Summary
3D Visualization
DebiChem - przeglądarki 3D
Ten metapakiet instaluje przeglądarki 3D, które mogą być przydatne dla
chemików.
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
Symulator molekularny do GNUstep-a (GUI)
|
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 |
|
License: DFSG free
|
Adun jest symulatorem biomolekularnym, który umożliwia także zarządzanie
danymi i ich analizę. Został stworzony przez Computational Biophysics
and Biochemistry Laboratory (laboratorium obliczeń biofizycznych i
biomedycznych), będące częścią Research Unit on Biomedical
Informatics (jednostki badawczej nad informatyką biomedyczną) na UPF.
Pakiet zawiera UL, frontend z graficznym interfejsem użytkownika do
symulatora Adun.
|
|
avogadro
System do molekularnego modelowania i wizualizacji
|
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 |
|
License: DFSG free
|
Avogadro jest systemem do molekularnego modelowania oraz wizualizacji
cząsteczek i biocząsteczek. Może wizualizować właściwości cząsteczek, takie
jak orbitale lub potencjały elektrostatyczne, a ponadto udostępnia
intuicyjne narzędzie do budowania cząsteczek.
Podstawowe możliwości:
- molekularne modelowanie z automatyczną optymalizacją opartą na
geometrii pól siłowych;
- mechanika molekularna obejmująca wyszukiwanie według ograniczeń i
konformacji;
- wizualizacja orbitali molekularnych oraz ogólnych izopowierzchni;
- wizualizacja drgań i kreślenie widm oscylacyjnych;
- obsługa krystalograficznych komórek elementarnych;
- generowanie wejścia dla pakietów chemii kwantowej Gaussian, GAMESS
i MOLPRO;
- elastyczna architektura wtyczek i skryptów Pythona.
Avogadro odczytuje formaty plików takie jak: PDB, XYZ, CML, CIF, Molden
oraz dane wyjściowe: Gaussian, GAMESS i MOLPRO.
|
|
ballview
free molecular modeling and molecular graphics tool
|
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 |
|
License: DFSG free
|
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.
|
|
cclib
Parsery i algorytmy dla chemii obliczeniowej
|
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 |
|
License: DFSG free
|
Biblioteka Pythona, która zapewnia analizatory składni plików dziennika
chemii obliczeniowej. Udostępnia także platformę do implementacji
algorytmów w sposób niezależny od pakietu.
Ten pakiet zawiera skrypty pomocnicze dla użytkowników końcowych.
Testy jednostkowe i pliki danych, zarządzane przez cclib, dystrybuowane są
oddzielnie np. w niewolnym pakiecie cclib-data.
|
|
drawxtl
|
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 |
|
License: DFSG free
|
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.
|
|
gabedit
graphical user interface to Ab Initio packages
|
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 |
|
License: DFSG free
|
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.
|
|
gamgi
Ogólny Interfejs Graficzny do Modelowania Atomistycznego
|
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 |
|
License: DFSG free
|
GAMGI (General Atomistic Modelling Graphic Interface) udostępnia
interfejs graficzny do budowania, przeglądania i analizowania
struktur atomowych. Program jest skierowany do społeczności naukowej
i zawiera interfejs graficzny do badania struktur atomowych i
przygotowywania obrazów do prezentacji oraz do nauczania budowy
materii atomowej.
|
|
garlic
visualization program for biomolecules
|
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 |
|
License: DFSG free
|
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)
|
|
gausssum
Analizowanie i wyświetlanie plików wyjściowych Gaussian, GAMESS itd.
|
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 |
|
License: DFSG free
|
GaussSum analizuje pliki wyjściowe ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar
i obliczenia z PC GAMESS, aby zdobyć użyteczne informacje.
GaussSum używa GNUPlot-a do wyświetlenia postępu optymalizacji geometrii,
gęstości stanów widma, widma UV-VIS, widma IR, widma Ramana,
i map różnic gęstości elektronowej. Może również wyświetlać wszystkie linie
zawierające dowolne wyrażenia i nie tylko to.
|
|
gdis
molecular and crystal model viewer
|
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 |
|
License: DFSG free
|
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)
|
|
gdpc
Wizualizator symulacji dynamiki molekularnej
|
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 |
|
License: DFSG free
|
Jest to program graficzny gpdc, służący do wizualizacji danych wyjściowych
pochodzących z symulacji dynamiki molekularnej. Obsługuje on standardowy
format xyz, a także inne formaty jako dane wejściowe oraz formaty plików
graficznych JPG i PNG jako dane wyjściowe.
|
|
jmol
|
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 |
|
License: DFSG free
|
Jmol to przeglądarka molekularna do trójwymiarowych struktur chemicznych,
napisana w języku Java. Jmol umożliwia odczytywanie różnych typów plików
i danych wyjściowych z programów chemii kwantowej oraz animację plików
wieloklatkowych i obliczonych trybów normalnych z tychże programów.
Program udostępnia funkcje do chemikaliów, kryształów, materiałów i
biomolekuł. Jmol może być przydatny dla studentów, nauczycieli oraz badaczy chemii i biochemii.
