEE Transactions on Visualization and Computer Graphics 12(5):1237-1244 (2006)
Registry entries: SciCrunch  OMICtools 
Screenshots of package qutemol
Rasmol
vizualizácia biologických makromolekúl
Versions of package rasmol
ReleaseVersionArchitectures
squeeze2.7.5-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy2.7.5.2-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie2.7.5.2-2amd64,armel,armhf,i386
stretch2.7.5.2-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,s390x
buster2.7.6.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2.7.6.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid2.7.6.0-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package rasmol:
fieldchemistry
interfacex11
roleprogram
scopeutility
uitoolkitgtk
uselearning, viewing
x11application
Popcon: 228 users (25 upd.)*
Versions and Archs
License: DFSG free
Git

RasMol je program na molekulárnu grafiku s účelom vizualizácie proteínov, nukleových kyselín a malých molekúl. Program je určený na zobrazovanie, výuku a tvorbu obrázkov v tlačovej kvalite.

Program načíta súbor so súradnicami molekúl a interaktívne zobrazuje molekulu na obrazovke v rozličných farebných schémach a reprezentáciách molekúl. Medzi momentálne dostupné reprezentácie patria hĺbkové drôtené modely, „Dreidingove“ paličky, gule vypĺňajúce priestor (CPK), gule a paličky, pevné a zreťazené biomolekulárne reťazce, označenia atómov a bodové povrchy.

Medzi podporované vstupné formáty patria Protein Data Bank (PDB), formáty Alchemy od Tripos Associates a Sybyl Mol2, formát (MDL) Mol od Molecular Design Limited, XYZ (XMol) od Minnesota Supercomputer Center (MSC), formát CHARMm, formát CIF a formát mmCIF.

Tento balík nainštaluje dve verzie RasMol, rasmol-gtk s moderným používateľským rozhraním založeným na GTK a rasmol-classic so starým rozhraním Xlib.

The package is enhanced by the following packages: rasmol-doc
Please register by following this link if you are using rasmol.
Please cite: Roger A. Sayle and E. James Milner-White: RasMol: Biomolecular graphics for all. (PubMed) Trends in Biochemical Sciences (TIBS) 20(9):374 (1995)
Registry entries: Bio.Tools  OMICtools 
Screenshots of package rasmol
Raster3d
tools for generating images of proteins or other molecules
Versions of package raster3d
ReleaseVersionArchitectures
squeeze2.9-1-1 (non-free)amd64,armel,i386,ia64,mips,mipsel,powerpc,s390,sparc
wheezy3.0-2-4amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie3.0-3-1amd64,armel,armhf,i386
stretch3.0-3-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster3.0-3-5amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye3.0-4-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid3.0-4-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package raster3d:
fieldbiology, biology:structural
interfacecommandline
roleprogram
scopeapplication
useconverting, viewing
works-with3dmodel, image, image:raster
works-with-formatjpg, png
Popcon: 14 users (14 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Please cite: E.A. Merritt and D.J. Bacon: Raster3D Photorealistic Molecular Graphics. (PubMed) Methods in Enzymology 277:505-524 (1997)
Registry entries: Bio.Tools  OMICtools 
Shelxle
graphical user interface for SHELXL
Versions of package shelxle
ReleaseVersionArchitectures
buster1.0.952-1amd64,arm64,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye1.0.952-1amd64,arm64,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.0.973-1amd64,arm64,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy1.0.564-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie1.0.677-1amd64,armel,armhf,i386
stretch1.0.816-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package shelxle:
uitoolkitqt
Popcon: 3 users (4 upd.)*
Versions and Archs
License: DFSG free
Git

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

Please cite: Christian B. Hübschle, George M. Sheldrick and Birger Dittrich: ShelXle: a Qt graphical user interface for SHELXL. (eprint) J. Appl. Cryst. 44(6):1281-1284 (2011)
Screenshots of package shelxle
V-sim
Visualize atomic structures
Versions of package v-sim
ReleaseVersionArchitectures
squeeze3.5.1-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy3.6.0-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
stretch3.7.2-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid3.7.2-6amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package v-sim:
fieldchemistry, physics
interfacex11
roleprogram
sciencevisualisation
scopeapplication
uitoolkitgtk
useviewing
x11application
Popcon: 23 users (4 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Screenshots of package v-sim
Viewmol
graphical front end for computational chemistry programs
Versions of package viewmol
ReleaseVersionArchitectures
jessie2.4.1-22amd64,armel,armhf,i386
squeeze2.4.1-15amd64,armel,i386,ia64,mips,mipsel,powerpc,s390,sparc
wheezy2.4.1-18amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc
stretch2.4.1-24amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster2.4.1-25amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye2.4.1-25amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid2.4.1-25amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package viewmol:
fieldchemistry
interface3d, x11
roleprogram
uitoolkitmotif
uselearning, viewing
x11application
Popcon: 31 users (42 upd.)*
Versions and Archs
License: DFSG free
Git

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.

Registry entries: SciCrunch  OMICtools 
Screenshots of package viewmol
Xbs
3D modely a filmy molekúl
Maintainer: Matthew Vernon
Versions of package xbs
ReleaseVersionArchitectures
wheezy0-8amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
sid0-10amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze0-8amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
bullseye0-10amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0-10amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch0-10amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie0-8amd64,armel,armhf,i386
Debtags of package xbs:
fieldchemistry
interface3d
roleprogram
scopeapplication
uitoolkitxlib
useprinting, viewing
works-withtext
works-with-formatpostscript
x11application
Popcon: 10 users (11 upd.)*
Versions and Archs
License: DFSG free

program xbs na kreslenie guľôčok a paličiek dokáže vytvárať nehybné a pohyblivé trojrozmerné modely molekúl. Je dostupný výstup na X11 a do PostScriptu. Modely je možné otáčať, meniť ich veľkosť atď. Sú dostupné rôzne možnosti označovania, tieňovania, osvetlenia a zafarbenia.

Screenshots of package xbs
Xcrysden
Crystalline and Molecular Structure Visualizer
Versions of package xcrysden
ReleaseVersionArchitectures
stretch1.5.60-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid1.5.60-1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy1.5.53-1amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
jessie1.5.60-1amd64,armel,armhf,i386
Popcon: 26 users (4 upd.)*
Versions and Archs
License: DFSG free

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.

Screenshots of package xcrysden
Xmakemol
program for visualizing atomic and molecular systems
Versions of package xmakemol
ReleaseVersionArchitectures
stretch5.16-9amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie5.16-7amd64,armel,armhf,i386
squeeze5.16-5amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy5.16-6amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
sid5.16-9amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye5.16-9amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster5.16-9amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package xmakemol:
fieldchemistry
hardwareinput, input:mouse
interfacex11
roleprogram
scopeapplication
uitoolkitmotif
useediting, viewing
x11application
Popcon: 17 users (21 upd.)*
Versions and Archs
License: DFSG free
Svn

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
Screenshots of package xmakemol
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 201087