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
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DebiChem 3D Visualization packages
Official Debian packages with high relevance
adun.app
simulátor molekúl pre GNUstep - grafické používateľské rozhranie
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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 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.
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avogadro
systém molekulárnej grafiky a modelovania
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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 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.
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ballview
slobodný nástroj na modelovanie a zobrazovanie molekúl
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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 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.
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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
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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 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.
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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
program na vizualizáciu biomolekúl
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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 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.
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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)
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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
prehliadač modelov molekúl a kryštálov
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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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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)
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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
periodická tabuľka a chemické nástroje
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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 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.
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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
vizualizácia biologických makromolekúl
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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
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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.
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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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