Formaty plików odczytywane przez Jmol obejmują: PDB, XYZ, CIF, CML, MDL
Molfile, Gaussian, GAMESS, MOPAC, ABINIT, ACES-II, Dalton i VASP.
|
|
kalzium
Układ okresowy pierwiastków i narzędzia chemiczne
|
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 | 24.08.3 |
Debtags of package kalzium: |
field | chemistry |
interface | 3d, x11 |
role | program |
suite | kde |
uitoolkit | qt |
use | browsing, learning, viewing |
works-with | 3dmodel |
x11 | application |
|
License: DFSG free
|
Kalzium jest w pełni funkcjonalną aplikacją chemiczną, obejmującą układ
okresowy pierwiastków, opis zagadnień z zakresu chemii, rozwiązywanie
równań chemicznych oraz podgląd cząsteczek w 3D.
Pakiet jest częścią modułu edukacyjnego KDE.
|
|
qutemol
interactive visualization of macromolecules
|
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 |
|
License: DFSG free
|
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.
|
|
rasmol
visualization of biological macromolecules
|
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 |
|
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.
|
|
raster3d
Narzędzia do generowania obrazów białek lub innych cząsteczek
|
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 |
|
License: DFSG free
|
Raster3D to zestaw narzędzi do generowania wysokiej jakości obrazów
rastrowych białek lub innych cząsteczek. Główny program renderuje kule,
trójkąty, cylindry i powierzchnie kwadratowe z podświetlaniem lustrzanym,
cieniowaniem i cieniowaniem Phonga. Stosuje wydajny algorytm programowy
Z-buffer, który jest niezależny od karty graficznej. Programy pomocnicze
przetwarzają współrzędne atomowe z plików PDB (Protein Data Bank) w celu
renderowania opisów obrazów składających się ze wstążek, atomów
wypełniających przestrzeń, wiązań, kulki + kija itp. Raster3D może być
również używany do renderowania obrazów utworzonych w innych programach,
takich jak Molscript, w środowisku 3D z podświetleniami, cieniami itp.
Dane wyjściowe zapisywane są w plikach obrazów pikselowych z 24-bitową
informacją o kolorze każdego piksela.
|
|
shelxle
Graficzny interfejs użytkownika dla SHELXLe
|
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 | 1.0.1697 |
Debtags of package shelxle: |
uitoolkit | qt |
|
License: DFSG free
|
ShelXle łączy edytor z podświetlaniem składni dla związanych z SHELXL
plików wejściowych .ins i plików wyjściowych .res z interaktywnym
wyświetlaczem graficznym wyświetlającym trójwymiarowe struktury, w tym
mapy gęstości elektronowej (Fo) oraz mapy różnic gęstości (Fo-Fc).
https://dx.doi.org/10.1107/S0021889811043202
|
|
v-sim
Wizualizacja struktur atomowych
|
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 |
|
License: DFSG free
|
V_Sim wizualizuje struktury atomowe, takie jak kryształy, granice ziaren,
cząsteczki itd. (w formacie binarnym lub w formacie zwykłego tekstu).
Renderowanie odbywa się w pseudo 3D z kulkami (atomami) lub strzałkami
(spinami). Użytkownik może wchodzić w interakcje za pomocą wielu funkcji,
aby wybrać widok, ustawić powiązania, narysować płaszczyzny cięcia,
obliczyć powierzchnie z pól skalarnych, zduplikować węzły, zmierzyć
geometrię itd. Ponadto, V_Sim umożliwia eksportowanie widoku jako obrazu
w formatach PNG, JPG, PDF (bitmapa), SVG (schemat) i innych formatach.
Dostępne są również narzędzia do kolorowania atomów z wartości danych
lub do animowania na ekranie wielu plików pozycji.
|
|
viewmol
graphical front end for computational chemistry programs
|
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 |
|
License: DFSG free
|
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.
|
|
xbs
3-d models and movies of molecules
|
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 |
|
License: DFSG free
|
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.
|
|
xcrysden
Crystalline and Molecular Structure Visualizer
|
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 |
|
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.
|
|
xmakemol
Program do wizualizacji układów atomowych i molekularnych
|
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 |
|
License: DFSG free
|
XMakemol jest programem obsługiwanym za pomocą myszki, napisanym przy
użyciu zestawu widżetów LessTif, służącym do przeglądania i zarządzania
układami atomów oraz innymi chemicznymi układami. XMakemol wczytuje dane
wejściowe XYZ i wyświetla atomy, wiązania i wiązania wodorowe.
Do jego funkcji należą:
- animowanie plików zawierających wiele klatek;
- interaktywne mierzenie długości wiązań, kątów pomiędzy nimi
oraz kątów skręcenia;
- kontrolowanie rozmiaru atomu/wiązania;
- eksportowanie do formatów XPM, Encapsulated PostScript oraz XYZ;
- przełączanie widzialności poszczególnych grup atomów;
- edytowanie pozycji podzbiorów atomów.
|
|
|